OPUS 5 BasePackage PDF

Spectroscopic Software
Version 5
Reference Manual
I 26039
© 2004 BRUKER OPTIK GmbH, Rudolf-Plank-Straße 27, D-76275 Ettlingen, www.brukeroptics.com
The text, figures, and programs have been worked out with the utmost care. However, we do not accept
legal responsibility nor any liability for either incorrect statements which may remain or their
consequences. The following publication is protected by copyright. All rights reserved. No part of this
publication may be reproduced in any form by photocopy, microfilm or other procedures or transmitted
in machine language, in particular for data processing systems without our prior written authorization.
The rights to distribution and to broadcasting as well as the rights to communication to the public are
also reserved. The software and hardware descriptions referred to in this manual are in many cases
registered trademarks and as such are subject to legal requirements.
This manual is the original documentation for the OPUS spectroscopic software.
Table of Contents
1 Starting OPUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
2 OPUS Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
2.1 Loading and Selecting a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 OPUS Browser Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.3 Spectrum Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.4 Report Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.5 Datafile History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.6 3D Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.7 Selecting Frequency Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.8 Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.9 Instrument Status Indicator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3 File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
3.1 Load File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.2 Unload File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.3 Undo Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.4 Save File/Save File As . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.5 Send File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.6 Send File to GRAMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.7 Send File to InStep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.8 Delete Data Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.9 External Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.10 VisualBasic Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.11 Load Data Point Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.12 Scan OPUS Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.13 Find OPUS Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.14 Clone Entry and Clone Original . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.15 Add Comment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.16 RS 232 Communication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.16.1 RS 232 Write/Read . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.16.2 RS 232 Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.16.3 COM1 Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.17 Copy Data Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.18 Change Data Block Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.19 New/Open . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.20 Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.21 Print Preview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.22 Print Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3.23 Exit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
iii
4 Edit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
4.1 Edit Parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.2 Replay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.3 Information Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.3.1 First-Time Information Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.3.2 Editing Existing INFO Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.3.3 Creating a New File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.3.4 Displaying and Printing INFO Data Blocks . . . . . . . . . . . . . . . . . . 45
4.4 Setup Info Mask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.5 Structure Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.6 Edit/Create Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.7 Attach Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
4.8 Convert 3dJcamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5 View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
5.1 Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.2 Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
5.3 Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
6 Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
6.1 New Spectrum Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
6.2 New Report Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
6.3 New Registered Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
6.3.1 Text View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
6.4 Cascade and Tile Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6.5 Arrange Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
7 Measure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
7.1 Configuring the Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
7.1.1 Optical Bench . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
7.1.2 Devices/Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
7.1.3 Interferometer/AQP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
7.1.4 Export Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
7.1.5 Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
7.1.6 Optic Communication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
7.1.7 Control Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
7.2 Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
7.2.1 Error and Warning Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
7.2.2 Basic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
7.2.3 Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
7.2.4 Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
7.2.5 Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
7.2.6 FT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
7.2.7 Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
7.2.8 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
7.2.9 Check Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
7.2.10 Beam Path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
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7.2.11 Raman Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
7.3 Repeated Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
7.4 Rapid Scan - Time Resolved Measurement . . . . . . . . . . . . . . . . . . . . . . . . . 96
7.5 Interleaved Time Resolved Measurements . . . . . . . . . . . . . . . . . . . . . . . . . 100
7.6 Direct Command Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
7.7 Optics Diagnostic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
7.8 Temperature Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
8 Manipulate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
8.1 Baseline Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
8.2 Spectrum Subtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
8.3 AB <-> TR Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
8.4 Straight Line Generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
8.5 Spectrum Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.6 Cut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
8.7 Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
8.8 Make Compatible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
8.9 Convert Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
8.9.1 Convert to Kubelka-Munk (KM) . . . . . . . . . . . . . . . . . . . . . . . . . 122
8.9.2 Convert to Reflectance Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 123
8.9.3 Convert to ATR Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
8.9.4 Convert to Absorbance Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 123
8.9.5 Logarithmize Reflectance Spectra . . . . . . . . . . . . . . . . . . . . . . . . 123
8.9.6 Convert Logarithmized Reflectance Spectra . . . . . . . . . . . . . . . . 123
8.9.7 Convert Single-Channel Spectra . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.9.8 Convert Raman Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.9.9 Raman Laser Wave Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.10 Smooth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.11 Derivative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
8.12 Frequency Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
8.13 Raman Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
8.13.1 Raman Correction Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
8.14 Black Body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
8.14.1 Black Body Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
8.15 Interferogram to Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
8.16 Inverse FT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
8.17 Post Zerofilling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
8.18 Fourier Self-Deconvolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
8.18.1 Fourier Self-Deconvolution Theory . . . . . . . . . . . . . . . . . . . . . . . 143
8.19 Symmetric FT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
8.20 Kramers-Kronig Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
8.20.1 Kramers-Kronig-Transformation Theory . . . . . . . . . . . . . . . . . . . 146
8.21 Spectrum from Interferograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
8.22 Extrapolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
8.22.1 Extrapolation to 0cm-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
8.22.1.1Theory of extrapolating n to 0cm-1 in case of
semiconductors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
v
8.22.1.2Theory of extrapolating n to 0cm-1 in case of
insulators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
8.22.2 Extrapolation to (infinity) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
8.22.2.1Approximation for extrapolating n . . . . . . . . . . . . . . . . 151
8.23 1/cm <-> µm, nm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
8.24 Averaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
8.24.1 Averaging Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
8.25 Merge Spectral Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
8.26 Atmospheric Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
8.26.1 Select Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
8.26.1.1Single-channel sample and single-channel
reference spectrum in one file . . . . . . . . . . . . . . . . . . . . . 161
8.26.1.2Single-channel sample and single-channel
reference spectrum in different files . . . . . . . . . . . . . . . . 161
8.26.2 H2O/CO2 Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
8.26.3 Calculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
8.26.4 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
8.26.5 Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
8.26.6 Atmospheric Compensation as part of the measurement process 164
8.27 Straylight Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
8.27.1 Select Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
8.27.2 Internal Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
8.27.3 Window Material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
8.27.4 Calculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
8.27.5 Create new correction spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
8.27.6 Using straylight correction as part of the measurement process . 170
8.28 Noise Generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
8.29 Moving Mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
8.30 Make Monotone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
9 Evaluate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .177
9.1 Curve Fit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
9.2 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
9.2.1 Set up Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
9.2.2 Interactive Method Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
9.3 Quantitative Analysis 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
9.3.1 Setup QUANT 1 Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
9.3.2 Quantitative Analysis 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
9.4 Signal-to-Noise Ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
9.5 Peak Picking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
9.6 Quick Identity Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
9.7 Quality-Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
9.8 Multi Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
9.8.1 Multi Evaluation Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
9.8.1.1 IDENT Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
9.8.1.2 Conformity Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
9.8.1.3 QUANT Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
9.8.1.4 Store Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
vi
9.9 Multi Evaluation Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
9.10 Quick Compare . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
9.10.1 Quick Compare Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
9.10.2 Quick Compare Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
9.10.3 Quick Compare . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
9.11 Spectrum Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
9.11.1 Starting a Spectrum Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
9.11.2 Search Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
9.12 NeuroDeveloper Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
10 Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253
10.1 Forward, Back . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
10.2 Stacked . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
10.3 Scale All, Scale Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
10.4 Page Forward, Page Backward . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
10.5 Zoom In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
11 Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .255
11.1 Installing Default Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
11.2 Print Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
11.3 Print Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
11.4 Quick Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
11.5 New Layout – Plot Layout Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
11.5.1 PLE Tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
11.5.2 Pop-up Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
11.5.3 PLE Page Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
11.5.4 Loading and displaying a spectrum . . . . . . . . . . . . . . . . . . . . . . . 269
11.5.5 PLE Spectral Frame Properties . . . . . . . . . . . . . . . . . . . . . . . . . . 271
11.5.6 PLE Table Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
11.5.7 PLE Text Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
11.6 Open Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
11.7 Print / Print Preview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
11.8 Print Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
12 Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .281
12.1 Script Recorded History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
12.2 Insert MyInstrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
12.3 Macro Converter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
12.4 Run Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
12.5 Debug Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
12.6 Macro Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
12.7 Compile Macro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
12.8 Add Macro to the Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
13 Validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287
13.1 OPUS Validation Program (OVP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
vii
13.1.1 OVP Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
13.1.2 Database Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
13.2 OPUS Setup (prior to OVP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
13.2.1 Preparing Default Measurement Experiment . . . . . . . . . . . . . . . . 290
13.2.2 OVP Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
13.2.2.1Confirming Correct Instrument Type. . . . . . . . . . . . . . . 294
13.2.2.2Adding Measurement Configuration . . . . . . . . . . . . . . . . 294
13.2.2.3Measuring Laser Wave Number . . . . . . . . . . . . . . . . . . 298
13.2.2.4Configuring Test Channel . . . . . . . . . . . . . . . . . . . . . . . . 300
13.2.2.5Selecting Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
13.2.2.6Deleting Optics Configuration from OVP . . . . . . . . . . . 303
13.2.2.7Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
13.2.2.8Exiting OVP Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
13.3 Validation Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
13.3.1 Starting Validation Measurement . . . . . . . . . . . . . . . . . . . . . . . . . 305
13.3.2 Test Protocol Wizards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
13.4 PQ Test Protocol Plug-in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
13.4.1 PQ Test Protocol Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
13.4.2 Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
13.4.3 PQ Tests Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
13.5 OQ Test Protocol Plug-in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
13.5.1 OQ Test Protocol Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
13.5.2 OQ Test Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
13.6 OVP Trends Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330
13.7 Running OVP in an Unattended Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
13.7.1 Running OVP via OPUS macro . . . . . . . . . . . . . . . . . . . . . . . . . . 332
13.7.2 Running AUTOOVP VB-Script . . . . . . . . . . . . . . . . . . . . . . . . . . 333
13.8 OVP Accessory Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
13.8.1 Accessories Influence on Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
13.8.2 Running Accessory Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
13.9 Adding New Test Channel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
13.9.1 OPUS Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
13.9.2 OVP Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
13.9.3 PQ Test Protocol Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
13.9.4 OQ Test Protocol Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
13.10 OVP Program Modules and Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
13.11 Instrument Status Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
13.11.1 Status Light Setup and Operation . . . . . . . . . . . . . . . . . . . . . . . . . 347
13.11.2 Instrument Status Icon Operation . . . . . . . . . . . . . . . . . . . . . . . . . 349
13.11.3 Status Indicator for Non-Ethernet Based Spectrometers . . . . . . . 351
14 Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .353
14.1 Logout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
14.2 Setup JCAMP/OPUS Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354
14.3 User Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
14.3.1 Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
14.3.2 Default User Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
14.3.3 Setting up User Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
viii
14.4 Change User Password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363
14.5 Setup User Macro List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
14.6 Register OPUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366
14.7 Customize Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
14.8 Customize Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
14.9 Display Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
14.10 User Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
14.11 New Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378
14.12 Save Workspace as . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
15 Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .381
15.1 Setting the Language . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
15.2 Rebooting the AQP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382
15.3 Abort OPUS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .385
Data Block Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
Icons Used For OPUS Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 390
Additional Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
List of File Name Extensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
ix
1 Starting OPUS
Before starting the OPUS installation, read the attached documentation.
To install OPUS, insert the OPUS installation CD into your CD drive.

Normally, the installation starts automatically. If the Windows Autostart option
is disabled, you have to start the installation manually by running the Setup
program from your CD. The installation program will guide you step by step.
You only need to follow the on-screen installation instructions shown in the
different dialog boxes.
At the end of the installation you will be asked to restart the computer. Note that
you need to restart your computer in order to complete the OPUS installation.
You may also be prompted to restart your computer when you install different
program components. In such a case do not restart until the OPUS setup has
been completed!
When the installation has been finished, an OPUS program icon is displayed in
the Windows Start menu. Click on this icon to start OPUS.
Figure 1: Windows start menu
The Login dialog box opens. Select your User ID from the drop-down list.
OPUS provides an independent user account system which regulates the access.
If you use OPUS for the first time, the User ID drop-down list includes two pre-
defined user records Default and Administrator. Select either one of them.
Enter OPUS in the Password entry field. The password is case sensitive. Once
you have assigned yourself a user record in OPUS, it is possible to determine
your own User ID and Password.
Bruker Optik GmbH OPUS Reference Manual 1

Starting OPUS
Figure 2: OPUS Login dialog
OPUS includes different accounts for operator and administrator rights. Users
defined as Operator have limited access rights compared to users defined as
Administrator. The rights depend on the User ID selected.
The Assigned Workspaces identify the user interface and access right. You can
always select those workspaces from the drop-down list which have been
defined for your User ID. When you use OPUS for the first time, we
recommend not to change the standard Default workspace.
Click on the Login button and the About OPUS window opens.
It shows the serial number of your OPUS copy and the registered user name.
The basic OPUS package integrates these additional licensed packages as an
all-in-one application.
2 OPUS Reference Manual Bruker Optik GmbH

Figure 3: About OPUS dialog
Click on OK to open the OPUS user interface. The interface appearance

depends on your screen settings and the operating system you use. Thus, the
screen display of the following dialog boxes may not show exactly the screen
contents displayed on your screen. BRUKER recommends a minimum graphic
resolution of 800 x 600 pixel and true color.

Starting OPUS
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Figure 4: OPUS user interface
The OPUS user interface header shows the type and status of the operator
currently logged in.
(a) The pull-down menus can be used to access all OPUS functions.
(b) The icon bars may be configured to quickly access frequently-used functions.
(c) The browser window of the OPUS file manager, similar to the Windows Explorer.
(d) The spectrum window for full views and zoom operations.
(e) The overview window always displays the full frequency range of the selected data files.
(f) A context sensitive online help.
(g) The status bar indicating background tasks.
(h) Instrument status (see section 2.9):
Gray = No spectrometer connected
Green = Spectrometer connected
Yellow = Warning
Red = Error
All settings (menus or icons) are individually configurable and will be reloaded
when you start OPUS next time.

2 OPUS Basics
This chapter introduces the basic OPUS functions, provides general information
on OPUS windows as well as on the processing of spectral data files. The
remaining chapters of this manual describe in detail all OPUS functions
according to their order on the different pull-down menus.
OPUS dialog boxes are similar to those of Windows. If you have already gained
experience in working with Windows, it will be easy for you to use OPUS.
OPUS supports drag & drop as well as shortcuts, e.g. copy (CTRL+C), cut
(CTRL+X) and paste (CTRL+V).
To use these shortcuts, you first have to select the text or file you want to
process. Drag & drop simplifies the copy and paste process, but can only be
applied on files. In this case click on the files icon in the OPUS browser and
press the left mouse button, while moving the file to the respective dialog box
(or window). If you release the mouse button, the file will automatically be
loaded into the dialog box selected.
Dialog boxes often consist of several tabs. Click on these tabs to change
between them. Buttons and menu items are only active, if they are displayed in
black. Grayed buttons are not available.
Figure 5: Example of a dialog box with two tabs

OPUS Basics
2.1 Loading and Selecting a File
Load Spectrum Dialog Box

If you load a file, either
• use the Load File command from the File menu,

• click on the icon in the tool bar or
• drag the file from the Windows Explorer into the spectrum window,
OPUS browser or any OPUS dialog box.
If you select the file you want to use, the Load Spectrum dialog box displays the
following features:
(a) (b) (c) (d) (e) (f) (g)
(h) (i) (j) (k)

Figure 6: Load Spectrum - active preview
a) The title bar shows the directory in which the file is stored.
b) The drop-down list includes directory paths to search for spectra files.
c) Using this arrow you can return to the last selection.
d) This icon allows to return to the parent directory.
e) Using this icon you can create a new directory.
f) Various options to display the file list.
g) The preview window displays a small spectrum range without indicating the axes. Data
blocks are displayed on top of the preview window. They include additional information
on the spectrum file.
h) File list of the path selected.
i) You can also manually type the name of the file you want to load into this entry field.

Loading and Selecting a File
j) It is also possible to load spectra of different formats, e.g. JCAMP-DX or GRAMS.SPC

files. These files will automatically be converted into the OPUS file format.
k) Parameters are additional information appended to the OPUS file. Sometimes not all
parameters to be selected by each drop-down list will be defined for each spectrum file.
This means that some parameter fields may remain empty.
You can select several spectra in the spectra list using the STRG or Shift key
while selecting the spectra. In this case the number of selected files will be
shown instead of the data blocks and spectra previews. Clicking on the Open
button will load the spectrum into OPUS and automatically close the Load box.
Select Files Option

You will encounter the Select Files option in various dialog boxes. Figure 7
shows an example of the Select Files tab in the Baseline Correction window.
Figure 7: Example of Select Files option
Select Files tabs include File(s) to... fields. Spectra files to be processed have to
be entered into these fields. You can use the Drag & Drop option to move spec-
tra files displayed in the OPUS browser window or Windows Explorer into
these selection fields. If you select spectra files before opening the Select Files
tab, or if you double click on the file data block in the OPUS browser window,
the spectra files will be automatically displayed in the specified entry field.
There are functions which cannot be used for all types of data. It is not possible,
e.g. to apply an AB<->TR Conversion to an interferogram. Sometimes, the
parameters of an OPUS function have to be set prior to loading a file, in order
to be able to select the file. If selected data blocks can principally be processed
by OPUS functions but the parameters do not match the data, the file name in
the File(s) to... field will be indicated in red and a warning symbol displayed
(see figure 8).

OPUS Basics
Figure 8: Convert Spectra – parameter mismatch
To remove data blocks from the File(s) to... field, select the data block and use
the Delete key on your keyboard. If you press the Shift or CTRL key, you can
select several files in one File(s) to... field.
2.2 OPUS Browser Window
The design and functionality of the OPUS browser is similar to the Windows
Explorer. To enlarge the spectrum window you can reduce the OPUS browser
window in size or relocate it. Left click on the upper edge of the browser
window and draw it underneath the icon bar. The OPUS browser window will
be displayed as drop-down list, including all the files loaded (see figure 9). To
undo this view click on the upper edge of the drop-down list and move the list to
the original browser window position, i.e. to the left side of the spectrum
window.

OPUS Browser Window
Figure 9: OPUS browser window displayed as drop-down list
When loading an OPUS file the file name, data blocks and file status
information are displayed in the browser window. If you position the cursor on
the file name, a small text field pops up indicating the complete data path. If you
place the cursor on a data block, the text field shows the operator name, sample
name and sample form.
(a) (b) (c)

Figure 10: Browser file list
a) If you have opened several spectrum windows you can switch between them. If
you click on the sign, the file name display will be minimized.
b) The blue document symbol indicates that the file has not yet been manipulated.
The number next to the file name indicates the number of copies made of the file
loaded. You can load a file several times into the OPUS browser window.
c) The small icon bar underneath the file name represents data blocks which are
part of the spectrum file. The data blocks displayed in figure 10 indicate a trans-
mission spectrum, single-channel spectrum, interferogram and single-channel
background spectrum. For further data blocks, see Appendix. If the data block
symbols are colored, this indicates that spectra or interferograms are displayed
within the spectrum window. Use the left mouse button to select one data block.
If you press the CTRL key, you can select more than one data block. Selected
data blocks are always indicated by a red frame.
The possibilities to select files are similar to those using the Load File option or
Windows Explorer.

OPUS Basics
If you select one file using the left

mouse button, press the Shift (⇑)
key and click on a second file
again. All the files between these
two files will also be selected.
Additionally selected by using

STRG
Figure 11: Select files
This kind of file selection causes the files to be automatically registered for
processing functions. If you have changed or added files using a processing
function, the blue document symbol will be hidden by a red one. If you have
loaded the same spectrum several times, the copies will be incremented.
If you right click on a file name, a pop-up menu opens.
Figure 12: Pop-Up menu for file manipulation
As changes made to a file are not automatically saved in the file directory, you
have to store these changes using the Save File option. Unload File means that
the file is removed from the spectrum window, but is still available in the file
directory. If you have modified the file using a processing function, you can
Undo all Manipulations. The Show Parameters option displays all information
on data acquisition which have been saved to the file. For details on parameters
and information data blocks, see chapter 4.
The Copy Entry and Clone Original options are used to duplicate spectrum
files. The difference between these two options is that Copy Entry copies a data
file which has been manipulated, e.g. if a baseline correction has been
performed. The Clone Original option copies the original spectrum file.
If you right click on a data block, the following menu pops up.

OPUS Browser Window
File has been

loaded twice
Figure 13: Pop-Up menu for spectrum manipulation
Using this menu you can change the layout of spectra within the spectrum
window. Apart from changing the color you can zoom selected spectra ranges.
Almost similar to this pop-up menu is the one displayed when you right click
into the spectrum window. The options will be described in the next section.

OPUS Basics
2.3 Spectrum Window
The spectrum window and overview window are on the right side of the OPUS
user interface. When you have loaded a file all spectra and interferograms
included in this file will be displayed.
The default settings for the spectral range are from 4,000 to 400 wave numbers
and from 0 to 1.5 extinction units. However, you can scale the spectrum to show
the complete data range. Use the Scale all command in the Display menu or
click on the icon. If a file consists of more than one data block, only the
first data block is displayed in the spectrum window.
In Figure 14 the Scale all command has not been used. Therefore, only the
overview window shows the total spectral range of data. The part shown in the
spectrum window is depicted on a white background, while the remaining data
range is grayed out. If you position the cursor on the gray area, the cursor will
change its form from to . Now you can move the borders of the spectral
range (white) by pressing the left mouse button.
Spectrum Window
Lock Window Size
Overview
Figure 14: Spectrum and overview window showing lock button

Spectrum Window
If you position the cursor between overview and spectrum window, the cursor
changes to . This allows you to re-size the windows. You can disable this
function using the Lock button, which becomes visible if you right click on the
this boundary. If the windows are looked, click again on the boundary to undo
this command by selecting Unlock.
If you right click on a spectrum within the spectrum window, a pop-up menu
will be displayed (Fig 15). This menu allows you to change the spectrum color,
to zoom a specific spectral range or to shift the complete spectrum.
Figure 15: Pop-up menu within the spectrum window
To magnify a part of the spectrum window, select the Zoom In option from the
pop-up menu. A crosshair is displayed in the spectrum window. Click on the left
mouse button to draw a frame around the spectral range you want to magnify. If
you click on the left mouse button a second time, the crosshair cursor disappears
and you can reposition the frame. Now, left-click again and the spectral range
selected will be resized to the spectrum window. Use the Zoom Out command to
decrease the magnification or the Scale all Spectra option to go back to the
original view by selecting Show Everything (XY) from the pop-up menu. The
Page back option in the Display menu allows you to have the last 10 spectral
ranges displayed again. For details on scaled spectra display, see chapter 10.
The Shift Curve command includes different options. You can either shift the
Whole Curve vertically or stretch the curve to the Top or Bottom in y direction.
Select the relevant option and shift the curve by clicking on the spectrum and
pressing the left mouse button. If several spectra are displayed, you can shift
each one of them using the Shift Curve option. Deactivate the Shift mode by
right clicking. To undo these changes, select Reset from the Shift Curve option.
The Crosshair command also includes different options. If you select Cursor, a
the cursor is displayed as crosshair. To follow the data points of a spectrum, use
the Follow Data option. This option allows to display the current crosshair

OPUS Basics
position (e.g. wavelenght or absorption unit) in the upper right corner of the
spectrum window. You can comfortably read out the x/y positions directly from
the spectrum. If you right click, the cursor changes into its regular form.
You can change the spectrum color and remove the spectrum from the spectrum
window by selecting the Change Color and Remove from Display options.
Use the Add Annotation command to identify peaks even more precisely. Right
click on the spectrum and select Add Annotation from the pop-up menu. At the
cursor position an arrow is inserted indicating the wave number of this data
point, by default. If you position the cursor onto the arrowhead and click on the
left mouse button, you can move the arrowhead.
To edit the annotation text, right click on the wave number and select Properties
from the menu which pops up. The Center text lines and With Arrows check
boxes are activated by default.
Add Region facilitates the selection of frequency ranges when using QUANT
methods.
Copy and Copy All as well as Paste can be used to copy files between different
spectrum windows. Special sections which have been copied can also be added
to different programs.
Properties opens the Display Settings dialog box.
Display Settings
Figure 16: Display Settings – Display Limits tab

Spectrum Window
Use the Display Limits tab to change the size of the displayed region.
Figure 17: Display Settings – Axes tab
The Axes tab allows to depict each spectrum with additional axes on top and on
the right side of the spectrum window. If the spectrum window includes more
than one spectrum and the spectra are displayed in stacked mode, you can
define separate axes for each spectrum if you select X between.
Figure 18: Display Settings – General tab

OPUS Basics
The General tab allows to change the background color and the default height
of the overview window. If you activate the Popup info check box, the path and
file name, or path name only, will be displayed as soon as you position the
cursor on the spectrum.
You can open more than one spectrum window by selecting the New Spectrum
Window option from the Window menu. You can either tile or stack windows.
Tiled windows are convenient to copy data between spectrum windows. You
can copy one spectrum from one window to another. Or you drag & drop the
spectrum from the OPUS browser window to one specific spectrum window.
2.4 Report Window
You can use the report window to display numerical or text information, e.g. to
display measurement parameters or evaluation results. This kind of information
is stored in report blocks. Double click on such a report block (except for peak
tables) to open a report window. A blank report window can be opened from the
Window menu (see chapter 6.3).
Figure 19: Report Window

Datafile History
The information included in the report block is displayed in form of a directory

tree on the left. If you select one item in the directory tree, the specific data are
displayed on the right. Click on the column title to sort the column data in
ascending or descending order. For report blocks which include headers, a
three-column window is opened and displays both the header and data matrix.
Right click on a report window and select Properties from the pop-up menu.
The View Properties dialog box opens. You can activate the Header preferred
check box and specify the font and font size if you click on the Printer Font
button.
Figure 20: Report Window - View Properties
2.5 Datafile History
A special type of report window is Datafile History. Any manipulation made in

the spectrum and even in the measurement parameters are recorded in a non-
editable, non-deletable history datafile. Figure 21 shows a Datafile History,
including several spectrum manipulations.
The first line of the datafile history states the operator as well as the OPUS
version and the name of the spectrum. Then, all manipulations and their
parameters are listed in the order of their performance.
All pieces of information are saved in a data block ( ) together with the
processed spectrum in one spectrum file. This ensures that all data
manipulations can be reproduced, as every kind of manipulation as well as the
operator name are automatically recorded.

OPUS Basics
History Datafile history History list

data block
Figure 21: Report Window showing datafile history
2.6 3D Window
3D windows can be used to plot contour graphics. These windows are part of
the OPUS MAP package and described in detail in the OPUS MAP manual. If
you load a 3D file it will be automatically displayed in a 3D window view.
2.7 Selecting Frequency Limits
In case of some OPUS functions you need to define frequency limits first to be
able to process a data file. You have got three possibilities to select a frequency
range:
• Select the frequency range interactively.

• Apply the current frequency limits of the spectrum window by click-
ing on the Get Display Limits button.
• Enter the limits manually.

Selecting Frequency Limits
If you want to interactively select the frequency range, load the spectra you
want to process, select the appropriate data manipulation and click on the
Interactive button in the Frequency Range tab. Figure 22 shows an example of
the Cut manipulation.
Figure 22: Frequency Range Selection
The Select Frequency Range(s) window opens and displays the loaded spectra.
Depending on the x-startpoint and x-endpoint defined (see figure 22), the view
of the Select Frequency Range(s) window may vary.
• If both frequency ranges are within the display limits, the area
between the boundaries will be white, the background gray.
• If the frequeny range displayed completely fits the display limits, the
entire range will be white.
• If the display limits are either above or below the frequency range
displayed, the background will be completely gray. In this case, close
the Select Frequency Range(s) window, define reasonable frequency
ranges and start the interactive mode again.
In Figure 23 shows pre-defined display limits which do not correspond to the

frequency range displayed. The frequency range between the current display
limits is white.

OPUS Basics
Figure 23: Select Frequency Range interactively - move frequency range
If you position the cursor on the boundary between the white and gray area, the
cursor changes into a double arrow. Press the left mouse button and move the
cursor to either the left or right side.
To define several frequency ranges right click on the gray area and select Add
Regions from the pop-up menu. Within the white section the cursor changes to a
cross arrow. If you press the left mouse button, you can move the entire
frequency range selected.

Toolbars
Figure 24: Select File Limits interactively – define endpoints
If you click on the OK button, you confirm the limits of the frequency range to
be used for data processing.
2.8 Toolbars
OPUS provides toolbars which can be individually configured to quickly access

frequently used functions. Next to each icon context-sensitive tooltips pop up
when you position the cursor over that icon.
Figure 25: OPUS Toolbar showing a tooltip
A double click on the icon immediately performs the selected function. The
icons are also displayed next to their respective function in the pull-down
menus.
You can customize the various tool bars to best suit your personal requirements.
The tool bar configurations are stored together with your workspace settings in
one file which has the extension .ows. OPUS default settings are stored in the
DEFAULT.OWS workspace. For details on tool bar configurations, see section
5.1 and 14.3. For a icons list, see Appendix.
OPUS Basics
2.9 Instrument Status Indicator
The instrument status is shown at the right end of the status bar (see figure 4). If
no spectrometer is connected, a gray status light will be displayed. A green
status light indicates that the instrument is OK and connected. When the
instrument status indicator turns yellow, a warning is indicated, e.g. the
instrument test has to be repeated. A red instrument status light indicates a
severe error, e.g. if a spectrometer component is defective. The instrument
status is also stored in a measured spectrum. If you click on the instrument
status light, a Diagnosis dialog pops up including additional information on the
status and specific help. Options for the diagnosis can be set up using the User
Settings options in the Setup menu.

Load File
3 File
The File menu includes all features necessary for your data file management.
Apart from basic commands such as loading, saving, printing and sending, the
File menu allows to start VisualBasic scripts and external software programs.
Figure 26: File Menu
3.1 Load File
The Load File command has already been described in section 2.1.

File
3.2 Unload File
The Unload File command removes files from the OPUS browser and spectrum
window. Note that when unloading files they will not be deleted from your hard
disk. Drag and drop the respective file into the File(s) to Unload field and click
on the Unload button.
3.3 Undo Changes
Use this command to undo all changes made in a data file since it has been
saved for the last time. The original data will be restored, but the History report
which includes all the previous manipulations will not be reset.
3.4 Save File/Save File As
The commands Save File and Save File As provide different options to store
files. Enter all files to be saved into the File(s) to Save entry field by drag and
drop.
Figure 27: Save Spectrum - Select File tab
The Select Files tab allows you to define spectral data to be stored, and the file
path. Use the Change Path button to browse the directory of your hard disk. If
you activate the Overwrite check box, existing files with the same file names
will be replaced by new files. This option cannot be activated when working in
GLP mode. It is also possible to increment file names. For details, see
section 14.10.

Save File/Save File As
On the Mode tab you can set the parameters for exporting OPUS data in a file
format. Apart from the OPUS and Data Point Table format there are also other
formats available, e.g. GRAMS1 or InStep2. JCAMP.DX as an additional ASCII
format can also be used. If you activate the respective check boxes in the
Options group field (figure 28), you can either move the original file, save all
data blocks or automatically remove all copies, provided that you have checked
the OPUS Format option box in the group field Output.
Figure 28: Save Spectrum – Mode tab
If you click on the Data Point Table tab, you can define the structure of the
output file. Enter the number format for x and y values, the number of decimals
as well as the separator format. Alternatively, you can activate the Separator is
TAB check box, to automatically separate the columns by tabs. You can limit
the output file size to 64KB by checking the Max. 64KB option button.
1. GRAMS is a registered trademark of Galactic Industries Corporation, 395 Main Street, Salem, NH 03079-9891.
2. InStep is a registered trademark of Infometrix Inc., 2200 Sixth Avenue, Suite 833, Seattle, WA 98121.

File
Figure 29: Save Spectrum - Data Point Table tab
3.5 Send File
You can also send OPUS files by e-mail. After loading the OPUS file into the
OPUS browser window you can send the file using the Send File command. The
respective file will be displayed in the File(s) to Send selection field. If not, drag
and drop it from the OPUS browser window into this field.

Send File to GRAMS
Figure 30: Send File - Select Files tab
If you check the Whole File option, the complete file content will be sent, even
if only one data block is displayed in the File(s) to Send selection field.
Alternatively, check the Only Selected Blocks option button if you want to send
specific data blocks only.
Clicking on the Send button will transfer the data to the Windows mail program.
You can specify an address and write a comment. If you use the mail program
for the first time, you will automatically be prompted to configure it.
The data will be attached to the letter. If the addressee uses an appropriate mail
program, it is possible to drag and drop the attachment from this program
directly to the OPUS spectrum window.
3.6 Send File to GRAMS
You can export a spectrum, loaded or measured by using OPUS, to GRAMS.

Similar to the Save File command data is loaded to the File(s) to Send selection
field and transferred to GRAMS via DDE (Dynamic Data Exchange). Make
sure that the GRAMS program has been started on the same computer.
3.7 Send File to InStep
Analog to Send File to GRAMS you can also send a file to the InStep program.

File
3.8 Delete Data Blocks
An OPUS file can consist of several data blocks. Use the Delete Data Blocks
command to delete single data blocks from an OPUS file. Peak tables,
integration results and other data blocks belonging to this file will also be
deleted. This does not entirely apply to GLP mode.
3.9 External Program
External programs, e.g. data evaluation programs, can be started from OPUS.
For further details, refer to the OPUS Programming manual.
3.10 VisualBasic Scripts
VisualBasic scripts can be started from OPUS. For further details, refer to the
OPUS Programming manual.
3.11 Load Data Point Table
The Load Data Point Table command enables to read in ASCII data tables. In
addition to the standard load data commands, it is possible to identify the table
columns, specify the data block type and limit the number of data points. Make
sure that you know the type of data point table (type of spectra, configuration of
x and y values). You can select the data range directly from the table by either
numeric entry or interactive mode. The preview window displays the data as
spectrum.
3.12 Scan OPUS Files
You can scan saved spectra selectively for character strings and text. Before you
can use this search command, you have to create a database. Use the Scan
OPUS Files command to do so.
Select the drive on which the spectrum files are saved. Generally, you should
select all drives which contain spectrum files. Click on the Scan Files button to
start creating the database. Depending on the number of spectrum files being
stored, the scanning can take a while. During scanning, the status bar indicates
this background task by Scan OPUS Files.

Scan OPUS Files
Figure 31: Scan OPUS Files – Path to Scan tab
If you click on the Parameter Evaluation tab you can limit the information
stored in the database by selecting the parameters you want to add or remove.
The smaller the number of parameters, the smaller the database.

File
Figure 32: Scan OPUS Files – Parameter Evaluation tab
3.13 Find OPUS Files
All spectrum files found are displayed in the Select File(s) to load selection box.
If you point the cursor on a spectrum, the selected parameters and information
from the info block are listed in the field on the right. Select a file from the
selection box and load it into the spectrum window by clicking on the Load
Selected Files Load button. If you have selected too many files, you will be
informed that the list has been shortened.
As soon as a database has been generated you can search for file names, text
strings in files or file parameters. In case you added spectra to your hard drive
after the database has already been generated, it is recommended to update the
database. Click on the Update Database now button prior to a search run. Date
and time of the last update is displayed to the left of this button.
Enter the string to be searched for in the Find Text in Files line. You can specify
whether to find exact wording only, any word, or all words you have entered.
You can even further narrow down the search by activating the Find in Period
check box. Specify the date and select between after, before or between this
date to narrow down your search. Start the query by clicking on the Update
Database now button.

Clone Entry and Clone Original
Figure 33: Scan OPUS Files tab
3.14 Clone Entry and Clone Original
Clone Entry and Clone Original are used to duplicate spectrum files. Use Clone
Entry to make a copy of a data file that has been manipulated (e.g. by baseline
correction). If you use the Clone Original command, you create a copy of the
original data file (manipulations made will not be stored). In either case drag &
drop the respective data file to the File(s) to Clone selection field. Click on the
Clone button.

File
Figure 34: Clone Entry - Select Files tab
3.15 Add Comment
If you want to add a comment to a spectrum, click on the Add Comment

command. Select the file(s) and drag and drop the file(s) into the selection field
File(s) to Comment. Then, enter the comment into the Comment Text entry
field. The comment will be displayed in the Report Display under Datafile
History.
Figure 35: Add Comment - Select Files tab

RS 232 Communication
3.16 RS 232 Communication
RS 232 Communication is a command which allows to communicate with

external devices using the serial port(s) of your PC (COM 1, COM 2, etc.).
In general, it is recommended not to use this command interactively, but in

combination with a macro or VB-Script. The interactive mode can be used to
test the communication.
3.16.1 RS 232 Write/Read

If you start the command interactively, the following dialog window will be
displayed:
(a) (g)
(b) (h)
(c) (i)
(j)
(d)
(e)
(k)
(f)
(l) (m) (n)
Figure 36: RS 232 Communication - RS 232 Write/Read tab
(a) This check box enables or disables the Write command.

(b) Indicates the status of the Write command (e.g. Writing..., Time-out etc.)
(c) Enter the text line(s) which are to be written to the external device. If you enter
more than one line, each line will be optionally terminated by the specified end-
of-line character. If you want to send single special characters to RS 232, which
cannot be used as strings as they are reserved for special purposes e.g. ’ (single
quote),{} (braces) etc., enter @(#) followed by the three digit ASCII code of
this special character.

File
Example: ABC@(#)039DEF will be sent as ABC'DEF

(d) The Line Separator options are used to specify the Line Separator for the Write
command. Whenever the specified line separator is detected the lines will be
separated accordingly. Carriage Return (CR) and Line Feed (LF) are already
pre-defined. If you need a different kind of line separator, check the Other
option button and enter the ASCII code of the desired line separator into the
entry field next to the option button. If no line separator is to be used, check the
None option button.
(e) You can specify a Terminator to be sent after the last character has been
entered. Either select None, if no character should be sent, or Other. In the latter
case you have to enter the ASCII code of the terminator into the entry field next
to the option.
(f) If you click on the Write button, the text entered in (c) will be sent to the RS 232
interface.
(g) This check box enables or disables the Read command.
(h) The status of the Read command is indicated here (e.g. Reading..., Time-out
etc.)
(i) The answer sent by the external device is displayed in this entry field
(j) These options are used to specify the Terminator for the Read command.
Whenever this terminator is detected the Read command will stop. Carriage
Return (CR) and Line Feed (LF) are already pre-defined. If you need a different
kind of terminator, check the Other option button and enter the ASCII code of
the desired terminator into the entry field next to the option button. If you check
the None option button, the Read command waits for answers until the time-out
has been reached.
(k) If you click on the Read button you activate the read command only.
(l) Exits the RS 232 Communication command and stores the current settings. No
write or read activity is started.
(m) Exits the RS 232 Communication command without saving the current settings.
(n) Shows the online help.
3.16.2 RS 232 Settings

The RS 232 Settings tab allows to set the different options for the serial
interface:

RS 232 Communication
(g)
(a)
(h)
(b) (i)
(c)
(d)
(e)
(f)
Figure 37: RS 232 Communication - RS 232 Settings tab
(a) The drop-down list includes all serial interfaces currently available. If a serial
interface is not available (e.g. if the mouse is connected to COM 1) this interface
will not be included in the drop-down list.
(b) The current interface settings are displayed.
(c) Enter an appropriate time-out value in milliseconds.
(d) If you activate this check box, the interface will be configured with a Mode
string. For details on the Mode command, refer to the operating system manual.
If the check box is deactivated, (e) and (f) will be disabled.
(e) Enter the mode string to be used for configuration (without specifying the serial
port) into this entry field.
(f) If you click on this button, the current settings according to the mode string. The
settings will be shown in (b).
(g) The Restore Default Settings button reads the current settings which have been
specified in the operating system as default.
(h) The Change Settings button activates the setup dialog of the operating system.
See section 3.16.3.
(i) The Store as Default button overwrites the operating system settings by using
the current settings.

File
3.16.3 COM1 Properties

The COM1 Properties dialog will be displayed if you click on the Change
Settings button (see section 3.16.2):
Figure 38: RS 232 Communication - Port Settings tab
Use this dialog to specify the following communication parameters:

• Bits per second
• Data bits
• Parity
• Stop bits
• Flow control
The same dialog opens if you set up the parameters of the serial interface by
using the System Settings command of the operating system.
3.17 Copy Data Block
Single data blocks can be copied from one OPUS file to another. This, however,
is only possible when using definite block types, e.g. INFO.

Change Data Block Type
Figure 39: Copy Data Block
Data blocks to be copied are entered into the Block(s) to Copy selection field,
e.g. by drag & drop from the OPUS browser window. Specify where to copy the
data blocks in the Destination File field.
3.18 Change Data Block Type
Changing the data block type is not required very often. Macros, however, may
need a definite data block type. If you select the Change Data Block Type
command, the data block type will only be renamed. The data, however, will
not be changed.
Drag & drop data blocks to be changed into the Block(s) to Change selection
field. Select the desired block type from the Choose Block Type drop-down list.
It may be possible that not all data block types are included in the list.

File
Figure 40: Change Data Block Type
3.19 New/Open
If you select the New command, a dialog opens which includes the OPUS, PLE
or VBScript options. OPUS generates a new OPUS workspace (see
sections 14.10 and 14.11), PLE a blank template for the Plot Layout Editor (see
chapter 11.5), and VBScript a blank VisualBasic script form. For details on how
to write VB Scripts, refer to the OPUS Programming manual.
Use the Open command to open available OPUS workspaces.
3.20 Print
You can print any report on your default printer using the Print command. The
report data are either printed on the printer or into another file.
3.21 Print Preview
This command is only available if a report window is displayed. You can print a
preview of a print-out by using the Print Preview command.

Print Setup
3.22 Print Setup
The default printing dialog can be used to define printer settings. You can
define the paper size and print-out format. These settings will be standard for
future OPUS print-outs. As the dialog box appearance depends on the printer
selected, it is not shown in this section.
3.23 Exit
If you select the Exit command, the OPUS program will close.

File

Edit Parameter
4 Edit
The Edit menu includes features for information input, options to edit structures
as well as the standard Windows commands such as Copy and Paste.
Figure 41: Edit Menu
4.1 Edit Parameter
Use the Edit Parameter command to edit the most important sample
parameters, e.g. sample name, sample form, operator name and sample number.
First, load the spectrum the parameters of which you want to edit into the OPUS
browser window. Select the Edit Parameter command. The following dialog
box opens:

Edit
Figure 42: Edit Parameter – Enter Parameter tab
Now, change the parameters accordingly. Note that you will not be able to
change these parameters if working in GLP mode.
On the Axes Labels tab you can set the axes labels and a scaling factor for the
axes. These settings are used when the spectra are printed out. The scaling
factors will only be considered in case of 3D spectra.
Figure 43: Edit Parameter – Axes Labels tab

Replay
4.2 Replay
When working in GLP mode a copy of the original spectrum is saved together
with the corresponding data. On the basis ofthis original spectrum, you can
repeat some of the manipulations performed.
Drag and drop the spectrum from the OPUS browser window to the
File for Replay entry field to repete some manipulations.
Figure 44: History Replay - Select File tab
Select the manipulation command up to which you want to restore the file. If
you select Smooth, as exemplified in figure 44, Baseline, Normalize and Smooth
manipulation command will be performed on the original spectrum, except the
Derivative command.
4.3 Information Input
Apart from OPUS parameters you can also save additional information, using
the Information Input command. This kind of information will be saved in a
separate INFO (information) data block , and can be integrated both into a
report window and in a plot. If you want to save spectra in your own search
libraries, information input is mandatory.
The so-called Info Mask (see section 4.4) includes the descriptions of up to 99
lines which can be saved in one INFO data block. You can define this Info Mask
according to your individual needs.

Edit
4.3.1 First-Time Information Input

Load a spectrum into the OPUS browser window and select the
Information Input command. The following dialog opens:
Figure 45: Information Input
You can only select one spectrum file at a time to enter additional information.
The name of the information mask, a file with the extension TXD is displayed in
the Text Definition field. To use a different information mask, click on the
Load Text Mask button. The Load Info Text Mask dialog pops up which you can
select a different information mask from.
Depending on the number of lines defined for the Info Mask selected, the
Information Input dialog (see figure 45) can include up to 7 pages. Enter the
requested information. You do not need to fill in all the fields.
Clicking on the Add Information button will create or modify the

INFO data block for the file selected. This new data block will be attached to
your spectrum file and displayed in the OPUS browser window. Right click on
this data block and select Show Report from the pop-up window. The report
window only includes data which have been filled into the lines of the
Information Input dialog (see figure 45).

Information Input
Figure 46: Report window with text information
4.3.2 Editing Existing INFO Blocks

If you load a spectrum file which already includes an INFO data block, the
information added to this data block will be displayed in the Information Input
dialog (figure 45) together with the appropriate information mask.
However, it may occur that the appropriate information mask cannot be found
on your data structure. Maybe the mask is based on a different data structure or
you have copied the information mask into a different directory, or even deleted
it. In this case the information mask reference will be highlighted in red in the
Text Definition field (figure 45).
Now, you can edit existing data or add new data. Alternatively, you can select a
different kind of information mask. In this case all inputs made so far will be
deleted in the dialog. If you have deleted or overwritten entry fields by accident,
click on the Restore Original button to read the original data again.
4.3.3 Creating a New File

Instead of attaching an INFO data block to an existing OPUS file you can also
create a new file, which only consists of an INFO data block. In this case
activate the New File check box (see figure 45). A new file, INFOx.0, will be
created, with x being either a single or multi-digit number.
4.3.4 Displaying and Printing INFO Data Blocks

As already mentioned the INFO data block can be displayed in a report window.
To print the INFO data block each data line of the block can be addressed as
OPUS parameter, using the parameter name Inn with nn being the line number
(e.g. I01 = first line, I12 = twelfth line). Similarly, you can also include
information mask texts into the plot, using Tnn as parameter name (e.g. T01 =
text in first line, T12 = text in twelfth line).

Edit
4.4 Setup Info Mask
When creating an information mask you define the kind of information

available for information input. Depending on the field of application you can
create different kinds of information masks. The contents and file name of the
information mask will be saved during information input. This enables all data
to be displayed on data systems which do not contain the appropriate Info Mask.
If you select the Setup Info Mask command, the corresponding dialog will be
displayed (figure 47), and the last-accessed Info Mask is automatically loaded.
The file name and path of the Info Mask is displayed in the Current Info Mask
line.
Figure 47: Setup Info Mask
Depending on the number of lines up to 7 pages can be displayed, similar to the

Information Input dialog. To create a new information mask click on the Clear
All button. All entries will be deleted and only the first page is available. All
entry fields will all be highlighted in red (see figure 48).

Setup Info Mask
Figure 48: Setup Info Mask - defining entry fields
As soon as you have started to enter data, the entry field color will change to
white. When entering data, make sure that the entry fields are filled in one after
the other. Be careful not to skip a line.

Edit
Figure 49: Setup Info Mask - defining entry fields
You have to define all entry fields on the first page before being able to open a
new page by the Next Page button. Save the information mask by clicking on
the Save Definition button. If an information mask with the same name already
exists, you will be asked whether you wish to overwrite the existing mask.
To load and edit an existing mask click on the Load Text Definition button.
Changes can easily be undone by clicking on the Restore Original button.
4.5 Structure Import
The Stucture Import command can be used for chemical structural formulae
created in Molfile format. These formulae can be imported to OPUS. If you
select the Structure Import command, the Structure Import dialog opens. Load
the corresponding files.
Files in Molfile format have the extension *.MOL. An OPUS file is created for
each structural file, using the same file name and a consecutively numbered
extension (starting with 0). This OPUS file is automatically loaded into the

Edit/Create Structure
OPUS browser window. Double click on the Structure data block to have the
structural formula displayed within the Structure window type registered in
OPUS. For details on how to attach a structural formula to an OPUS file, see
section 4.7.
4.6 Edit/Create Structure
The Edit/Create Structure command provides a general interface to any

software that supports the Molfile format. You can use an editor of your own
choice. Bruker provides an editor suited for this interface.
OPUS files with structural formulae are automatically converted into Molfile
format and stored in the Search sub-directory, using the BIRSY.MOL file name.
The file name, including the path, is transferred to the editor using the command
line. If your editor supports command line parameters, the structural formula
will automatically be displayed. You can edit the structural formula and store it
in Molfile format. The file edited in Molfile format will automatically be
converted into the OPUS format.
Figure 50: Edit/Create Structure – Edit Structure tab
On the Edit Structure tab you can create a new structural formula, or edit an
existing one. In the first case, activate the New Structure File check box. An
empty file will be created and transferred to the structure editor. Define the file
name, including the path. To edit an existing structural formula drag and drop
the file into the entry field displayed (see figure 50), and click on the
Edit/Create Structure button.

Edit
Figure 51: Edit/Create Structure – Choose Editor tab
Click on the Choose Editor tab to specify which structure editor you want to use
in combination with the Edit/Create Structure interface. Enter the program
name, including the path, into the Structure Editor entry field or use the Browse
button to search the directories for the editor program. The Scaling Factor
determines the size of an imported structural formula.
4.7 Attach Structure
Having imported a structural formula you can assign this formula to an OPUS
spectrum file. The structural formula will automatically be converted into the
OPUS format.

Convert 3dJcamp
Figure 52: Attach Structure
Load the spectrum into the OPUS browser window and drag and drop it into the
Select OPUS Spectrum entry field. Specify the name of the structural formula
file. You can also use the Browse button to locate the file. Click on the Attach
Structure button to include the structural formula into the OPUS file.
4.8 Convert 3dJcamp
The Convert 3dJcamp command allows to convert JCAMP spectra files into the
OPUS format. A JCAMP file can consist of several spectra. Each spectrum of a
JCAMP file has to have a specific format. The following file extract exemplifies
such a format:
##TITLE=Butanoic acid
...
...
##CAS REGISTRY NO=107-92-6
...
450.0 637 638 621 624 638 665 702 723 741 798
490.0 839 862 888 935 928 967 1021 1000 996 1098
530.0 1133 1222 1328 1382 1488 1531 1571 1558 1559 1570
570.0 1572 1637 1678 1756 1802 1942 1924 1905 1927 1920
...
The "..."characters represent additional information lines, all starting with "##"
(exceptions see below), or additional lines of data points.
For further details on how to convert information lines into OPUS parameters,
refer to chapter 14.2.

Edit
The CAS REGISTRY NO information line is obligatory if a structure formula

JCAMP file also exists. For the reason that the spectrum is assigned to the
molecular structure according to the CAS number. The structure of this
spectrum is available in OPUS in the form of the STR (structure) data block
( ).
If you click on the Convert3dJcamp command, the following dialog opens:
Figure 53: Convert 3d-JCAMP-Files - Select File(s) tab
In the Select 3-D JCAMP files group field you define the file name of the 3-D
JCAMP file which includes the spectra information. You either type in the file
name manually with the complete path or click on the Browse button to select
the file in the directory structure.
Optionally, you can enter the file name of the molecule structure file. If you
skip the Molecule structure file entry line, the OPUS spectra created will not
include a STR data block.

Convert 3dJcamp
Format of JCAMP structure formulae

The format of a molecular structure may be as follows:
c:75014
C2H3Cl
2:(303,155,320,165;2)(337,156,320,165;1)
1:(3,Cl)
0:
The first line includes the CAS number followed by the sum formula, bonding
data and the names of foreign atoms.
You can also add the melting and boiling points of the different substances to
the OPUS file INFO data block. Make sure that you add the data at the end of
the JCAMP structure file, line by line as follows:
,CAS_NO,MELTINGPOINT,BOILINGPOINT,
Example:
,1571864,75.0,263.0,
Always write a comma at the beginning and at the end of the lines.
In the Target group field (figure 53) you specify the OPUS format which the
JCAMP spectra have to be converted to. You can select between three option
buttons:
• 1-D OPUS files:
Each JCAMP spectrum is stored separately as OPUS spectrum. The
file name is a combination of the TITLE and CAS REGISTRY NO
information lines used in the JCAMP file. If you check the 1-D
OPUS files option button, you also have to specify the target path.
Either type in the target path name manually or click on the Browse
button to select the path from the directory structure.
• 3-D OPUS files:
The 3-D-JCAMP file is converted into a 3-D-OPUS file. This is
useful if the spectra have been acquired by chromatography, or if all
spectra are a compound of always the same substance which comes
in different concentrations. You can also define this substance
concentration in the information line for each spectrum. The format
in the JCAMP file must be as follows:
##CONCENTRATIONS= (NCU)
(<Glucose>, 2.100, %)
(<Lnvisco104>, 1.131, %)
In this case the substance name, quantity and quantity unit will be
included in a text file (in table format) which will be created apart
from the OPUS file and with the same file name. This is helpful if the
data are used to perform a QUANT analysis. In this case the

Edit
concentration data can be used from the text file by means of the
clipboard.
Either type in the target path name manually or click on the Browse
button to select the path from the directory structure. You also have
to specify the OPUS target file name without extension. If the 3-D
OPUS file already exists, it will not be overwritten, but the name
incremented.
• OPUS library
All spectra are stored in an OPUS library, including spectra
information and possible structure data blocks. Either type in the
target path name manually or click on the Browse button to select the
path from the directory structure. You also have to specify the OPUS
target file name without extension. If the OPUS library already
exists, it will be overwritten.
Click on the Convert button to start the conversion. The conversion progress
will be indicated by the status bar on the bottom right. If one of the information
lines includes the sum formula, the molecular mass will be calculated from this
formula, indicated in atomic units and entered in the INFO data block of the
respective spectrum.
To undo the settings click on the Cancel button and the dialog will be closed.

Toolbars
5 View
The View menu allows to configure the OPUS user interface. You can define
the toolbars, hide or unhide the status bar or the browser window.
Figure 54: View Menu
5.1 Toolbars
Use the Toolbars option from the View menu or right click onto the OPUS
toolbar to open the Toolbars dialog box. This dialog box allows to configure
single icons or even complete toolbars.
Figure 55: Toolbars Configuration
If you check the different boxes, you activate or deactivate the different toolbars
on the user interface. Click on the New button to create a new toolbar.
Customize allows you to adjust the toolbar according to your individual
preferences. A second dialog box will open, see figure 56.

View
Figure 56: Customize Dialog
Click on the Toolbars tab and select the toolbar you want to customize. If you
activate the Show Tooltips check box, additional info text pops up which
describes the function of a specific icon when you position the cursor on it. New
Look means that the line between the icons on the toolbar will not be displayed.
This is set by default. To enlarge the icons displayed, activate the Large Buttons
check box.
Click on the Commands tab and select the categories you want to customize.
Each category selected is exactly described on the lower part of the dialog box,
see figure 57. You can drag the icons directly into the toolbar. If you want to
remove an icon from the toolbar, simply drag the specific icon from the toolbar
and drop it outside the bar.

Status Bar
Figure 57: Customize – Commands
5.2 Status Bar
The status bar informs you about the background tasks of programs running in
the OPUS, and displays their current status. To activate or deactivate the status
bar, check or uncheck the Status Bar option.
5.3 Browser
By default, the OPUS user interface always displays the browser window on the
left side. If you deactivate the Browser option, only the spectrum and overview
window will be displayed on the screen. Apart from this option you can also
reposition the OPUS browser window (see section 6.4).

View

New Spectrum Window
6 Window
The Window menu allows you to open new windows and to customize their
position and appearance. If you load a file, OPUS automatically opens the
appropriate window to this file. For example, if you open a 3D file, OPUS
directly opens a 3D window and displays the spectrum accordingly.
Figure 58: Window Menu
6.1 New Spectrum Window
OPUS allows to display several spectra in one spectrum window, and to display
spectra in different windows. If you select the New Spectrum Window option, a
new spectrum window opens, indicated by the tab at the bottom
of the spectrum window. Click on the respective tab to switch between the
windows.
6.2 New Report Window
Apart from spectra and interferograms OPUS files store different data as well.
For example, the results of a peak picking evaluation and its parameters used
can be listed numerically. The data are displayed by dragging the PEAKS (peak
pick) data block into the report window.
6.3 New Registered Window
If you click on the New Registered Window option, a drop-down list opens
which includes all possible types of OPUS windows. The number of windows
may vary, according to the additional software packages installed. Therefore,
the list in this manual may not exactly reflect the list contents displayed on your

Window
screen. You can open any type of blank window by selecting the window from
this list.
Window Name Type

3d, 3d+ To display three-dimensional plots.
Cluster Analysis To display a dendrogram or histogram (part of OPUS
IDENT).
Display To display spectra.
Library To display libraries and their detailed information.
OldReport Shows report in the OPUS/OS2 format.
Process Control To display a standard trend chart (part of OPUS PROCESS).
Report To display report blocks.
SearchResults To display the result of a search performed using Spectrum
Search and other Search functions.
SingleReport To display a report without the tree structure.
Structure To display molecular structures, generated with a structure
editor (part of OPUS SEARCH).
Text View To enter text. See section 6.3.1.
6.3.1 Text View

Select Text View from the drop-down list. The Text View window is indicated
by the tab. There are three possibilities to enter text into the
OPUS Text View window:
1) Keyboard
Place the cursor into the window and enter text using your keyboard.
2) Copy and Paste
It is possible to copy and paste text in the Text View using the shortcuts
Ctrl+C and Ctrl+V.
3) Drag and Drop a text file
Drag and drop a text file into the Text View window.
You can only drag one file into the Text View window. If there has
already been a text file in the Text View window, this file will be
replaced and the text is overwritten unless you press the CTRL key dur-
ing the Drag and Drop operation. In this case the text of the dragged file
is appended to the content of the file which has already been open.
To select a text passage within the Text View window, move the cursor to the
relevant text passage and press the left mouse button. You can also use the Shift
and one arrow key to mark a text passage. If you want to delete a text passage,
you can either use the Backspace ( ← ) or Delete key, or you select the text and
use the CTRL+X shortcut. It is also possible to use the Cut command from the
Edit menu.
Cascade and Tile Windows
To save a text file, right click on the Text View window and select the Save
option from the pop-up menu.
6.4 Cascade and Tile Windows
You can either cascade or tile the different windows, see Figure 59 and 60.
Figure 59: OPUS User Interface – Tiled Windows

Window
Figure 60: OPUS User Interface – Cascaded Windows
In connection with the OPUS browser pop-up menu you can further configure
the appearance of your OPUS interface. Right click on the browser window.
The following menu pops up:
Figure 61: Browser Pop-Up Menu
If you select Allow Docking, the windows (browser, spectrum and overview
window) are displayed next to each other within the OPUS interface. If you
deactivate this option, you can remove the browser window from the OPUS
interface and position it somewhere else on the Windows desktop.
The Hide option makes the browser window invisible. To undo this setting,
activate Browser in the View menu.
Float In Main Window opens the browser and spectrum window in equal size
on the OPUS user interface. You can switch between these two windows by
clicking on the corresponding tabs at the bottom.

Arrange Icons
6.5 Arrange Icons
If you have minimized several spectrum or report windows, you can have their
icons arranged according to the Windows settings. By default, the icons are
arranged at the bottom of the OPUS user interface.

Window

Configuring the Optics
7 Measure
OPUS supports the configuration and adjustment of spectrometers. You can
immediately start measurements as well as define, save and reload measurement
experiments. Additionally, you can use OPUS to control external spectroscopic
devices, and you can have your data acquisition triggered by external signals. If
an Ethernet interface is used to communicate with the spectrometer, you have to
install the Microsoft Internet Explorer 5.0 or higher.
Figure 62: Measure Menu
When installing the optics a Bruker service engineer has already saved the
optics configuration in OPUS. If you change or modify the spectrometer, you
have to adjust these settings accordingly.
7.1 Configuring the Optics
To define the type of your spectrometer use the Configuration selection box on
the Optical Bench tab of the Optic Setup and Service command. Figure 63
shows Vector 22 as configuration. If a spectrometer is connected to the PC, it
signalizes the firmware version (i.e. software inside the spectrometer) to OPUS.
Additionally, the acquisition processor (AQP) type, AQP software version
number and AQP memory size are displayed (see figure 63), provided no
Ethernet connection has been used.

Measure
7.1.1 Optical Bench
Figure 63: Optic Setup and Service – Optical Bench tab with VECTOR configuration
If the AQP simulates an Optic Bench check box is activated, the communication
between OPUS and your spectrometer will be disabled. This check box is used
for test purposes only, as all measurement commands are performed in
simulation mode and not on the optics bench. The AQP generates
interferograms which include a simulated noise signal.
Spectrometers with Ethernet connection, e.g. MATRIX or TENSOR series have

no AQP installed. These instruments are connected via a network and use a
URL (Uniform Resource Locator) that needs to be defined during the setup. The
Optical Bench tab looks slightly different in case of these spectrometers (see
figure 64).

Figure 64: Optic Setup and Service – Optical Bench tab with MATRIX configuration
7.1.2 Devices/Options
On the Devices/Options tab you specify the components installed in your
spectrometer. Make sure that the settings correspond to the spectrometer
configuration. To activate a component, select the respective check box (see
figure 65).

Measure
Figure 65: Optic Setup and Service – Devices/Options tab
All available options can be configured using the Setup button. Figure 66
exemplifies a detector configuration.
Figure 66: Detector Configuration

Figure 66 shows as common configuration a Test Ramp for test purposes, and a
DTGS detector for measurements. These options are displayed in blue. As
special feature the spectrometer defined has been equipped with an MCT
detector.
Click on the Add New Item button and enter the 2=MCT definition into the
respective line. This entry is now displayed in black. Entries displayed in black
can always be edited and deleted. If an option has not yet been available (or
should not to be used at the moment), deactivate the respective check box.
Some detectors, e.g. MCT detectors, show non-linearity between sample

concentration and peak intensity. If these detectors are used to perform a
quantitative analysis, it is necessary to know this non-linearity to be able to
correct it.
If you edit a line, it will be displayed inversely (e.g. white on black). A line
selected can be vertically moved by clicking on the Item UP and Item DOWN
buttons. Confirm your changes by clicking on the OK button, or discard them
by clicking on the Cancel button.
The direct result of a data acquisition is always an interferogram. This

interferogram can be transformed into spectra of various types, e.g. absorbance,
transmittance or reflectance spectra. A result spectrum type will only be
available if you activate the respective result type check box in the Setup Result
Spectrum list (figure 67).
Figure 67: Setup Result Spectrum

Measure
If a result spectrum type is not available in the list or deactivated, it cannot be

requested in the method.
Note: If you have created a measurement method and subsequently edited the
optics configuration, this may cause the method to be incompatible to the optics
settings. A red error symbol on the different Measurement dialog tabs indicates
this kind of problem.
Special features in case of Raman experiments

If you use a laser as light source, you have to define its wavelength and
maximum power output. A special format is required for this kind of entries.
Click on the Devices/Options tab of the Optic Setup and Service dialog.
Activate the Source check box and click on the Setup button. The special format
will be displayed on the bottom of the dialog box (see figure 68).
Figure 68: Source settings in case of Raman instruments

7.1.3 Interferometer/AQP
On the Interferometer/AQP tab of the Optic Setup and Service dialog (see
figure 69) you can set the values for the absolute peak position, laser wave
number, resolution, data rate and the maximum FT size.
Figure 69: Optic Setup and Service - Interferometer/AQP tab
You have to experimentally evaluate the Absolute Peak Position of your system
by using the Check Signal tab of the Measurement dialog. This value has to be
re-adjusted if the detector or laser have been replaced, or if the optics has been
completely re-adjusted. In case of multi-channel measurement, the laser wave
number can be specified individually for each channel if a channel-specific IT-
Test is possible.

Measure
7.1.4 Export Options

You define the file format of an OPUS data file on the Export Options tab (see
figure 70). The OPUS option box is checked by default. Optionally, you can
also export the data to GRAMS format. Make sure that the GRAMS software
runs on the main memory of your computer, together with OPUS, while
exporting data.
Figure 70: Optic Setup and Service - Export Options tab

7.1.5 Service
The Service tab (see figure 71) includes the OPUS diagnostic functions, i.e.
diagnostic results and statistics of the spectrometer. Clicking on the buttons on
the right side resets the parameters displayed. Note that the diagnostics test must
have been performed at least once after the installation of OPUS, otherwise no
test results will be available. You can repeat the diagnostics test by clicking on
the Repeat Diagnostics Test button.
Figure 71: Optic Setup and Service - Service tab
The upper two buttons refer to the HeNe laser parameters. Some lasers show
sporadic power fluctuations during operation, which influence the
interferometer control. These fluctuations are automatically recorded by an
internal counter. The fluctuation value should always be 0, other values would
indicate an error. If the fluctuations increase, you have to replace the laser. Use
the Reset Laser Dropouts button to reset this counter to 0.
If you have replaced the laser, you can set the laser operating time meter to 0 by
using the Laser Replaced (Reset Parameters) button. At the same time, the
value of the laser start intensity is read again.
The Source Replaced (Reset Parameters) button resets both the counter of the
total source operating time and the counter of the on/off source cycles if you
have replaced the source.

Measure
The remaining buttons determine the control parameters of the spectrometer

stepper motors. The number and position of stepper motors depend on the
spectrometer type. To read the parameters of all motors click on the Update
whole Motor Table button. The other buttons read the status of specific motors:
• Update Aperture Motor Table – motor to control the aperture
• Update Channel Motor Table – motor to switch beam ports
• Update Detector Motor Table – motor to switch detectors
• Update Source Motor Table – motor to switch sources
• Update Calibration Filter Motor Table – motor to control the
calibration filter
• Update Polarizer Motor Table – motor to control the polarizer
• Update Sample Changer Motor Table – motor to move the sample
wheel
• Update Flaps Motor Table – motor to control the flaps
7.1.6 Optic Communication

To monitor the AQP communication click on the Optic Communication tab
(figure 72). Check the Auto Scroll box if you want the list to automatically
scroll.
Figure 72: Optic Setup and Service - Optic Communication tab
In case of spectrometers connected by a network the Optic Communication tab

includes the appropriate URLs.

Measurement
Figure 73: Optic Setup and Service - Optic Communication With URLs
7.1.7 Control Panel

This option applies to the IFS 125HR spectrometer only and is described in the
IFS 125HR user manual.
7.2 Measurement
After you have configured your spectrometer you can start to set up an
experiment. Basically, two types of measurement modes are possible:
Advanced Measurement and Routine Measurement. The difference between
these two modes is the number of parameters to be set up. The
Advanced Measurement mode provides access to all parameters, and the
Routine Measurement mode provides only a pre-selection of parameters most
reasonable for the spectrometer. In this case you only have to select very few
parameters to perform a measurement. Note that the Routine Measurement
mode is not available for all instruments.
When working in a validated environment (see chapter 14.10), the

Setup Measurement Parameters command allows to load and edit a
measurement without actually performing this measurement.
Special considerations and conditions in case of Raman measurements will be

explained in section 7.2.11.

Measure
If you start OPUS, the parameters used for the last OPUS experiment will be
loaded by default. If this is exactly the experiment you want to use, just
continue, otherwise you will have to load a new experiment.
By clicking on the Exit button you save all parameter settings made in the
Measurement dialog box, except the interferogram peak position. The peak
position has to be saved separately by clicking on the Save Peak Position button
on the Check Signal tab (see figure 88). If you click on the Cancel button, you
exit the dialog box without saving the changes made. You can use the Cancel
command as an Undo command for all changes made, except for peak positions
saved.
7.2.1 Error and Warning Symbols

Configuration errors are indicated by colored entry fields, and warning symbols
on the corresponding tab. Errors during measurement may be caused by:
a) The method loaded is not compatible with the spectrometer configuration.
b) A parameter value is beyond the allowed limit.
Example 1:
Figure 74: Error caused by wrong selection
The red symbol on the Optic tab indicates a parameter mismatch with the
existing hardware. The Source Setting entry field is marked in red. If you place
the cursor on the drop-down list, a help text pops up indicating Globar (MIR).
This means, that Globar (MIR) has been entered as source in the method, but
the spectrometer is not equipped with a globar. Open the Source Setting drop-
down list to see the sources available. After correcting the entry, the warning
symbol will disappear.

Measurement
Example 2:
Figure 75: Error caused by wrong parameter
If the value of a parameter is beyond the allowed limits, the symbol will be
displayed. If you place the cursor on the respective entry field, a help text pops
up indicating the cause of error. In the example shown in figure 75 the
resolution of 0cm-1 is too small as the resolution has been set to 0.25cm-1 in the
optics configuration for the spectrometer.
Example 3:
A warning symbol will not necessarily be displayed on the tab on which the last
change has been made. In the following example the Wanted High Frequency
Limit on the Acquisition tab has been changed from
to
Consequently, the symbol will be displayed on the Advanced tab. Place the
cursor on the respective entry field, to have the help text displayed.
Figure 76: Error caused by wrong frequency limit

Measure
Example 4:
In this example the resolution has been set to 1cm-1 on the Advanced tab, and
the frequency range has been set from 4000cm-1 to 400cm-1. In the Aperture
Setting drop-down list an aperture size of 10mm has been selected.
Figure 77: Information about restrictions on measurement
The measurement can be performed, but the resolution desired cannot be

achieved above a wave number of more than 1300. This will be indicated by the
symbol on the Optic tab, and a yellow entry field.
Example 5:
If you select User settings from the Setup menu, you can disable the parameter
change function. Deactivate the Change Parameters check box on the
Rights tab.
This may cause that a wrong parameter cannot be corrected. In this case the
error will be indicated by the symbol.
Figure 78: Error caused by limited user rights
Use a different measurement experiment.

Measurement
7.2.2 Basic
The basic parameters for data acquisition can be found on the Basic tab of the
Measurement dialog box.
Figure 79: Measurement – Basic tab
On the Basic tab you specify:

• Experiment
• Operator name
• Sample name (e.g. identification for the sample)
• Sample form (short description)
• Path (where the measurement result is to be saved)
• File name (of the result)
The information about sample name and sample form is optional and will be
stored in the INFO data block of the spectrum. If the measurement parameters
differ from the parameters used in the loaded experiment, the experiment name
is displayed in yellow. These parameters are additionally listed in the
HISTORY data block of the spectra acquired.

Measure
If you accept the default settings of the measurement parameters specified on

the remaining tabs, you can directly start measurement. Either click on the
Background Single Channel or Sample Single Channel button. As soon as the
measurement has been finished, the parameters used will automatically be
stored together with the results. These parameters can be accessed by the OPUS
browser pop-up menu (see chapter 2.2).
During measurement the progress is indicated by the status bar at the bottom
right of the OPUS workspace. To interrupt the measurement right click on the
status bar, and a menu pops up including three different options.
Figure 80: Pop-Up Menu to Stop Tasks
The Stop Task option interrupts a running measurement (a repeated

measurement will be continued by the next spectrum). To completely abort a
repeated measurement select the Abort Task option. If you click on the Task
Window option, an additional menu pops up including the current OPUS tasks
running.
Figure 81: OPUS Task List
Select one task from the list and click on the Stop Task or Abort Task button. If
the measurement has been completed, the No Active Task message is displayed
in the status bar.
Except for emission, Raman or single-channel spectra it is always necessary to

acquire a background spectrum to eliminate frequency characteristics of the
source, spectrometer or sample matrix. This correction is automatically
performed after the sample measurement has been completed.

Measurement
7.2.3 Advanced
On the Advanced tab you can specify the directory path, and the data file name
of the spectra to be saved. Starting with the second measurement, the data file
name will be incremented, indicating the current number of measurements.
All parameters can be saved in an experiment file on the Advanced tab. Click on
the Save button. The Select Experiment File Name dialog opens. Specify a name
for the measurement experiment defined. This name can be used to re-load the
experiment.
On the Advanced tab you define the resolution and spectral range.
Alternatively, you can determine the number of scans per spectrum, or the total
time of all scans.
Figure 82: Measurement – Advanced tab
Do not set the resolution higher than necessary to minimize the total acquisition
time. Improving the resolution, e.g. by a factor of 2, requires a four- times
higher acquisition time at a constant signal-to-noise ratio of the spectrum. This
is due to the fact that the signal-to-noise ratio is proportional to the square root
of the acquisition time.

Measure
Possible result spectrum types have already been determined when configuring
the optics. You can now select the result spectrum type from the drop-down list.
In figure 82 Transmittance has been defined as result spectrum, and is
automatically checked as first data block in the Data blocks to be saved group
field. You can check further data blocks. A background spectrum can, of
course, only be saved if it has been acquired before.
Use the Exit button to save the settings.
7.2.4 Optics
Depending on the optics configuration the number of entry fields displayed in
figure 83 may be different.
Figure 83: Measurement – Optics tab
Select an aperture setting from the Aperture Setting drop-down list. The
aperture size defines the spectral resolution. An A aperture diameter causes a δσ
spectral peak broadening1 at a σ wave number (provided an F fixed focal length
of the collimated mirror in front of the interferometer is given):
A2
δσ ≥ --------2- ⋅ σ
8F
1. More precisely: a convolution with a delta function of width δσ.

Measurement
Select the channel you want to use for the measurement (e.g. Front, Back or
External). If your spectrometer is equipped with several detectors, select the
detector to be used in the Detector Setting drop-down list.
The scanner velocity depends on the detector type installed and the current
experiment. Select a slow scanner velocity (<10kHz) for photoaccoustic
experiments. For DTGS detectors and photodiodes 10kHz are adequate, while
you should use a higher velocity (>10kHz) if your spectrometer is equipped
with MCT or InSb detectors.
We recommend to set the Sample Signal Gain and Background Signal Gain
values to Automatic. The optimal value is automatically determined by a
separate short scan before the measurement starts, to ensure that the complete
dynamic ADC range will be covered.
The Switch Gain setting allows to amplify the interferogram by 2N within the
spectral ranges which are quite off the centerburst. This has almost the same
effect as if you enhance the ADC dynamic from, e.g. 16 to (16 + N) bit, which
reduces digital noise. This aspect is important for data acquisition in high
resolution when using a broad-band source. The window width around the
centerburst can be specified in the Window in Points field.
You can define time intervals before a measurement start or device change.
Enter the respective time intervalsin seconds into the Delay after Device
Change or Delay Before Measurement entry fields. The Delay after Device
Change option will only be performed if certain parameters, e.g. sample
changer position, detector, measurement channel, have been changed to avoid
problems especially in case of slow detectors (DTGS). A Delay Before
Measurement avoids detector saturation if certain parameters (e.g. detector,
measurement channel) have been changed.
7.2.5 Acquisition
Set the high and low frequency limit on the Acquisiton tab. The actual
frequency limits will then be calculated and may deviate from the values set and
are therefore displayed next to the Wanted High or Low Frequency Limit entry
field on the right (see figure 84).
Restricting the sampling bandwidth reduces the amount of data and may be
useful when recording high resolution spectra. However, electronic and/or
optical filters have to be used to ensure that signal intensity is 0 beyond the
selected frequency limits. Otherwise, the signals may be convoluted or folded to
the selected range, and may adulterate the intensity.

Measure
Figure 84: Measurement – Acquisition tab
Additionally, you can specify the Low Pass Filter, High Pass Filter,
Acquisition Mode and Correlation Mode settings. The acquisition mode defines
whether one or both sides of the interferogram is measured, and the correlation
mode checks the data integrity.
As the interferometer mirror continuously moves, all frequency components of

the IR spectrum are depicted in a detector-response spectrum. This kind of
spectrum is in a lower frequency range, its bandwidth can be limited by using
electronic filters.
The high pass filter limits the bandwidth within the high frequency ranges.
Activate the filter by selecting On from the drop-down list, deactivate the filter
by selecting Open. Note that this electronic filter is not available for all
spectrometers.
Use the low pass filter to limit the bandwidth in the low frequency ranges. As
the mapping of IR wave numbers to frequencies in the low frequency range is
proportional to the scanner velocity v, the fixed cut-off frequency f of the filter
(in Hz) corresponds to a wave number σ which depends on v as follows:
σ [ cm –1 ] = f [ Hz ] ⁄ v [ cms – 1 ]

Measurement
In case of the acquisition mode you can select between several options:
• Single Sided: this option only allows the measurement of one-sided

interferograms, data acquisition is performed only during the forward
mirror movement.
• Double Sided: the interferogram is measured on both sides, data
acquisition is performed during the forward mirror movement. In this
mode the time resolution amounts to half the value achieved in Single
Sided mode. The signal-to-noise ratio shows an improvement of 2 ,
and the ordinate accuracy is higher compared to the Single Sided
mode. The Double Sided acquisition mode is suitable for Raman,
Emission, phase correction measurements and high-resolution
quantitative measurements.
• Forward/Backward: data acquisition is performed during the forward
and backward mirror movement. Forward and backward scans are
separately co-added, calculated and added. This option reduces dead
time, improves the signal-to-noise ratio, but requires twice as much
computation time.
• Fast Return: this mode offers a fast mirror retrace without data
acquisition. This causes less dead time and a better signal-to-noise
ratio.
Fast Return and Forward/Backward modes are not available for all types of
spectrometers. On condition that the measurement times are identical, the
signal-to-noise ratio improves in the following order:
S/N (no Fast Return) < S/N (Fast Return) < S/N (Forward/Backward)
The correlation mode determines whether a data integrity check is performed

during data acquisition. You can select between the following options:
• No: data will not be checked.
• Around Peak, Low: is only available, if several scans are averaged.
Each new interferogram is compared to the first one within a range
around the centerburst. If the deviation exceeds the threshold the
interferogram will be discarded. Otherwise, the interferogram will be
used for averaging.
• Around Peak, High: same as Around Peak Low, but the limit is more
sensitive to minor changes (e.g. caused by thermal drift in case of
long-term measurements).
• Full Igram Length: all interferogram points are compared to each
other. An interferogram is discarded if the points contain more than
ten defective areas or if the number of defective points exceeds one
eighth of the total number of interferogram points.
Activate the Interferogram acquisition directly to hard disk check box if you
want to save the data acquisition results directly to hard disk.

Measure
7.2.6 FT
On the FT tab you define the phase resolution. Set the phase resolution in such a
way that the number of Phase Interferogram Points amounts to at least 250.
The phase correction increases the interferogram symmetry. Phase correction is

always necessary as the interferogram measured is never perfectly symmetric.
For details on the phase correction method, see chapter 8.15. Select the
Phase Correction Mode and Apodization Function from the respective drop-
down list.
The Zerofilling Factor value has to be of 2n order within the range between 1
and 512.
Figure 85: Measurement – FT tab
7.2.7 Display
On the Display tab you can define the axes settings for the spectrum display
during measurement. It is possible to define upper and lower limits for the x-
and y-axis.
If you activate the Display single scans before measurement check box, the
spectrum will be calculated by single scans and displayed, before the actual data
acquisition starts. The actual data acquisition is performed as soon as the
operator starts measurement.

Measurement
To display intermediate results during measurements, activate the Display

during measurement check box.
Figure 86: Measurement - Display tab
7.2.8 Background
Normally, the background spectrum remains in the AQP. Use the Background
tab to transfer the background spectrum from the AQP to the PC and save it
there. Click on the Clear Background button to delete the background spectrum
from the AQP.

Measure
Drag & drop the saved background spectrum from the OPUS browser window
or Windows Explorer into the selection field below the Load Background
button. If you click on the Load Background button, the background spectrum
will be transferred to the AQP and can be used for spectra calculations.
In case of MATRIX and TENSOR spectrometers the background spectrum is

saved in the OPUS.BG file within the OPUS directory. When starting OPUS the
last-used background spectrum, i.e. the OPUS.BG file, will automatically be
loaded to the AQP.
Figure 87: Measurement – Background tab
7.2.9 Check Signal

The appearance of the Check Signal tab depends on the spectrometer
configuration. Besides the options and commands displayed in figure 88 you
may have additional functions available for your system.
To determine and save the exact interferogram peak positionyou have to open
the Check Signal tab at least once after you have installed your spectrometer.
The purpose of checking the signal is to either achieve a maximum
interferogram signal or optimize the shape of the single-channel spectrum.

Measurement
Figure 88: Measurement - Check Signal tab with interferogram
Similar to the spectrum display in the spectrum window you can also zoom in a
particular section. The interferogram shown in figure 88 and 89 has been
created by the AQP simulation mode. Therefore, the interferograms of your
spectrometer used may be different.
Figure 89: Interferogram zoomed-in

Measure
To undo the zooming click on the Scale Display button and the interferogram
will be scaled on the intensity axis.
If the maximum interferogram value is not displayed, move the range by using
the and buttons.
In the upper right corner of the interfergram plot the amplitude and zero-
crossing position of the interferometer are displayed. If the peak position is
constant, you can save it by clicking the Save Peak Position button.
To monitor the amplitude and zero-crossing position even when adjusting the
interferometer from a considerable distance, check the ADC Count option
button in the Show group field. The graphical display of the interferogram will
be replaced by a numerical one.
Figure 90: Numerical display of ADC count
Check the Interferogram option button to return to graphical display. To Fourier

transform the interferogram during adjustment and have it displayed as single-
channel spectrum, check the Spectrum option button.
Stepper Motor Adjustment

In case of spectrometers providing a software-controlled adjustment of the
interferometer by using stepper motors, the motor control panel is displayed at
the top on the left.
(a) Automatic alignment
(b) Manual fine alignment
(c) Motor display and control
(d) Restore (0,0) position of motors
Figure 91: Menu to adjust stepper motors

Measurement
The motors can be controlled manually by using the arrow buttons. Click on
the Auto Align button to start an automatic adjustment. Use the Fine Auto Align
button to correct minor misalignments within the near range of the current xy-
coordinates. This is especially recommended if you measure spectral regions of
higher frequency (NIR to UV). The Fine Auto Align function produces the same
result as the Auto Align function, however, it performs faster than Auto Align as
it covers a smaller frequency range.
7.2.10 Beam Path

Whether the Beam Path tab is available or not depends on the spectrometer
type. Use the Beam Path tab to visualize the spectrometer beam path which is
based on the parameters defined on the Optic tab.
If you position the cursor on a beam path component, e.g. source, the
component description pops up. Double click on the source component to have
the beam path displayed. Figure 92 shows a TENSOR 27 beam path. Depending
on the spectrometer used it is also possible to interactively change the
measurement parameters (e.g. source, detector, measurement channel) on the
Beam Path tab. Left click on one of the beam path components to activate or
deactivate it. All the changes made will be automatically stored on the Optic
tab.
Figure 92: Measurement - Beam Path tab (Tensor 27)

Measure
7.2.11 Raman Measurements

In case of Raman measurements you can also specify the laser power on the
Basic tab (see figure 93).
Figure 93: Raman Measurement - Basic tab
In standard configuration the laser will automatically be switched off after each
measurement. For some applications, e.g. series measurements, you can
deactivate this laser option. Uncheck the Auto Laser OFF check box.

Measurement
On the Advanced tab the frequency range for data storage will be displayed in
relation to the laser excitation frequency on a yellow background.
Figure 94: Raman Measurement – Advanced tab

Measure
On the Acquisition tab all frequencies are displayed in relation to the laser
excitation energy.
Figure 95: Raman Measurement – Acquisition tab

Repeated Measurements
The laser power can be set using the slider on the Check Signal tab. The actual
performance will be displayed.
Figure 96: Raman Measurement - Check Signal tab
7.3 Repeated Measurements
The Repeated Measurements command allows you to define a measurement

series to automate data acquisition. The Repeated Measurements dialog box
differs from the Measurements dialog box only in the Basic tab. This tab
includes two additional entry fields:
a) Repeat the Measurement: define the total number of measurements
b) Delay between Measurements: define the total number of scans and the delay
between single measurements.

Measure
Figure 97: Repeated Measurements – Basic tab
7.4 Rapid Scan -

Time Resolved Measurement
The Rapid Scan Time Resolved Measurement command allows you to acquire
spectra in quick succession (not available for TENSOR, MATRIX, MPA,
IFS125 HR or VERTEX spectrometers). Typically, time-resolved
measurements (TRS) are performed to record sample changes or environmental
fluctuations, to achieve an absolute time resolution (i.e. maximum possible
number of measurements) or to repeat measurements with high time constant.
The result of this measurement is stored in a 3D file which includes all spectra
measured.
Contrary to the OPUS/CHROM software, no spectrum or chromatogram will be

calculated during data acquisition. Therefore, TRS measurements do not require
any additional computational power or any additional CPU capacity on your
AQP board. However, the AQP has to have sufficient RAM to store all
averaged interferograms. The following table lists the maximum number of
interferograms per run, using a bandwidth from 0 to 7900cm-1 and single-sided
data acquisition:

Rapid Scan - Time Resolved Measurement
AQP Memory Max. Number of Interfero- Max. Number of Interfero-

grams (8cm-1) grams (4cm-1)
1 MB 67 33
4 MB 480 240
16 MB 2130 1065
Basically, the Rapid Scan Time Resolved Measurement dialog box includes the
same commands as the Measurement dialog box (described in chapter 7.2, ff),
except for the Method Editor tab. Before you start a TRS measurement you
have to create an experiment.
Figure 98: Rapid Scan Time Resolved Measurements – Method Editor tab
The Method Editor tab is used to define the timer parameters of your
experiment. Time-resolved measurements are controlled by the following
components:
• Measuring single scans
• Measuring several scans (average)
• Waiting for an external TTL1 signal
• TTL signal output
• Optic commands output
1. Transistor-transistor-logic signal

Measure
• Message to the operator (wait for response)

• Wait times
• Start loop/end loop (repetition of a sequence)
You can directly program these components by using the respective buttons
displayed in figure 98 on the right. The commands and their corresponding
parameters are displayed on the left and can later be edited manually. It is also
possible to exclusively perform the command input manually. In the following
the commands of the different buttons will be explained.
• Message Box: enters the Message box xxxx command with xxxx being
a wildcard which can be edited. The text edited will be displayed
when running the TRS method.
• Comment: creates a comment line to make the method program code
readable.
• Optic Command: allows to send text commands to the optics during
run time to change certain parameter values.
• Set Buffer: specifies the memory area which has to be accessed. You
can use the same memory area several times, i.e. you do not need to
define a new memory area for repeated measurements or loops.
Example:
Measure 10 Scans to Buffer 5
Writes 10 scans to buffer 5
Buffer=1
Start Loop=100
Measure 1 Scan
End Loop
Writes 10 scans to buffer 1 to 100
• Start Loop: indicates that a loop starts. All commands enclosed
between Start Loop and End Loop will be repeated an n-times. You
can nest these loops as often as you want, provided that each Start
Loop statement is assigned to an equivalent End Loop statement.
• End Loop: marks the end of a loop.
• Wait (ms): the execution of the subsequent command will be delayed
by the specified period of time (in milliseconds).
• Reset Time Base: the time information stored with the spectra refers
to the start time of the measurement. If a Reset Time Base command
is executed, the waiting time is reset to 0.
• Wait Input “High”: delays the subsequent command until the 5V
TTL level is detected in the input bit specified. The following table
explains the correlation between the bits and pins of the 50-pole I/O
plug. The bit marked by an (s) is read by an especially fast command
and should therefore be preferably used in case of extreme time
resolution.

Rapid Scan - Time Resolved Measurement
Bit Number Pin Number Socket Pin Number Plug
4 13 5
5 14 38
6 15 22
7 (s) 16 6
• Wait Input “Low”: delays the subsequent command until the 0V TTL
level is detected on the input bit specified.
• Set Output “High”: sets the 5V TTL level to the output pin specified.
The following table explains the correlation between the bits and pins
of the 50-pole I/O plug. The bit marked by an (s) is read by an
especially fast command and therefore should preferably be used in
case of extreme time resolution.
Bit Number Pin Number Female Pin Number Male
Connector Connector
0 5 35
1 6 19
2 7 3
3 (s) 8 36
• Set Output “Low”: sets the 0V TTL level to the output pin specified.
• Measure NSS Scans: the total number of scans that will be averaged
is read from the Measurement dialog. The advantage is that there is
no need of rewriting a new TRS method, if the same method has to
be used with different numbers of scans.
• Measure N Scans: starts the measurement. The total number of single
scans to be averaged will be displayed after the Measure command.
Figure 98 shows the program code generated by these buttons. Below these
button there are the following three check boxes:
• Use Buffer 1 as Background: the background spectrum is measured
during TRS measurement and used to calculate the spectra. If this
check box is not activated, the background spectrum of the preceding
standard measurement will be used, which is the arithmetic average
of all forward and backward scans.
• Split Forward/Backward Interferogram: this check box can only be
activated if the Single Sided Forward/Backward or Double Sided
Forward/Backward option has been selected as Acquisition Mode. In
this case a buffer is split into a forward and backward scan, and the
scans are stored separately. This leads to a time resolution increased
by factor 2.

Measure
• Split Double-Sided Interferogram: this check box can only be

activated if the Double Sided Forward/Backward, Double Sided Fast
Return or Double Sided option has been selected as Acquisition
Mode. In this case a double-sided interferogram is split into two
single-sided interferograms, which increases time resolution once
again by factor 2.
If both check boxes, i.e. Split Double-Sided Interferogram and Split Forward/
Backward Interferogram, have been activated and the Double Sided Forward/
Backward option has been selected as Acquisition mode, 4 interferograms
(spectra) are generated per buffer. This yields to the maximum possible time
resolution at a given mirror velocity.
Enter a description of the method you have created into the Description entry
field (figure 98). Use the Save button to store the description. To access
previous methods click on the Load button. If you want to create a new method,
click on the New button. After creating the method you can check the syntax
programmed by using the Check Syntax button.
If you have defined a Rapid Scan measurement, start this measurement by

clicking on the Start Rapid Scan Measurement button on the Basic tab. The
measurement progress is displayed on the status bar. If the Split Forward/
Backward Interferogram mode is used, the status bar displays wice the
number of scans. The Measure 4 scans message, e.g., produces 4 forward and
4 backward scans, i.e. a total number of 8 scans.
7.5 Interleaved Time Resolved

Measurements
The electronics of several BRUKER spectrometers can generate up to 16 data

points (equidistant in time) per standard interferogram data point. This can be
used to analyze the kinetics of rapid processes which are completely
reproducible with as many as 16 time intervals. If the time required to digitize
n time intervals is higher than the time available between two normal
interferogram data points, the time intervals can be distributed over several
scans (interleave factor >1). The Interleaved Time Resolved Measurement
function is not available for TENSOR, MATRIX, MPA, IFS 125 HR or
VERTEX spectrometers.
If you select the Interleaved Time Resolved Measurements command, a dialog

opens including tabs which are quite similar to the other measurement dialogs
already described. Enter all parameters for interleaved measurements on the
Timing/Interleave tab.

Direct Command Entry
Figure 99: Interleaved Time Resolved Measurement - Timing/Interleave tab
• Time Resolution: Distance between two time slices in microseconds.

• Number of Time Slices: Number of n time slices which are to be
measured for each normal interferogram data point. Values between
1 and 16 are possible. n time slices will create n spectra.
• Trigger Delay: Delay between the trigger of a normal data point and
the digitalization of the first time slice in microseconds.
• Max. Experiment Repeat Rate: Maximum measurement repetition
rate. The actual repetition rate will be below this value.
After the measurement, the data are sorted into n interferograms which are
assigned to the respective time slices. If desired, the corresponding single-
channel spectra are calculated. Similar to TRS-measurements the results are
stored in a 3D data file.
7.6 Direct Command Entry
The Direct Command Entry command is especially used for test purposes and
in case of macros. Commands sent to the optics will be logged, and also be
displayed on the screen. If you click on a certain line in the entry field next to
the Send Command button, this command line can be repeated. The answers
sent by the optics are displayed in the field below.

Measure
Figure 100: Direct Command Entry
7.7 Optics Diagnostic
The Optics Diagnostic command allows a quick check of the spectrometer

components. In the Diagnose dialog the hardware components, e.g. source,
laser, interferometer etc. are displayed in the upper line. If the test has been
finished, the test result is displayed in the lower line according to the number of
test channels (IT RESULT) defined. For details on how to define test channels
refer to chapter 14.10.
A green check mark indicates that the test has been successful. The yellow
WARNING note means that the test time has been expired. If the test has not
passed, a red ERROR is displayed.
The instrument test, the so-called PQ test (Performance Qualification Test)

proves that the spectrometer measures correctly in terms of routine laboratory
work, and has to be performed every day.
For details on the diagnostics result log select the Optic Setup and Service
command and click on the Service tab.

Temperature Control
Figure 101: Optics Diagnostic - Instrument Status
7.8 Temperature Control
The Temperature Control command allows the operation and control of

external equipment, e.g. temperature-controlled stage.
Figure 102: Temperature Control – Basic tab

Measure
Select the respective serial port which the stage is connected to from the Serial
Port drop-down list. Specify the type of thermo-sensor in the
Temperature Control Device drop-down list. If you activate the
Use Serial Port default settings for this device check box, the default port
parameters will be set as specified in the operating system.
To set the required temperature click on the Set Temperature button. The
current temperature of the stage can be read by clicking on the
Read Temperature button. If macros are used to control the temperature, click
on the Wait for Temperature (Macro Only) button to stop the makros until the
desired temperature is achieved.
Figure 103: Temperature Control – Extended Commands tab
The Extended Commands tab allows command input. For details on the
corresponding commands, refer to the control unit manual. The following
syntax applies:
To read a command: R <command>

To write a command: W <command>
The command will only be transmitted if you press the Send button. Clear
provides a blank entry field. Save your command sequence using the Save
Settings button.

8 Manipulate
This chapter describes all OPUS data manipulation options. The term
Manipulate involves all arithmetic methods which modify or create new
spectral data of a spectrum acquired.
Figure 104: Manipulate Menu
The dialog boxes of the different Manipulate commands almost look like the
same. Each dialog box consists of the following tabs:
• The Select Files tab allows to select the files to be manipulated, as
well as to define the most important manipulation parameters. For
details, see section 2.1.

Manipulate
• The Frequency Range tab allows to define the spectral limits of

manipulation. For details on how to interactively select frequencies,
see section 2.7.
As the calculation results are only temporary files (work files), you need to
directly save them by using the Save File command of the File menu. If you exit
OPUS without saving the work files, the manipulation data get lost. Normally, a
warning pops up when you want to exit OPUS indicating the existence of data
which have not yet been saved.
8.1 Baseline Correction
You can perform a baseline correction for several spectra at the same time.
First, load the spectrum file(s) you want to correct by clicking on the Load File
command in the File menu. Select the Baseline Correction command in the
Manipulate menu. The file name will be automatically displayed in the File(s)
to Correct selection field. If not, drag and drop the spectrum file(s) from the
OPUS browser window into the respective selection field.
Figure 105: Baseline Correction – Select Files
You can either accept the baseline points automatically set by OPUS, or set
them manually. Click on the Start interactive mode button. A new window
opens which shows the original spectrum on top and the baseline correction at
the bottom. Check the Straight lines or Polynomes option button to adjust
straight lines or polynomes to the baseline.

Baseline Correction
Figure 106: Baseline Correction – Interactive Mode
Double click on the original spectrum to add a baseline point. The result of this
correction will be immediately displayed in the lower spectrum window. If you
want to remove a baseline point, double click on this point again.
You can also zoom spectra. Right click on the original spectrum and select the
Zoom In or Zoom Out command from the pop-up menu. For details, see
section 2.3. Click on the Store button to save the correction results (figure 106).
To automatically correct the baseline of your spectrum select the Select Method
tab (figure 105). A different dialog box opens and allows to specify the
correction method, e.g. Scattering or Rubberband, and the number of baseline
points. Optionally, you can exclude the spectral ranges which contain CO2
bands (between 2400 ... 2275cm-1 and 680 ... 660cm-1). This is only possible in
case of an automatic baseline correction.

Manipulate
Figure 107: Baseline Correction – Select Method
Specify the number of baseline points. Enter a value between 10 and 200
(unless the frequency range selected is too small). The default value is 64.
Select a correction method and start the calculation by clicking on the Correct
button.
Both baseline correction methods divide spectra in n ranges (n being the

number of baseline points) which are of equal size. In the case of absorbance
spectra the minima are determined within these n ranges. The baseline points
are connected by straight lines. From the bottom up a rubberband is stretched
over this curve. Each baseline point which is not exactly on the rubberband is
omitted. The rubberband serves as baseline.
If you check Scattering Correction, the rubberband is created in such a way that
at each point the slope of the baseline must be negative for an absorbance-like
spectrum (provided that the spectrum is displayed in decreasing wave numbers
from left to right).
Baseline corrections can also be performed on transmittance spectra. First,

maxima are determined in the transmittance spectrum and the rubberband is
calculated. Then, the original spectrum is divided by the rubberband. You will
get the same result if you convert the transmittance spectrum into an absorbance
spectrum, perform the baseline correction and re-convert the result spectrum
into a transmittance spectrum.
Figure 108 shows an original absorbance spectrum and a baseline-corrected

spectrum, using the Rubberband Correction method and 64 baseline points.

Baseline Correction
Rubber Band
Scattering Correction
Figure 108: Spectrum prior to and after Baseline Correction
If you subtract the corrected spectrum from the original spectrum, the baseline
can be determined, see figure 109.

Manipulate
Figure 109: Original Spectrum and Rubberband Baseline
8.2 Spectrum Subtraction
This kind of calculation subtracts spectra, with one multiplication factor each,
from a multi-component spectrum. An additive constant can be determined.
Click on the Spectrum Subtraction command. Figure 110 and 111 show the
Spectrum Subtraction dialogs:

Spectrum Subtraction
Figure 110: Spectrum Subtraction - Select Files
Figure 111: Spectrum Substraction - Frequency Range
The result of this calculation which can be attributed to different components is

as follows:

Manipulate
Result spectrum (ν) = multi-component spectrum(ν)

– Factor1 * single-component spectrum (ν)
– Factor2 * single-component spectrum (ν)
...
– Offset
Note: This kind of calculation is only appropriate for absorbance spectra.

Transmittance spectra are automatically converted to absorbance spectra during
calculation. Only if the original spectrum has been of transmittance mode, the
resulting spectrum will be converted to transmittance when the subtraction has
been finished.
Example:
First, generate an example spectrum using the Spectrum Calculator (see

chapter 8.5). The spectrum has to consist of 0.7 ABBOE12.0 spectrum parts, 1.3
ABBOE08.0 spectrum parts and 2.3 ABBOE05.0 spectrum parts. Save the
spectrum as CALC.6. This spectrum should represent a generic sample
consisting of an unknown amount of these three components and be analyzed
by using Spectrum Subtraction. The automatic subtraction mode minimizes the
least squares deviation in the difference spectrum.
The optimum result can only be achieved if all single components are
simultaneously subtracted from one mixture spectrum. This yields to a result of
almost zero.
If you click on the Start Interactive Mode button, the following dialog box will
be displayed:
(a)
(b)
(f)
(c)
(d)
(g)
(e)
Figure 112: Interactive Spectrum Subtraction

AB <-> TR Conversion
a) Shows the name of the multi-component spectrum.

b) If you click on the drop-down list, you can select the spectra to be subtracted.
c) Depending on your spectra selection in (b), the adjusted factors are displayed.
The factor value can be increased or decreased, using the control elements on the
right. The value can also be entered manually. Click into the entry field and
overwrite the value given.
d) If you check this option button, the displayed spectra will be scaled.
e) Use this slider to define the number of decimals which vary the components of
(c).
f) This window shows both the single-component spectra and the multi-component
spectrum.
g) The display is autoscaled and shows the difference between the multi-component
spectrum and the weighted single-component spectra.
If you right click into the windows (f) and (g), you can zoom in specific spectral
ranges using the pop-up menu. The Auto Subtract button would start the
automatic single-component subtraction. If you click on the Store button, you
exit this dialog box and the difference spectrum is stored as Principal File (a).
The numerical values used are attached to the spectrum in the form of a
subtraction data block . This data block contains the factors used to
subtract the spectra, and the result spectrum. If you right click on the subtraction
data block, the Show Report option pops up. Select this option to open the report
window:
Figure 113: Spectrum Subtraction Report
The first column on the right shows the factors and the mark in the Modified
column indicates the spectrum which the subtraction report has been attached
to.
8.3 AB <-> TR Conversion
The AB<->TR Conversion command converts absorbance spectra to

transmittance spectra and vice versa. The conversion direction can be set
automatically, or individually pre-defined.

Manipulate
Figure 114: AB <-> TR Conversion
If you definitely determine a conversion direction, only those spectra will be

converted which do not have the requested format. The option buttons in the
Conversion Direction group field allow to create a uniform data block type for
several spectra. Click on the Convert button to start the conversion.
Figure 115: Converted Absorbance Spectrum into a Transmittance Spectrum

Straight Line Generation
The spectrum displayed by a dotted line (figure 115) has be generated by an

AB → TR conversion.
The equation required for an TR → AB conversion is:
AB = – log ( TR )
Transmittance values less than 10-5 are set to 5 absorbance units.
The equation required for an AB → TR conversion is:
TR = 10 – AB
8.4 Straight Line Generation
The Straight Line Generation command allows to eliminate fringe effects in the
interferogram or artifacts detected in a spectrum. Select the spectrum files and
define the frequency range on the Frequency Range tab (figure 116). You can
either select the frequencies interactively, manually or accept the current
frequency limits of the spectrum. When you have finished setting the frequency
limits, click on the Generate button.
Figure 116: Straight Line Generation - Frequence Range tab
Figure 117 shows a straight line generated between 2,550 and 2,360 wave
numbers, which replaces the original peak (dotted line).

Manipulate
Figure 117: Spectrum Before and After Generating a Straight Line
8.5 Spectrum Calculator
The Spectrum Calculator is used to calculate spectra and numerical results. You
can also enter algebraic terms.

Spectrum Calculator
(a)
(b)
(c)
(d)
(h)
(e)
(i)
(f)
(j)
(g)
Figure 118: Spectrum Calculator
a) Use the button to delete your input.

b) These buttons provide trigonometric functions. The following functions are available if
you use the Shift and Hyp button:
c) Additional mathematical functions, e.g. square function 2 (e.g. 32 = 9) and “^”, as well as
π and special function x are made available.
sqrt is the square root function √
ln is the natural logarithm
lg is the logarithm to the base 10
exp is the exponential function e
dxp takes the following entry to the power of x (i.e. 10x)
d) C clears the display (h) and (i). You can use the brackets ( ) to form mathematical groups
that will be calculated first.
e) The four basic arithmetic operations.
f) Numerical block which consists of the figures 0 - 9, the decimal point and exponential
function E (e.g. 4.321E3 = 4321).
g) This button starts the calculation. The result will be displayed in the entry field (h).

Manipulate
h) You can drag & drop spectra from the OPUS browser window to the entry field (h). They
are directly made available for mathematical calculations. You can also enter algebraic
terms and numerical values into this entry field.
i) Select the result data block from the drop-down list.
j) The display field shows the calculation results or indicates ERROR in case of an
incorrect entry.
You can enter figures, signs and functions either using the numerical keypad of
your keyboard or clicking on the spectrum calculator keys. In the latter case
inputs will always be added to the entry field (h). Delete inputs by using the
button.
If the calculation results in a spectrum, the original spectrum file will be

overwritten by the new result spectrum. This also applies to data blocks.
If two spectra are divided, a transmittance spectrum is generated in the

numerator of these two spectra. The transmittance spectrum may overwrite the
original spectrum.
In some cases it may be necessary to calculate frequency-dependent terms. This

can be done using the x function, which represents the frequency values of the
spectral data points. The term
sin(x/100) + [4:TR] – [4:TR]
uses the group ([4:TR] – [4:TR]) to generate a spectrum with 0 intensity. The x
function causes the frequency limits and data point (frequency) spacing to be
applied. The result will be a sine wave. If you calculated
sin (x/100) + [4:TR], the spectrum intensity values would be added to the sine
wave.
The spectrum calculator cannot be compared with a normal pocket calculator. If

you enter 100√ into the pocket calculator you expect the result to be 10. The
spectrum calculator, however, operates with algebraic formulae. Therefore, you
need to enter sqrt(100).
It is also possible to use the spectrum calculator in case of 3d data. For details,
see the OPUS 3D or OPUS VIDEO manual.
8.6 Cut
Use the Cut command to minimize the frequency range of a data file. Select the
spectrum file and define the frequency range. Click on the Cut button to start the
command. Figure 119 shows a frequency range (thicker curve line) generated
by using the Cut command.

Normalization
Figure 119: Original Spectrum (Thin Line) and Cut-Out Range (Thick Line)
You can also use the Cut command to invert the frequency limits of spectra.
Select upper and lower limits which are beyond the spectral range and define
them as new frequency limits in reverse order. Right click on the spectrum and
select Properties from the pop-up menu. Invert the axes settings using the Axes
tab. This change may not immediately appear in the spectrum window.
8.7 Normalization
The Normalization command allows to normalize spectra and perform offset

corrections on spectra. Select the files to be normalized and click on the
Normalization command. Three different methods are available for spectrum
normalization:

Manipulate
Figure 120: Normalization - Select Files tab
• Min/Max normalization – This method scales spectrum intensities to

the effect that the minimum absorbance unit will be 0 and the
maxium 2. In case of transmittance spectra the normalization is
between 0 and 1.
• Vector normalization – This method calculates the average y-value
of the spectrum. The average value is subtracted from the spectrum
decreasing the mid-spectrum to y = 0. The sum of the squares of all
y-values is calculated and the spectrum is divided by the square root
of this sum.
NPT 2
The vector norm of the result spectrum is 1: ∑ ( xi )
i=1
= 1
• Offset correction – This method shifts spectrum intensities to the

effect that the minimum absorbance unit will be 0.
8.8 Make Compatible
The Make Compatible command changes the data point grid of the selected files
to adapt it to the Principal File grid. The files to be processed are manipulated
to make the x-values of the spectra compatible to those of the principal file. This
causes the frequency base points to be shifted. If the frequency range of a
spectrum selected is larger than the range of the Principal File, the frequency
range will be cut. Many OPUS commands make spectra automatically
compatible to each other.

Make Compatible
Figure 121: Make Compatible
There are two methods to calculate the intensities of new frequency base points.
The original intensities serve as a basis.
• Interpolation – The method of quadratic interpolation can always be

used.
• Reduce Resolution – The new intensities are calculated by
integrating the original ones.
In case of the Interpolation method the curve shape is better preserved, while
Reduce Resolution keeps the peak positions more constant.
Example:
The Principal File frequency limits are between 1,000 and 5,000cm-1. The
number of data points is 4,001 (i.e. 1cm-1 resolution). The frequency of the first
point is 4,000.5, of the last 200.5cm-1. The number of data points is 1,901 data
points (2cm-1 resolution). The Make Compatible command creates a new
spectrum on the basis of the original one. The first frequency point of this new
spectrum is at 1,000cm-1 and the last one at 4,000cm-1. The number of data
points is 3,001 (1cm-1 interpolated resolution).
The x-direction (high-to-low or low-to-high) of the new spectrum always

depends on the Principal File.

Manipulate
8.9 Convert Spectra
The Convert Spectra command performs several data conversions which

mainly involve the y-axis. When selecting spectrum files for conversion certain
restrictions may apply. If you try to select a spectrum which does not comply
with the conversion method selected, a warning symbol will be displayed. The
file name in the File(s) to Convert selection field on the Select Files tab will be
red.
Figure 122: Convert Spectra – Mismatch of Method and Spectrum
Define the spectrum, select a conversion method and click on the Convert
button to start the command.
8.9.1 Convert to Kubelka-Munk (KM)

The KM conversion type is appropriate for spectra which have been measured
in diffuse reflectance. Compared to AB conversion the intensities are more
linear to concentration. The conversion uses the following equation:
( 1 – Refl ) 2-
KM = -------------------------
( 2 ⋅ Refl )
Rfl also means TR in this case. Absorbance spectra are first converted to
transmittance spectra. The smallest value allowed for transmittance or
reflectance is 0.001%. This corresponds to a Kubelka-Munk value of about 500.

Convert Spectra
8.9.2 Convert to Reflectance Spectra

The following conversion formula is applied:
Refl = 1 + KM – ( 2 ⋅ KM + KM 2 )
8.9.3 Convert to ATR Spectra

X
ATR = AB ⋅ ------------
1000
X represents the wave number. Transmittance spectra are first converted to

absorbance spectra. As in case of Attenuated Total Reflection measurements
the penetration depth is inversely proportional to the wave number (frequency),
the spectra are normalized to a constant penetration depth.
8.9.4 Convert to Absorbance Spectra

1000
AB = ATR ⋅ ------------
X
8.9.5 Logarithmize Reflectance Spectra

Spectra reflectance values below 0.00001 will be levelled to a lg(Refl) intensity
of 5.
logRefl = -log(Refl)
8.9.6 Convert Logarithmized Reflectance Spectra

R = 10 – log ( R )

Manipulate
8.9.7 Convert Single-Channel Spectra

The start and end frequencies of a single-channel Raman spectrum will be
converted using the following equations:
FXV ( Raman ) = RLW – FXV ( ScSm )

LXV ( Raman ) = RLW – LXV ( ScSm )
RLW stands for Raman Laser Wave number. This value is registered within the
instrument parameter block of the Raman file created. OPUS uses the ScSm
abbreviation to indicate a single-channel sample spectrum. FXV represents the
starting frequency, LXV the end frequency.
8.9.8 Convert Raman Spectra

The following equation applies for the respective conversion direction selected:
FXV ( ScSm ) = RLW – FXV ( Raman )
LXV ( ScSm ) = RLW – LXV ( Raman )
The RLW parameter belongs to the instrument parameter block of the Raman
spectrum.
8.9.9 Raman Laser Wave Number

This value will be used for the ScSm → Raman conversion.
8.10 Smooth
The Smooth command allows to smooth spectra. The smoothing is based on the
Savitzky-Golay algorithm. Possible values for smoothing points are between 5
and 25. If you select a spectrum file and click on the Smooth command the
following dialog box opens:

Smooth
Figure 123: Smooth – Select Number of Points
Define the number of smoothing points and click on the Smooth button to start
the command. You can also start the interactive mode. The following view is
displayed:
Figure 124: Interactive Smoothing

Manipulate
Figure 124 shows the original spectrum in the upper window and the smoothed
spectrum in the lower. Use the slider to set the smoothing points interactively.
The currently used number of smoothing points is shown below the slider. If
you click on the Store button, the loaded original spectrum file will be changed.
If you click on Cancel button, the changes made will not be stored. In both
cases the view will close.
Smoothing reduces noise but also distorts signal intensities. Figure 125 directly
compares the original spectrum with the smoothed one. The original spectrum
band shows more pronounced peaks.
After Smoothing
Before
Figure 125: Smoothing Effects on a Spectrum
8.11 Derivative
The Derivative command calculates the first to fifth derivative of a spectrum,

using the Savitzky-Golay algorithm. This algorithm allows a simultaneous
smoothing of the spectrum. The smoothing effect reduces the noise generated
by derivation.

Frequency Calibration
Figure 126: Derivative - Select Files tab
The minimum number of smoothing points depends on the derivative order. The
higher the derivative order, the more smoothing points need to be set. You can
set a maximum of 25 points.
Select a spectrum file, define the number of smoothing points and the derivative
order. Click on the Process button to start.
As a result, a data block is generated indicating the actual derivative order of the
original spectrum. If a spectrum of 1st order is subject to a 1st order derivation
again, the result will be a 2nd order spectrum. The kind of derivative order is
displayed in the data block of the resulting spectrum.
3rd and higher order derivations are symbolized as n derivation. The derivative
order is stored in the parameters of the derivation data block. Right click on the
spectrum file and select show parameters from the pop-up menu.
8.12 Frequency Calibration
The Frequency Calibration command re-calibrates the x-axis of a spectrum.

You have to enter the two parameters M and A. These parameters change all
νold x-values of the data points:
νnew = νold⋅M + A (or fnew = fold⋅M + A)

Manipulate
Select a spectrum file and click on the Frequency Calibration command. The
following dialog box opens:
Figure 127: Frequency Calibration - Select Files
After the calibration the two parameters M and A are stored in the spectrum data
block. This enables you to undo the calibration.
The original data set before the calibration looked as follows:
Figure 128: Original Set of Data Parameters
After the calibration the frequencies of the first and last data point have
changed. Two additional parameters, i.e. factor M (Mult. for Freq. Calib.) and
addend A (Add for Freq. Calib.) have been included in the list.

Frequency Calibration
Figure 129: Set of Data Parameters after Frequency Calibration
The x-axis of a spectrum can be modified several times as follows:
νold,1 = νold⋅M1+A1
and later by
νnew,2 = νnew,1⋅M2+A2
For the first run select the parameters M1 and A1, and for the second the param-
eters M2 and A2. The parameter list displays the parameters Mtotal and Atotal,
which represent the total change compared to the original calibration:
νnew,1 = νold⋅M1 + A1
νnew,2 = νnew,1⋅M2 + A2
νnew,2 = νold⋅Mtotal + Atotal
⇒(νold⋅M1 + A1)⋅M2 + A2 = νold⋅Mtotal + Atotal
⇒Mtotal = M1⋅M2
Atotal = A1⋅M2 + A2
You can undo these changes all at once.

Manipulate
8.13 Raman Correction
The special features of the optics and the frequency dependent scattering that
occur in Raman spectra can almost be eliminated by using the Raman
Correction command. To undo the Raman Correction, click on the symbol
on the toolbar.
Select a spectrum file, only Raman spectra, and click on the Raman Correction
command.
Figure 130: Raman Correction - Correction Method
The Correction Method tab allows to define the correction method and the
reference spectrum which is to be used as well as the temperature. If you check
the Reference Correction option, you correct the influence which the optics has
on the spectrometer. This requires a current spectrum of the reference lamp
installed in the sample compartment. The spectrum should not be older than two
weeks to reflect the ageing of the lamp.
The correction spectrum (almost similar to the one acquired by Black Body can
be selected if you click on the Change Reference File button. If the sample
spectrum and the reference lamp spectrum do not match in your data point grid,
click on the Make Compatible command of the Manipulate menu. Scatter
Correction corrects the dependence between scattered radiation and excitation
frequency.
Click on the Correct button to start the correction. The correction parameters
are stored in the Instrument parameters list:

Black Body
Figure 131: Raman Correction Flags
Thus, it is avoided that the same correction is used several times. Ensure that the
Raman laser wave number and the source temperature have not changed just
before performing the correction.
8.13.1 Raman Correction Theory

Rayleigh's υ4-law relates the scattering as a function of the wave number. This
effect increases with the spectral distance of the line of interest to the wave
number of the Raman laser. In case of Scatter Correction the Raman spectrum
is multiplied point by point using:
υ Laser⎞
⎛ --------------
4
-
⎝ υ ⎠
In case of the Reference Correction the point-to-point multiplication for the

Raman spectrum to be corrected will be as follows:
( Black Body Spectrum ) ( Raman Spectrum )-

-------------------------------------------------------------------------------------------------------
( Reference Spectrum )
8.14 Black Body
The Black Body command calculates the emission spectrum of a black body.
The frequency range and data point grid used to calculate the curve are both
based on a reference spectrum. This also applies to the units of the x-axis
(frequency or wave number).
The black body (light source) temperature will be indicated in Kelvin. It is

stored as TMP parameter together with the calculated distribution. Optionally,
the energy distribution or flux density of the photons (depending on the
frequency or wave number) can be calculated.
In case of Raman spectra the x-axis is displaced so that the Raman laser signal
is at 0 wave numbers and the Stokes spectrum range includes positive wave
numbers. The Raman laser wavelength is determined by the RLW parameter of
the spectrum measured, and can be manually set to 9394cm-1.

Manipulate
Figure 132: Black Body
Select a spectrum file and indicate the temperature of the black body. Activate
the respective option button for the type of distribution and click on the
Calculate button to start the calculation.
8.14.1 Black Body Theory

The radiative properties of a black body are only determined by its temperature.
This enables an approximation of the true light source spectrum, assuming that
a single-channel spectrum of the light source is available. Figure 133 shows the
radiation spectrum of a black body at a temperature of 1000K.

Black Body
Figure 133: Radiation emitted by a black body at 1000K
The energy and photon flux of a black body is determined by:
8
2 ×10 hc 2 ν 3-
Energy per wave number: y = -----------------------------
100νhc⎞
⎛ ------------------
⎝ kT ⎠
e –1
– 15
2 ×10 cν 2
Photon flux per wave number: y = -----------------------------
-
⎛ 100νhc
------------------⎞
⎝ kT ⎠
e –1
where:
T = Temperature [K]
c = 2.99792458⋅108 [ms-1]
h = 6.626176⋅10-34 [m2kgs-1]
k = 1.380662⋅10-23 [m2kgs-2K-1]
ν = Wave number [cm-1]

Manipulate
8.15 Interferogram to Spectrum
The Interferogram to Spectrum command converts an interferogram into a

spectrum and performs the same operations which immediately run after AQP
data acquisition:
• Apodization
• Phase computation
• Zerofilling
• Fourier Transformation of the interferogram
• Phase correction
This allows to repeat spectra calculation after measurement, using different

parameter settings for apodization, zerofilling and phase correction.
The original data files have to be interferograms. You specify these data files on
the Select Files tab. The frequency range of these files has to be between the
upper and lower folding limit parameters used during measurement.
In addition to the spectrum calculated, which is always a single-channel

spectrum, you can also save the phase and power spectrum on the Store tab. The
latter two spectra are calculated by the double-sided known part of the
interferogram, using the phase resolution setting.
Figure 134: Interferogram to Spectrum – Store tab

Interferogram to Spectrum
Use the Apodization tab to select the apodization function and zerofilling factor.
Due to the finite mirror travel, the interferogram is only recorded up to a certain
point (i.e. a finite resolution). This leads to artificial side lobes on spectral lines,
the natural width of which is smaller than or comparable with the measured
resolution. By multiplying the interferogram by an apodization function, these
side lobes can be suppressed, however at the expense of line broadening.
Figure 135: Interferogram to Spectrum – Apodization tab
A detailed description of the apodization function would go beyond the scope of

this manual. In case of standard measurements in liquid or solid phases the
Blackman-Harris-3-term is recommended. To obtain the highest resolution, you
either select no (Boxcar) or at best a weak apodization function (Norton-Beer,
Weak).
Zerofilling means adding zeros to both ends of the interferogram before

performing Fourier transformation. This increases the number of data points in
the spectrum, which is equivalent to an interpolation. The number of data points
can be increased by zerofilling using the factors selected (e.g. 2, 4, 8,..., 512).
In case of a zerofilling factor of 1 zeros are added up to the next power of two. If
the number of data points has already been a power of two, no zeros will be
added.
Single-sided interferograms require a minimum zerofilling factor of 2. In case

of double-sided interferograms, the zerofilling factor can be halved in
comparison to single-sided interferograms. By increasing the number of data
points in the spectrum the depiction improves by sharper lines (a mere cosmetic

Manipulate
effect). However, an n-fold zerofilling requires an n-fold computing time and n-

fold storage space (depending on the computing method).
Select the Limit Data tab to define the resolution.
Figure 136: Interferogram to Spectrum – Limit Data tab
If you activate the Limit Resolution to check box, you can vary the resolution by
entering a value which is greater than or at least equal to the value used during
measurement. In this case only a fraction of the measured interferogram is used
for computation.
In the Phase Resolution group field you specify how precise the phase has to be
determined. Generally, you should enter the same value as being used for the
measurement. The value is limited by the length of the double-sided part of
interferogram.
In case of interferograms recorded in forward/backward mode you can specify

which direction(s) of mirror travel have to be evaluated during transformation.
If both mirror travels should be evaluated, the forward and backward scans will
be transformed separately, phase corrected and averaged.
If data have been recorded in multiplex mode, the interferogram contains

alternating data from two analog-to-digital converters (ADCs). The Even and
Odd option allow the data from both ADCs to be evaluated separately. There is
no such option in case of backward scans. Therefore, record multiplex
measurements only by using the Forward mode.

If you activate the Even option button, the intensity values I0, I2 ... of the first
ADC will be transformed. If you activate the Odd option button, the intensity
values I1, I3 ... of the second ADC will be transformed.
The phase correction can be compared with an interferogram symmetrizing,

which is always necessary due to the asymmetry of any measured
interferogram. Click on the Phase Correction tab.
Figure 137: Interferogram to Spectrum – Phase Correction tab
Several phase correction modes are available:

• Mertz: this is the standard procedure for phase correction.
• Mertz Signed: modified Mertz function which is used if the single-
channel spectrum is expected to contain negative contributions.
• Power Spectrum: this can be used instead of Mertz or Foreman, but
only for double-sided interferograms, if the spectrum includes
wide ranges of low light intensity (total absorption, Raman,
emission). Disadvantage: up to √2 more noise compared with Mertz
or Forman.
• Mertz/Stored Phase: like Mertz, whereas the phase is not re-
calculated but based on previously existing data which have been
calculated by using the regular Mertz method. This method can be
useful, if the single-channel spectrum includes less-defined ranges
(i.e. an undefined phase), which frequently occurs in case of
emission measurements. Furthermore, it can also be useful if the
spectra are expected to contain negative contributions. In this case,
the phase stored should derive from a spectrum with absolute
positive values.

Manipulate
• No/Save Complex Data: the data will not be phase corrected but
Fourier transformed in complex form and stored as real and
imaginary parts.
• Forman: a method mathematically equivalent to Mertz, offers a
slightly higher precision at the cost of higher computational costs.
Figure 138: Interferogram to Spectrum - Non-linearity tab
In a single-channel spectrum there should be no signal below the absorption

edge of the detector. The non-linear detector response causes the signal to be
non-zero below this edge. The non-linearity of the detector can be calculated
from the ratio of the intensity of these artifacts and the total energy flow in the
detector. As soon as the non-linearity is known a corrected spectrum can be
calculated showing less artifacts. As a rule, the interferograms stored will not be
modified. The non-linearity correction only effects the spectra.
To ensure a successful non-linearity correction the following conditions have to

be fulfilled:
• The spectrum must be recorded from 0cm-1 up to the maximum wave
number at which the detector can send a signal.
• Electronic filters must not be used. Spectra have to undergo a broad-
band recording to avoid aliasing.
• The Phase resolution FT parameter should be set to result in at least
500 phase interferogram points. Too low a phase resolution results in
an inaccurate non-linearity correction.
After phase correction the non-linearity correction coefficients are calculated,

using all the data points of the single-channel spectrum.

The modulation efficiency causes an additional multiplicative correction of the

entire spectrum. It can be set either to the correct value (typically between 0.7
and 1.0), or to 1.0 if the correct value is unknown. If you use a preamplifier
which reverses the signal polarity, the value of the detection limit has to be
multiplied by -1.
Use the Peak Search tab to select the position of the zero path difference (ZPD):
Figure 139: Interferogram to Spectrum - Peak Search tab
• Absolute largest value searches the peak with the highest absolute
intensity.
• Maximum searches the highest peak with the largest positive value.
• Minimum searches the lowest peak, if known that the peak has a
negative intensity.
• Mid between Min./Max. calculates a value between the minimum and
maximum limit.
• No peak search uses the position saved in the interferogram. If this
value is known, it can be entered manually.
• Mid between largest two searches the peak between the two largest
values.
• Take from stored phase uses the value calculated for the phase stored.
The position of the peak can be influenced by considering additional data points
apart from the range evaluated by one of the algorithms mentioned before. Each
position will be tested for its symmetry or asymmetry. The position with the
highest symmetry will be defined as ZPD. Check the respective option button in
the Symmetry of the Interferogram group field.

Manipulate
8.16 Inverse FT
The Inverse FT command transforms a spectrum into an interferogram, and can

be used for all types of spectra.
Figure 140: Inverse FT
You have to specify whether the spectral data are part of a symmetric or
antisymmetric interferogram. Generally, you activate the Normal Symmetry
option button, as antisymmetric interferograms only occur in special cases, e.g.
complex spectra. Interferograms symetrically generated only contain values on
the positive side of the x axis. Therefore, in case of Fourier transformation you
have to define how these values have to be completed on the negative side.
Select the spectrum file and frequency range as usual and specify the symmetry.
Start the procedure by clicking on the Inverse FT button.
8.17 Post Zerofilling
The aim of post zerofilling is to increase the digital resolution of a spectrum, i.e.
to create more data points per wave number. This is especially useful for the
peak picking in case of high-resolution spectra, as the result will be smoother
spectra plots. When calculating spectra a zerofilling is performed by indicating
the Zerofilling factor. This kind of zerofilling increases the digital resolution of
spectra within the entire spectral range. The advantage of post zerofilling is that
only the spectral range of interest will be interpolated, which allows to save
storage space.

Post Zerofilling
Figure 141: Post Zerofilling - Select Files tab
Specify the Additional Zerofilling Factor. The possible values range from 1 to
512.
Example 1
A spectrum with a digital resolution of 8cm-1 is post zerofilled by an additional

zerofilling factor of 2. The digital resolution after the interpolation is 4cm-1.
Example 2
A spectrum with a digital resolution of 8cm-1 is post zerofilled by an additional

zerofilling factor of 8. The digital resolution after the interpolation is 1cm-1.
In both cases the digital resolution has been 8cm-1. To avoid artifacts allow at
least 50 more data points on each side of the desired interval. This frequency
range must also contain meaningful spectral information.
If you click on the Zerofill button (figure 141), the spectra file(s) selected will
be interpolated using the Additional Zerofilling Factor specified.
Figure 142 exemplifies a post zerofilling factor of 4. The interpolated curve

definitely includes more (quadruple) data points as the original data.

Manipulate
Before zerofilling
Figure 142: Digital resolution before and after post zerofilling
8.18 Fourier Self-Deconvolution
The aim of Fourier Self-Deconvolution is to enhance the apparent resolution of

a spectrum, or to decrease the line width. Spectral ranges comprising broad and
overlapping lines can thus be separated into sharp single lines. The Fourier
Self-Deconvolution is only useful in case of lines which are substantially
broader than the spectral resolution.
Select the respective spectra file(s) on the Select Files tab. On the Adjust
Parameter tab you have to define the line shape. Check either the Gaussian or
Lorentzian option button. The appropriate line shape type depends on the line-
broadening procedure. In case of doubt it is recommended to assume a
Lorentzian shape.
Specify a deconvolution and noise reduction factor, or alternatively define a

factor for the band width and resolution enhancement. The effect will be the
same. Start the self-deconvolution by clicking on the Deconvolute button.

Fourier Self-Deconvolution
Figure 143: Fourier Self-Deconvolution
8.18.1 Fourier Self-Deconvolution Theory

The Fourier Self-Deconvolution (FSD) assumes that the spectrum to be
measured consists of well-resolved lines which have been convoluted
(broadened) by the same type of line-broadening function (LBF). If the shape
and width of the LBF are known, its effect can be arithmetically excluded from
the spectrum. It is recommended to perform this arithmetic exclusion on the
basis of the interferogram as in this case the deconvolution is equivalent to a
simple interferogram division caused by the LBF Fourier transformation.
In general, the deconvolution corresponds to a multiplication of the

interferogram I(x) using the exp(a*x) deconvolution function for Lorentzian
and exp(a*x*x) for Gaussian shapes, which intensifies the interferogram edges.
The deconvolution factor is the maximum value of these functions at the end of
the interferogram.
The amplification of the interferogram caused by self-deconvolution also

amplifies both the signal and noise. However, especially on the interferogram
edges the signal-to-noise ratio is worse than at the centerburst. To avoid the
increase of noise, a Blackman-Harris apodization is simultaneously performed
such that the interferogram is multiplied by the result of an ascending
deconvolution function and a descending apodization function. The apodization
function value is 1.0 at the beginning and 0 at the end of the interferogram.
Between these two limits the value exhibits a maximum.
Deconvolution factors of 100, 1000 and 5000 correspond to a maximum

amplification of 3.4, 12.8, and 40 in case of Lorentzian shapes, and 1.06, 3.2
and 16 in case of Gaussian shapes. If you work with Lorentzian shapes it is

Manipulate
recommended to increase the deconvolution factor in the order 50, 100, 1000,
5000, and to stop if the resultant spectrum shows artificial oscillations.
The noise reduction factor should range from 0.0 to 1.0. It is the fraction of the
interferogram, which apodization function has been decayed to 0 and thus used
for evaluation. A value of 1.0 corresponds to the full interferogram length. It is
recommend to start with a value of 0.5 (half interferogram length). If the
spectrum has been calculated using a zero filling factor >2, a start value of 1/
(zerofilling factor) is recommended to reduce noise.
Figure 144 shows a spectrum before and after a deconvolution, using the
parameters shown in figure 143. The intensity at the maximum of a
deconvoluted spectrum line is usually higher, in relation to its edges, than of an
original spectrum. However, the peak ratios are not changed. The deconvoluted
spectrum always depicts the higher maxima.
Deconvoluted spectrum
Original spectrum
Figure 144: Spectrum before and after Fourier Self-Deconvolution
8.19 Symmetric FT
Symmetric Fourier Transformation is used if a phase correction is not

necessary, e.g. if the interferogram has been generated by inverse Fourier
Transformation, or does only include one half of a scan, relative to the highest
maximum.

Kramers-Kronig Transformation
Figure 145: Symmetric FT - Select Files tab
Define the symmetry assumption on the Select Files tab. Generally, you check
the Normal Symmetry option button. If, however, the interferogram has been
generated by inverse Fourier transformation using the antisymmetric function,
check the Antisymmetric option button.
Select the frequencies on the Frequency Range tab and start the transformation
by clicking on the Symmetric FT button. The result will be a single-channel
spectrum. In case of an antisymmetric transformation only the positive part of
the single-channel spectrum will be saved.
8.20 Kramers-Kronig Transformation
The Kramers-Kronig Transformation command extracts from a sample

reflectance spectrum either the complex refractive index, complex dielectric
constant, an absorption spectrum or the phase change of the IR beam due to
reflection. This requires the following conditions:
• The sample has to consist of a pure, homogeneous material (neither
mixtures, layered systems nor powders).
• The beam has to be measured in specular (not diffuse) reflection at
nearly normal incidence (e.g. 10° unit).
• The sample must be thick enough (“half-space“) to ensure that no
light returns from the inner sample to the sample surface (e.g. after
reflection on one back edge). Especially, multiple reflections and
interferences have to be avoided. If the sample is not thick enough to
absorb all radiation, roughen the backside to prevent possible
reflection.

Manipulate
• The spectral cut-off has to fall in a moderately flat and unstructured

range. It must not be interrupted among significant structures.
Figure 146: Kramers-Kronig Transformation - Select Files tab
On the Select Files tab you select the spectra to be processed and specify the
desired result function. You can either calculate the Refractive Index (complex),
Dielectric Function (complex), Absorbance or Phase spectrum. In case of the
first two options the result file includes two data blocks: the real and imaginary
part of the functions (indicated by “R” or “I” in the file symbol).
If an absorbance spectrum is calculated, it only includes pure absorption

contributions, but no reflection losses. To be able to compare the absorbance
spectrum directly with a transmission spectrum, you have to consider the
reflection losses at both boundaries of the sample layer by adding the correction
-2lg (1-[Input - Reflectance spectrum] using the OPUS spectrum calculator.
8.20.1 Kramers-Kronig-Transformation Theory

The real and imaginary parts of complex physical quantities describing the
interaction between radiation and sample, e.g. the complex refractive index
n = n + ik , dielectric constant ε = ε′ + iε″ and the logarithm of the
amplitude-reflectivity ln ( re iφ ) = ln ( r ) + iφ ), depend on each other due to the
causality principle. The two parts can be transformed into each other by the so-
called Kramers-Kronig Transformation (KKT). OPUS uses this to first calculate
the phase rotation angle φ ( ν ) (a function of the wave number ν) from the
measured reflectance spectrum R ( ν ) = r 2 ( ν ) of an optically thick sample
using KKT. Then, the reflectivity of the air/sample edge (vertical incidence) is
calculated from r ( ν ) and φ ( ν ) using the Fresnel equation:

Spectrum from Interferograms
iφ ( ν )
Γ ( ν )e = [n(ν) – 1] ⁄ [n(ν) + 1]
The real and the imaginary parts of the refractive index are calculated as
follows:
1⁄2
n ( ν ) = [ 1 – R ( ν ) ] ⁄ [ 1 + R ( ν ) – 2R ( ν ) cos ( φ ( ν ) ) ]
κ ( ν ) = 2R 1 ⁄ 2 ( ν ) sin ( φ ( ν ) ) ⁄ [ 1 + R ( ν ) – 2R 1 ⁄ 2 ( ν ) cos ( φ ( ν ) ) ]
If desired, the dielectric function is calculated:
ε′ = n 2 – κ 2
ε″ = 2nκ
From the imaginary part of the refractive index, the so-called absorption index
κ ( ν ) , the absorptivity A ( ν ) of a layer with a thickness d can be calculated by:
A ( ν ) = log ( e )2πνdκ ( ν )
In principle, KKT enables to determine all important optical sample properties

on the basis of one single measurement (reflectance spectrum R ( ν ) ).
Note: A separate description on how to use the KKT and some exemplary spectra
are available on request.
8.21 Spectrum from Interferograms
The Spectrum from Interferograms command can be used to create a spectrum

by comparing a sample interferogram with a reference interferogram. The result
spectrum can either be displayed in absorption or transmission.

Manipulate
Figure 147: Spectrum from Interferograms - Select Files tab
Drag & drop the sample and background interferogram into the corresponding
selection field. Note that the interferogram files include the parameters set
during measurement. Select the respective result spectrum format from the
drop-down list and start the calculation by clicking on the Calculate button.
8.22 Extrapolation
You can extrapolate reflectance spectra to 0cm-1 or to an upper frequency limit

selectable by the user. The previous wave number ranges are used without being
modified. In case of extrapolation to 0cm-1 it is distinguished between
insulators and semiconductors. OPUS interprets the sample as semiconductor if
the input for R (0cm-1) is 1.
Select the spectrum and the frequency range as usual. Specify a limit for R at the
At infinity and At 0 entry field. Start the calculation by clicking on the
Extrapolate button.

Extrapolation
Figure 148: Extrapolation
8.22.1 Extrapolation to 0cm-1

The R0 and i1 parameters are used for the extrapolation to 0cm-1. R0 can be any
value between 0 and 1. i1 represents the inner limit of the wave number interval
which the approximate function for the extrapolation has to fit to. The
beginning of the original spectrum will be automatically selected as the second
limit i2. If in case of i1 a wave number smaller than the lower wave number of
the original spectrum has been specified (i.e. no overlapping range), i1 will be
set to include two data points to fit the function.
R
new Orginal Spectrum new
1
R0
R∞
0
0 i1 i2 νend ν[cm-1]
Figure 149: Parameters used for extrapolation

Manipulate
8.22.1.1 Theory of extrapolating n to 0cm-1 in case of

semiconductors
The approximation function is:
a 42
Φ 4 = 1 – a 4 ν + ----- ν + a 5 ν 1.5
2
As R ( s ) = Φ ( s ) has already been specified (s being wave number of the

spectrum beginning), the a5 coefficient can be eliminated:
a 42
R ( s ) = 1 – a 4 s + ----- s + a 5 ν 1.5
2
a2
R ( s ) – 1 + a 4 s – ----4- s
2-
a 5 = --------------------------------------------------
s 1.5
The remaining function is:
a 42 ⎛ a 42 ⎞ ⎛ ν⎞ 1.5
Φ4 = 1 – a4 ν + ν + R ( s ) – 1 + a 4 s – - s ---
----
- ----
2 ⎝ 2 ⎠ ⎝ s⎠
Now, specify a4 in a way that the sum of all error squares within the
overlapping area can be minimized.
8.22.1.2 Theory of extrapolating n to 0cm-1 in case of

insulators
Φ1 = R ( 0 ) + a1 ν 2 + a2 ν 4
As R ( s ) = Φ ( s ) has already been specified (s being the wave number of the

spectrum beginning), the a2 coefficient can be eliminated:
R ( s ) = R ( 0 ) + a1 s2 + a2 s4
R ( s ) – R ( 0 ) – a1 s2
a 2 = ---------------------------------------------
s4
ν 4
Φ 1 = R ( 0 ) + a 1 ν 2 + ( R ( s ) – R ( 0 ) – a 1 s 2 ) ⎛ ---⎞
⎝ s⎠

1/cm <-> µm, nm
Now, specify a1 in a way that the sum of all error squares within the
overlapping area can be minimized.
8.22.2 Extrapolation to ∞ (infinity)

The R∞, i1 and νend parameters are used for extrapolating to ∞. R∞ and i2 are
equivalent to R0 or i1 used in case of extrapolating to 0cm-1. νend represents the
wave number up to which the extrapolation has to be performed.
8.22.2.1 Approximation for extrapolating n to ∞

a a
Φ 3 = R ( ∞ ) + ----1- + ----2-
ν2 ν4
As R ( s ) = Φ ( t ) has already been specified (t being the wave number of the

spectrum end), the a2 coefficient can be eliminated:
a a
R ( t ) = R ( ∞ ) + ----1- + ----2-
t2 t4
a
a 2 = ⎛⎝ R ( t ) – R ( ∞ ) – ----1-⎞⎠ t 4
t2
a t 4
Φ 3 = R ( ∞ ) + a 1 ν 2 + ⎛ R ( t ) – R ( ∞ ) – ----1-⎞ ⎛ ---⎞
⎝ t 2 ⎠ ⎝ ν⎠
8.23 1/cm <-> µm, nm
The 1/cm <-> µm, nm command changes the x-axis (abscissa) unit of a
spectrum. Wave numbers can be converted into micrometer and nanometer, or
vice versa. Load the spectrum file and drag and drop it from the OPUS browser
window to the File(s) to Convert selection field. Define the conversion direction
by using the Conversion Direction drop-down list on the right.

Manipulate
Figure 150: 1/cm <-> µm, nm – Select Files tab
On the Frequency Range, Precision tab you can individually define the
frequency range or use it from the original spectrum.
Figure 151: 1/cm <-> µm, nm – Frequency Range, Precision tab
The maximal compression factor (MCF) can be specified by using the slider in
the Precision group field. In case of fixed frequency limits define the number of
data points in the result spectrum. If, however, the frequency limits of each
input spectrum are used, the interpolation is determined by the MCF.

1/cm <-> µm, nm
Figure 152: 1/cm <-> µm, nm – Scaling tab
On the Scaling tab you define the scaling of intensities. If you check the
Preserve y-Values option button, the intensities will generally not be changed.
Only interpolation effects play a more or less important role. The spectrum
appearance does not change, with the x-axis being substantially distorted.
If you check the Preserve Integrals option button, the y-values are multiplied by
a frequency or wavelength-dependent factor (proportional to 1/x2). This
preserves the integrals, provided the original spectrum and the new spectrum
both use equivalent integral limits.
Frequency Conversion Theory:
The connection between wave number [cm-1] and wavelength [µm] is based on
the following formula:
Wavelength [µm] x wave number [cm-1] = 10000.
Each wave number can be converted into a wave length. Digitally recorded
spectra have no continuous data, but discrete data points. OPUS saves these
equidistant data points, e.g. two data points per wave number. After the
conversion, however, the data points are no longer equidistant.

Manipulate
Wave number [cm-1] Wavelength [µm] Difference [µm]
400 25.00
1.19
420 23.81
1.08
440 22.73
0.99
460 21.74
0.91
480 20.83
0.83
500 20.00
Since OPUS always saves spectra as a set of equidistant data points only, an
interpolation must be performed after the abscissa conversion.
The interpolation type for frequencies (or wavelenghts) is determined by the

MCF or the number of resulting data points. The minimum number of data
points for the micron spectrum created is equivalent to the number of data
points found in the cm-1 spectrum. The MCF defines the conversion properties
in the high frequency end of the wave number spectrum which is converted to
the low wavelength end of the micron spectrum.
If, e.g., a factor of 5 is selected, 5 frequency intervals are converted to 1

wavelength interval (distance between each data point), which causes the loss of
spectral information. The ratios get better if lower wave numbers (higher
wavelengths) are selected.
The MCF can vary between 0.5 and 50. However, the new spectrum has never
fewer data points than the original spectrum. Therefore, it may occur that the
number of data points, e.g. starting from a factor of 20, remain unchanged.
In case of a small MCF the number of data points of the new spectrum may
become quite large. This depends on the upper and lower frequency limits as
well as on the distance of data points in the original spectrum. By reconverting
the new spectrum and comparing it with the original one it can be verified
whether the factor selected has been reasonable.
The upper left spectrum in figure 153 shows the original data scaled in wave
numbers. On the right it has been converted to wavelengths, with the intensities
remaining unchanged. In the lower left spectrum the intensities have been
converted without changing the integrals. The lower right spectrum shows the
original spectrum (B) which has been converted from wave numbers to
wavelengths and reconverted for comparison. Spectrum (A) uses an MCF of 1,
spectrum (C) an MCF of 15. The number of data points in (A) is about ten times
higher than in (C), and comes very close to the original data.

Averaging
Figure 153: Original data and converted spectra after abscissa conversion
8.24 Averaging
The Averaging command generates a new spectrum from a set of original

spectra of the same type. The intensities of this new spectrum are calculated by
averaging the intensities of the original spectra.

Manipulate
Figure 154: Averaging - Select Files tab (select by symbol)
The Files to Average group field provides two different options to select the
respective data file. Check the Select by Symbol option button if you want to
select the file by Drag & Drop from the OPUS browser window into the
respective selection field.
Check the Select by Name option if you want to select the file by specifying its
path and data block. In this case the dialog looks different (figure 155).

Averaging
Figure 155: Averaging - Select Files tab (select by name)
The average spectrum calculated includes the largest wavelength range which is
common to all original spectra.
Activate the Update Av. Spectrum check box to save the average spectrum on
your hard disk. An additional entry field will be displayed next to this check box
function in which you have to enter the name of the file to be saved. If a file
with the same file name already exists, it will automatically be added to the set
of spectra to be averaged and overwritten by the result file.
To weight spectra files proportional to their number of scans measured for each
file before the average spectrum will be calculated, activate the Weighting with
No of Scans check box.
Calculate the standard deviation of single-spectra intensities from the average

spectrum intensities by activating the Create/Update Std.-Dev. Spectrum check
box. An additional entry field will be displayed next to this check box function
in which you have to enter the name of the file to be saved.
The Compute Av. Report check box function performs an identity comparison
between the original set of spectra and the average spectrum. This will result in
an average report which includes information on the single spectra used to
create the average spectrum. The report also outlines the deviation of each
single spectrum from the average spectrum, and the frequency range and
averaging method selected.

Manipulate
The single-spectra deviation is indicated in multiples of the standard deviation

to make the detection of outliers easier.
Click on the Report Method... button to select the respective kind of method
used to calculate the spectral distance.
8.24.1 Averaging Theory

Averaging means to calculate the arithmetic mean of y identity values included
in n original spectra:
n
∑
i=1
yi
y = --------------------
n
The σ standard deviation is:
n
2
∑
i=1
( yi – y )
σ = ------------------------------------
n–1
When comparing standard deviation spectra, calculated with and without

weighting the number of scans, the results will slightly differ even if the number
of scans is the same for all original spectra. The reason is that the sum of 1 to n
in the above equation is not divided by n, but n-1. As n does not represent the
number of spectra but the number of scans when weighting, the results will
differ by a constant factor. This factor approaches 1 the more the number of
single spectra increases.
8.25 Merge Spectral Ranges
Several spectra of the same type (e.g. transmittance spectra) can be merged to a
new spectrum. Any gap in the frequency region is filled by a straight line.
If the original spectra overlap within one or more frequency ranges, linear
weighting is performed to avoid a step. If the frequency range of one spectrum
is completely overlapped by a second one (i.e. one spectrum is obsolete), a
warning message pops up and stops the merging. The parameter set of the first
spectrum on the list of spectra to be merged is used as result spectrum.
To merge spectra, drag them from the OPUS browser window into the File(s) to
Merge Spectra Ranges entry field on the Select Files tab. Click on the Merge
button.

Merge Spectral Ranges
Figure 156: Merging Spectra Ranges
Result of Merging Spectra Range
Two Separate Spectra
Figure 157: Original and merged spectra

Manipulate
8.26 Atmospheric Compensation
The Atmospheric Compensation command eliminates disturbing H2O and/or

CO2 bands in ratio spectra. These bands arise due to different H2O/CO2 vapor
concentrations in the beam path if you measure reference or sample spectra,
respectively.
To perform Atmospheric Compensation a single-channel reference spectrum

and single-channel sample spectrum are analyzed and transformed into a ratio
spectrum without any (or hardly any) H2O and/or CO2 bands.
If you select the Atmospheric Compensation command the following dialog box
opens:
Figure 158: Atmospheric Compensation - Select Files tab
8.26.1 Select Files

The Atmospheric Compensation command requires two single-channel spectra
to calculate one compensated ratio spectrum. Drag the single-channel sample
spectrum into the Single-channel Sample block(s) field, and the single-channel
reference spectrum into the Single-channel Reference block(s) field.

Atmospheric Compensation
If you want to compensate several spectra simultaneously, the two single-

channel spectra which belong together have to be uniquely defined. To do so,
you have two possibilities which are described in the following:
8.26.1.1 Single-channel sample and single-channel refer-

ence spectrum in one file
If the single-channel sample and single-channel reference data block are stored
in one file, select the desired file and drag and drop it into the respective
selection fields on the Select Files tab. Only the correct data block type will be
accepted (see figure 158).
If you have selected several files, a data block for each file selected will be
displayed in both selection fields.
8.26.1.2 Single-channel sample and single-channel refer-

ence spectrum in different files
If the single-channel sample and single-channel reference data block are stored
in different files, select the single-channel reference spectrum and drag and drop
it into the Single-channel Reference block(s) field. Select the single-channel
sample spectra and drag and drop them into the Single-channel Sample block(s)
field.
If you want to compensate several sample spectra simultaneously, which belong

to one single-reference spectrum, drag and drop all single-channel sample
spectra in the upper selection field and the single-channel reference spectrum in
the lower selection field, see figure 159.

Manipulate
Figure 159: Atmospheric Compensation - Single-Channel Spectra in Different Files
8.26.2 H2O/CO2 Compensation
You can define the atmospheric gas you want to be compensated. If you
deactivate both compensation check boxes on the left side (see figure 159), you
will get an uncompensated transmission spectrum, i.e. the ratio between a
single-channel sample spectrum and a single-channel reference spectrum.
Activate the Aqueous solution check box if your measurement sample is an

aqueous solution (e.g. proteins in water). A different compensating algorithm
optimized for aqueous solutions will be used for calculation.
8.26.3 Calculate
Click on the Calculate button to start the Atmospheric Compensation command.
For each single-channel sample block the appropriate ratio block will be
calculated and added to the original spectrum file.
If a ratio data block already exists, it will be overwritten by the calculated ratio
data block and the original data will be replaced. Figure 160 shows Atmospheric
Compensation effects.

Figure 160: Atmospheric compensation effects
The upper curve is the transmission spectrum of a polystyrene film. H2O and
CO2 bands can be clearly seen in several wave number ranges. The lower curve
is the result of atmospheric compensation. Disturbing absorption lines of H2O
and CO2 have nearly been eliminated.
8.26.4 Requirements
• Single-channel spectra have to include wave number ranges starting

from 3600 to 4000cm-1 for H2O compensation, and
2300 to 2400cm-1 for CO2 compensation.
• Sample absorption within these wave number ranges will result in
poorer quality with regard to compensation.
• The sample and reference spectrum have to be acquired using the
same spectrometer resolution. Different zero-filling factors are
possible.
• The spectrum should not end at a wave number which shows strong
absorption of atmospheric gases. To get a similar H2O compensation
(see figure 161), the lower wave number limit must not be around
1700cm-1.
• For compensation in aqueous solutions the spectrum has to include
wave number ranges of 2300-2400cm-1 and 1800-1900 cm-1 for both
CO2 and H2O.
• These wave number ranges must be free of sample absorption bands.

Manipulate
8.26.5 Limits
The Atmospheric Compensation command uses physical models to estimate the
amount of atmospheric gases in the single-channel spectra and therefore
compensates disturbing H2O and/or CO2 bands. Atmospheric Compensation is a
kind of data manipulation and has to be used with due care.
8.26.6 Atmospheric Compensation as part of the

measurement process
If you want to use Atmospheric Compensation to manipulate spectra
immediately after the measurement process, you have to perform the following
steps:
1) Select the Advanced Measurement command in the Measure menu and
set the parameters for your experiment. Click on the Advanced tab.
2) Activate the Single Channel and Background check boxes in the Data
blocks to be saved option field.
3) Check Additional Data Treatment and click on the button.
4) The following window pops up:
5) Select Atmospheric Compensation from the Manipulate menu. The

Atmospheric Compensation dialog box opens.

Figure 161: Atmospheric Compensation - Select Files
6) Select [<FILE>:ScSm] from the Single channel Sample block(s) drop-

down list and [<FILE>:ScRf] from the Single channel Reference
block(s) drop-down list. Activate the different check boxes, if required.
7) Click on the Calculate button.
The Additional Data Treatment option on the Advanced tab of your

Measurement dialog has to be similar to figure 162. If the sample measurement
has been successful, Atmospheric Compensation will be performed immediately
after the measurement.

Manipulate
Figure 162: Measurement - Activated Post-Measurement Manipulation
8.27 Straylight Correction
The Straylight Correction command allows to correct two phenomena which

normally occur in case of diffuse reflection measurements:
1) Diffuse reflection of the measurement light at the window, mainly due
to scratches and contaminations.
2) Multiple reflections between sample and window, which lead to
increased absorption.
The Straylight Correction eliminates these errors of ratio spectra (i.e.

transmission, absorbance, Kubelka-Munk, reflection) partly by intrinsic
correction spectra and partly by using mathematical algorithms. The result will
again be a ratio spectrum.
If you select the Straylight Correction command the following dialog box
opens:

Straylight Correction
Figure 163: Straylight Correction - Select Files
8.27.1 Select Files

Drag and drop the desired spectra files from the OPUS browser window into the
Spectra to apply straylight correction field. Only ratio blocks, e.g. absorbance,
transmittance, Kubelka-Munk, reflectance or log-reflectance will be accepted.
8.27.2 Internal Background

Activate or deactivate the Internal background was used check box to specify
whether your reflection measurement has been performed by an internal or
external background. External means that you have used your own standard,
e.g. a gold stamp or certified Labsphere standard during background
measurement. Internal means that you have used built-in features of the
Ulbricht sphere to determine the background spectra (i.e. Sphere Background-
Channel in case of an MPA spectrometer).

Manipulate
8.27.3 Window Material

The correction of multiple reflections depends on the refraction index of the
window material. To specify the window material used, activate either the
Quartz or Sapphire check box. In most cases quartz has been used as standard
window material. MPA and MATRIX spectrometers, e.g. are always delivered
with quartz windows. Some Vector and TENSOR spectrometers are supplied
with sapphire windows. If you are not quite sure about the material of your
spectrometer window, contact your Bruker Service.
8.27.4 Calculate
Click on the Calculate button to start Straylight Correction. The ratio spectrum
will be calculated for each ratio block which is displayed in the Spectra to apply
straylight correction field. The ratio block data will be overwritten by the
calculation result.
The correction algorithm considers the following effects:

1) Straylight effects caused by diffuse reflection of the incoming light at
the measurement window. These effects will be corrected by calculating
a corrected ratio spectrum:
TM − Stray
TM corrected = If TM has been recorded using an inter-
Extref − Stray nal background.
TM − Stray / Extref If TM has been recorded using an

TM corrected =
1 − Stray / Extref external background (nearly
100%).
TM is the original transmission spectrum, TMcorrected the resulting

spectrum. Stray stands for transmission spectrum of a measurement
performed without sample (open channel). Extref is the ratio between
the single-channel spectra of the external reference and single-channel
spectra of the internal reference.
2) Multiple reflections between the measurement window and sample:
After the first diffuse reflection of the light at the sample, a fraction of
this light can be reflected again both at the window and the sample. This
leads to incorrect measurement results, especially in case of a mid-range
sample absorbance ratio (30-70%). This effect is compensated by
multiplying the transmission spectrum by the following factor:
1+ c (
c = R ⋅ 1 + (1 − R )
2
)
1 + TM ⋅ c where

TM is the original transmission spectrum and R is the reflection

coefficient of the window material.
3) The ratio spectrum may have different values when using an internal
background instead of an external standard.
The difference between internal and external background is the portion
of light reflected directly at the measurement window. This part of light
leaves the Ulbricht sphere by the input. This effect is taken into account
by a correction spectra which quantifies this background difference.
Figure 164 shows straylight correction effects.
Figure 164: Straylight correction effects
8.27.5 Create new correction spectra

Each OPUS release includes a set of correction spectra which can be used for
straylight correction. It is, however, important that these spectra reproduce the
properties of your spectrometer. Therefore, it is recommended to create your
individual set of correction spectra before using the OPUS Straylight
Correction command. Correction spectra should be created regularly (e.g. each
month).
To proceed successfully you need a standard material, e.g. gold standard or

certified Labsphere standard (99%). Even if no standard is available it is still
possible to create new correction spectra but not reasonable, because you may
obtain correction spectra which are even worse than the OPUS default spectra.
The correction algorithm assumes that the standard used has a diffuse reflection

Manipulate
of about 100% within a wave number range of 15,000 to 3,000cm-1.
To create new correction spectra, click on the Create new correction spectra
button. A new dialog opens. Follow the on-screen instructions. If you have
finished, the new correction spectra will be automatically stored on hard disk.
The Straylight Correction command always uses the latest correction spectra
measured.
When running the New correction spectra script three different single-channel
spectra are measured:
• SCintBG: Single-channel measurement of internal background
• SCextBG: Single-channel measurement of external background
• SCStray: Single-channel measurement without sample
Note: If you use an MPA spectrometer, two additional single-channel spectra

will be measured for the External Transmission channel.
The following ratio spectra are calculated from the three different single-
channel spectra:
• ExtRef: SCextBG/SCintBG
• Stray: SCStray/SCintBG
The ratio spectra are stored by the ExternalReference_macro.0 and

EmptyChannel_macro.0 file name in the (OPUS-Dir)\StrayCorr directory.
Note: If you use an MPA spectrometer, two additional spectra will be created
which have the extension _micro.
The ExtRef and Stray single-channel spectra are used to perform straylight
correction on the spectra measured.
8.27.6 Using straylight correction as part of the

measurement process
If you want to use Straylight Correction to manipulate spectra immediately
after the measurement process, you have to perform the following steps:
1) Select the Advanced Measurement command in the Measure menu and
set the parameters for your experiment. Click on the Advanced tab.
2) Use the Result Spectrum drop-down list to define the result spectrum
type. This type has to be one of the following: transmittance, absor-
bance, Kubelka-Munk, reflectance or log reflectance. Activate the
appropriate check box in the Data blocks to be saved option field.
3) Check Additional Data Treatment and click on the button.

4) The following window pops up:
5) Select Straylight Correction from the Manipulate menu. The Straylight

Correction dialog box opens.
Figure 165: Straylight Correction - Select Files
6) Select the result spectrum, e.g. [<FILE>:TR] from the Spectra to apply
straylight correction drop-down list. Activate the check box and radio
buttons, if required.
7) Click on the Calculate button.
The Advanced tab of your Measurement dialog may be similar to figure 166. If
the sample measurement has been successful, additional spectra manipulation,
e.g. Straylight Correction will be performed immediately.

Manipulate
Figure 166: Measurement with Activated Post-Measurement Manipulation
8.28 Noise Generation
The Noise Generation command adds artificial noise to a spectrum. It adds

random positive or negative numbers to the spectrum values. Select a spectrum
file and click on the Noise Generation command. The following dialog box
opens:

Moving Mean
Figure 167: Noise Generation - Select Files
In the Noise level entry field you enter the maximum value by which the
spectral values will be changed. Click on Generate to start this kind of
manipulation.
8.29 Moving Mean
Moving Mean performs some kind of smoothing on a spectrum. Select a file and
click on the Moving Mean command. The following dialog box opens:

Manipulate
Figure 168: Moving Mean - Select Files
Two different types of manipulation are possible. In both methods the Number
of points parameter always represents the number of subsequent spectrum
points. These spectrum points are used for the calculation to be able to create
new spectrum values.
If you check Calculate moving mean, spectrum values being next to each other
are averaged over and replaced by their mean value. If you check Calculate
moving slope, the first and the last point of a sequence of data points are used to
calculate a straight line between these two data points. The spectrum values
between these two data points are replaced by values which are on the straight
line. These steps are repeated using the next sequence of data points. The
number of data points are defined in the Number of points entry field.
Click on the Calculate button to start this manipulation command.

Make Monotone
8.30 Make Monotone
Depending on the options selected and the spectrum curve shape, the Make
Monotone command allows to correct a trace or spectrum such that the resulting
curve increases or decreases in a monotonic manner. Select a file and click on
the Make Monotone command. The following dialog box opens:
Figure 169: Make Monotone - Select Files
You can select between three manipulation directions. If you check Upwards,
the spectrum values will be changed to the effect that the resulting spectrum
values increase in a monotonic way. If you check Downwards, the resulting
spectrum values will decrease in a monotonic way. Activating the Automatic
option automatically determines whether the resulting curve increases or
decreases, considering two data points at the boundary of the wave number
interval.

Manipulate

Curve Fit
9 Evaluate
The command included in the Evaluate menu primarily intend to calculate
results from existing spectra. This could be a quantitative data analysis, peak
identification or a library search. These calculations do not alter the spectrum
files.
Figure 170: Evaluate Menu
9.1 Curve Fit
The Curve Fit command allows to calculate single components in a system of

overlapping bands. A model consisting of an estimated number of bands and a
baseline should be generated before the fitting calculation is started.
The model can be set up interactively on the display and is optimized during the
calculation. As the result of this calculation highly depends on the model
selected, make sure that the model is reasonable from the chemical point of
view.

Evaluate
Setup Model
Select the Curve Fit command and a dialog box opens which you use to specify
spectrum to be fitted, and the frequency range.
Figure 171: Curve Fit - Select Spectrum
Drag & drop the spectrum to be fitted from the OPUS browser window into the
File to Fit selection field on the Select Spectrum to Fit tab. Make sure that the
spectrum is of absorbance type and baseline corrected.
If you activate the Save Single peaks Too check box, every fitted peak will be
stored as a separate file. You can also start a new fit using the last result.
On the Frequency Range tab you define the frequency range of the spectrum
you want to fit. If you click on the Interactive button, a new window opens
which allows to define the area to fit interactively. To take the limits from the
respective display window click on the Get Display Limits button. Activate the
Use File Limits check box if you want to take the original frequency range of
the file. The previous two options will then be disabled.
Once a suitable model has been found (see next paragraphs), it can be applied to
other spectra of the same kind, there is no need to set up a new model for each
spectrum. The spectra to be analyzed must always be defined in the File to Fit
selection field. The Fit Report block ( ) of the already fitted spectrum will
then be dragged into the Fit Report selection box. Click on the Fit button to start
the Curve Fit procedure of all spectra with the method selected.

Curve Fit
Figure 172: Curve Fit - Frequency Range
To perform a curve fit you first have to create a fit method first. Click on the
Start Interactive Mode button on the Select Spectrum to Fit tab and the
spectrum you selected will be opened in the curve fit setup window (see
figure 173).
In the upper window, the spectrum to be fitted is displayed, whereas in the

bottom window the difference between the original spectrum and the fitted
spectrum is shown. As there was no fitting carried out at this point, both
windows show the same spectrum.
You can create a curve fit model by moving the cursor into the top window. The
mouse pointer will change from an arrow to an ADD symbol ( ). By
clicking onto the peak, a curve will appear close to the selected peak. Each left
click will generate a new curve. The intensity of the curve corresponds to the
cursor position. The generated curves will appear in red.

Evaluate
Figure 173: Curve Fit Window before Fit
When the cursor is positioned close to the top of the peak, the MOVE symbol
( ) is displayed. You can now move the curve by clicking and dragging it to
the desired position.
To change the width of the peak, position the cursor slightly below the top of
the curve. The WIDTH symbol ( ) will appear. By clicking and dragging to
the left, the curve will become wider, whereas dragging to the right makes the
curve narrower.

Curve Fit
Figure 174: Curve Fit Window after Fit
Peak Parameters
In the bottom half of the window, various parameters can be edited. Position,
Intensity and Width can here be manipulated more precisely than with the
cursor. To change the values of a curve, it must be selected first by clicking
onto the respective field. Than the values can be directly typed in or changed
with the respective arrow key above the field.

Evaluate
Peak Shape
Several different options exist for the peak shape. The default setting is Lorentz,
i.e. a pure Lorentzian curve. A single click on the upper arrow key switches
immediately to a pure Gaussian function. The next click on the same arrow sets
the peak to Baseline. If, beginning again with the Lorentz type, the down arrow
is clicked on instead, the peak shape changes to 100%Lorentz + Gauss. In
principle the peak shape simulated is also a pure Lorentzian function but it
represents the special case of a mixture of Lorentzian and Gaussian functions.
Repeated clicking, on the down arrow manually decreases the Lorentz function
percentage. This type of manipulation is typically left to be performed by
OPUS.
Baseline
In some cases it may be necessary to use a Baseline in addition to the peaks. A
baseline is always a straight line defined by a reference point and a slope. The
baseline can be defined by the operator or calculated by OPUS. The parameter
Width is replaced by Slope in the peak list. Baseline parameters can be set
interactively with the mouse or directly in the peak table.
The parameters of the baseline are automatically modified only if the

Levenberg-Marquardt algorithm is used. If the Local Least Squares algorithm
is selected, the parameters are set manually.
Peak List
Each peak is shown in one line of the peak list including all peak parameters.
The lines with non-selected peaks are green and the currently selected peak is
marked in violet. The peaks in the list are always sorted by peak position.
Algorithm
Two different algorithms are available for the optimization of the model:
• Levenberg-Marquardt
• Local Least Squares
The algorithm can be selected before starting the calculation but can also be
changed during the calculation. The algorithm principles are described below.
Status Line
The status line is activated after starting the calculation. It shows the iteration
time and the error of the fit.
Example: 12 sec: Residual RMS error 0.009109

Curve Fit
The smaller the error value the smaller the deviation between measured and
calculated curve.
Message: * Bad Fitting Model! *
Sometimes an additional message *Bad Fitting Model!* is displayed in the

status line. This message is displayed if the program was not able to fit one or
more peaks. These peaks are found at the left or right end of the frequency range
and usually have very small intensities. These bands needs to be deleted before
the calculation is continued. To delete a band, click on its band number (left
row) to select the band and press Delete on your keyboard.
Max Iter. Time (sec)

The maximum iteration time for Auto Fit in seconds is specified in this field.
Auto Fit
The Auto Fit button is used to start the calculation. After clicking on this button
the calculation begins and the button text changes to Stop. During the iteration
the newly calculated peaks are shown on the display in real time. The
calculation can be interrupted at any time by clicking on the button. To restart,
click the button again.
Autoscale
At any time, the standard display functions can be used to zoom, expand or roll
the contents of the display. To return to the original frequency and intensity
limits click on the Autoscale button.
Save Report
Select the Save Report button to save the current report. The resulting sum-
spectrum is stored as a temporary work file. This fit report can be used for the
curve fit of new spectra.
Save Peaks and Reps

In addition to the previously described functions for the Safe Report button, the
fit report is added to the original spectrum.

Evaluate
Theoretical Background
Two different algorithms are used for the curve fit:
• Levenberg-Marquardt
• Local Least Squares
Both algorithms are based on the least squares method. The difference between
the original and the calculated curve are kept as small as possible. The fitting
model is described by: Y G = y ( x ;S )
YG Measured data
y Model
x Frequency
S Set of curve parameters
Levenberg-Marquardt Algorithm
The quadratic equation
N for the deviation between measured and calculated
2 2
curve is: χ ( S ) = ∑ [ Y G – y ( x ;S ) ]
i=1
χ2 Quadratic deviation
N Number of points
The function is minimized by iteration. The gradient of the function χ2 is

calculated for the current set of peak parameters. The gradient is then used to
determine a new set of parameters S.
Some additional restrictions have also been implemented to make the

calculation more effective:
• All peaks must lie within the specified frequency range.
• The width of a peak must not be greater than the specified frequency
range.
• Peak intensities must be positive.
• The contribution of Lorentz- and Gauss functions for mixtures must
lie within the range 0% to 100%.
• The sum of both parts must always be 100%.
Local Least Squares Algorithm

The Local Least Squares algorithm performs an independent fit for each
individual peak. The calculation is thereby restricted to the range around the
peak maximum. This dramatically reduces the amount of data required for the
calculation, enhancing the speed compared to the Levenberg-Marquardt
method. Some loss of precision vs. the Levenberg-Marquardt method occurs.
The Local Least Squares algorithm has some conditions:

Integration
• The parameters for the baseline are taken from the model, not calcu-
lated.
• The peak parameters are always variable, none of them can be fixed.
The given model can be looked at as an area in a n-dimensional space with n

being the total number of peak parameters. In most cases this area has one
absolute minimum and several local minima. The quality of the calculation
depends on the quality of the selected model, i.e. does the calculation find the
absolute minimum or does it orbit in the vicinity of the local minima. The latter
case can be detected by a relatively large error and an visually obvious poor fit.
In case of a poor fit, start again with a new optimized model.
Criteria for the selection of an algorithm

The Levenberg-Marquardt algorithm in most cases gives a better fit compared
to the Local Least Squares algorithm, but needs significantly more calculation
time. If the number of points in the selected region and the number of peaks in
the model is small the Levenberg-Marquardt algorithm can be used
immediately.
If the amount of data is large or many peaks need to be fitted, start with the
Local Least Squares algorithm which converges very quickly. As soon as the
variation of the error becomes small, switch to the Levenberg-Marquardt
algorithm for the final fit.
9.2 Integration
This Integration command allows the integration of peaks as well as the

calculation of peak heights. There are 18 different integration modes available.
Click on the Integration command to open the following dialog:

Evaluate
Figure 175: Integration - Select Files tab
Drag & drop the file(s) to be integrated from the OPUS browser window into
the File(s) for Integration selection field. Before you can start an integration
you have to load a method previously created, or set up a new one.
The integration method includes the integration type and the frequency ranges
to be considered to integrate spectra. Integration methods have the extension
*.INT and can be stored separately. The integration method previously loaded
will be displayed by default in the Loaded Method group field, unless you load a
different method or create a new one. If no integration method has been loaded,
the text reads No Integration Method loaded.
To load a method click on the Load Integration Method button and select the
respective method from the dialog that opens. When creating a new integration
method, you can define an integration method for each peak of interest, also
see 9.2.1.
The integration result is stored in the INTEG data block ( ). Right click on
this data block and select the Show Report option from the pop-up menu. The
report displayed includes the frequency limits as well as the integration method
used.

Integration
Figure 176: Integration Report
The integration report displayed in figure 176 is based on an absorption

spectrum (AB) and includes two bands (peak 1 and peak 2) which have been
integrated by mode A (also see 9.2.1). In case of this mode the result will be an
integral which is indicated by the Result column. Mode A requires 2 frequencies
per area, indicated in the Freq 1 and Freq 2 columns.
If the same spectrum is integrated a second time, e.g. by using a different

method, you can select between three different options available to store the
report. Click on the Report tab.
Figure 177: Integration – Report tab
• The Overwrite option button is activated by default. By means of this

option you can replace an existing integration report.
• If you activate the Merge option button, you add the results to an
existing report.
• If you activate the Append option button, a new single report will be
created and appended to the existing file.

Evaluate
Figure 178: Appending a new integration report to an existing one
9.2.1 Set up Method

An integration method specifies the frequencies for one or more areas which are
to be integrated. Click on the Setup Method button of the Integration dialog to
create a new method.
(a) (b)
(d)
(e)
(f)
(g)
(h)
(c) (i)
Figure 179: Integration Method Setup
a) Determines the left and right edge used to perform an integration or search an
extremum. If you click on the Interactive button, you can set the limits
interactively.
b) Shows the total number of integration areas.
c) Shows the integration mode used for the current area.
d) Shows the number of the current integration region.
e) Use the forward and backwards buttons ( ) to switch between the
integration areas.
f) If you click on the Clear button, you can delete limits, baseline points and the
label of the area defined by (d), as well as undo the integration mode selected.
g) Shows the label of the current area.
h) If you click on the Clear Method button, all areas with the relevant information
will be deleted. Before you create a new method click on this button to delete
possible default settings caused by the previously loaded integration method.

Integration
i) Click on the Load Method button if, e.g. you want to add new areas to an existing
method, or to edit methods which have been previously created.
Note: Save possible changes by clicking on the Store Method button before you
exit this dialog. If you fail to do so, the changes will be discarded.

Evaluate
A) The integration will be performed between the band, abscissa and the
frequency limits defined.
B) A straight line is drawn between the peaks of the two frequency limits
defined. The area above this line will be integrated.
C) The baseline is determined by the first and second baseline point. The
area within the band will be integrated.
D) The baseline is horizontal and determined by the baseline point

defined.
E) To eliminate noise the average peak values between the 1st and 2nd as
well as the 3rd and 4th baseline point are averaged. These average val-
ues form the baseline in combination with the abscissa of the 2nd and
3rd baseline point.
F) The baseline is determined by a least square fit of a parabola to the
data points between the 1st and 2nd, and between the 3rd and the 4th
baseline point.
G) Looks for the highest peak between the left and right edge, and for the
minima on the left and right of this highest peak. The baseline connect
these minima.
H) Integrates from the maximum to the left minimum.
I) Integrates from the maximum to the right frequency minimum.
J) Highest absolute peak intensity
K) Peak intensity relative to the local baseline
L) Peak intensity relative to the baseline, same as D
M) Peak intensity relative to the horizontal baseline
N) Peak intensity relative to the baseline defined by the minima
O) Minimum between the frequency limits
P) Intensity at the specified frequency
Q) Peak intensity relative to the baseline, same as E
R) Peak intensity at a given frequency
Figure 180: Integration Modes

Integration
9.2.2 Interactive Method Setup

To interactively set up a new method first load a spectrum file and click on the
Interactive Method Setup button of the Integration dialog.
II
Figure 181: Integration - Interactive Method Setup
The integration modes A and B (see chapter 9.2.1) are available to interactively
set up an integration method. Select either one of them by the Integration Mode
drop-down list. For integration mode B a straight line (baseline) is drawn
between the intensity values of the frequency limits specified. The area above
this line will be integrated. In case of integration mode A the integration will be
performed using zero as baseline.
The limits are exactly defined by the frequency range set. There will be no
minimum. To set new baseline points click on a certain band position, press the
left mouse button and draw the line. The frequency limits will always be
indicated by the exact wave number (see figure 181). A black help line
additionally indicates this value on the abscissa.
To change between the different integration areas use the forward ( ) and
backward ( ) arrow buttons. Each integration area is defined by a certain
name displayed in the Area selection field. The number next to this selection
field indicates the order in which the integration areas have been defined. The
activated integration area is displayed in red (I in figure 181), non-activated
areas are displayed in light red (II in figure 181).

Evaluate
To move an integration area you first have to select it. If you position the cursor
on the area edge, it will change into . Now, move the area to the position
desired.
If you want to delete an area, select it and click on the Delete Area button. To
delete all areas click on the Delete All button.
You can also load a method and apply it to the current integration mode, or
define new areas and store them as integration method.
9.3 Quantitative Analysis 1
Quant 1 is the software algorithm used to determine component concentration

values for unknown samples. To quantify the components of a multicomponent
sample, calibration measurements are required.
Quant 1 is only suited for spectra with well separated peaks. In case of peak
overlap the use of Quant 2 is recommended.
9.3.1 Setup QUANT 1 Method

Several samples are necessary for calibration. These calibration samples should
contain each component of interest in various concentrations. Furthermore, the
concentrations have to be known, i.e. were determined by a different analytical
method. Using these calibration samples their spectra can be correlated with the
compound concentration.
Each component is assigned to exactly one peak in the spectrum; there are 17
different possibilities (different baselines, intensity or area) to evaluate a peak.
Finally, a calibration function (linear, quadratic or polynomial) is fitted to the
data obtained from the calibration samples, and this function is then used to
determine the concentrations of the unknown sample.
IR spectra are usually depicted as absorption spectra. Ideally, for weakly

absorbing compounds, a linear correlation between the concentration and the
absorption is to be expected (Beer’s law).
A wizard will guide you through the setup of a Quant 1 calibration. Each step
will be performed on a separate tab of the dialog. Using the arrows you can flip
through the pages.
On the first tab a short overview of the necessary steps is given. You can also
load and edit an existing method; this can also be a method created with OPUS-
OS/2. In the following we will generate a new method:

Quantitative Analysis 1
Figure 182: Setup Quant 1
Switch to the next page. Here you can enter the name of the components and
their units. Start by clicking on the Add Component button.

Evaluate
(a) (b)
(c)
(d)
(e)
Figure 183: Define Components
The default name of the first component and the unit mg appears in the entry
fields (a) and (b). If you like, choose a name representative of the compounds
you use and save it using button (c). To include additional compounds use Add
Component (e); list (d) displays all components and weights. To remove a
component, select it with the mouse and press the delete key on your keyboard.
On the next page you load the calibration spectra and enter the value of each
component for each sample of the calibration set (mg). The example includes 10
spectra and two components.

Figure 184: Component List – Component Value Input
Using the Add Spectra button you can include spectra in the list. Navigate to the
directory holding the spectra by clicking on Change Path. If you want to
exclude a spectrum do so by selecting the spectrum and press Remove Selected
Spectra. You can also print this table for your records by means of the Print
button.
Previously, you have defined the number of components, their name and value
for each sample. Now, you have to define one isolated peak for each
component, whose peak height or integral is to be used for calibration.

Evaluate
Figure 185: Setup Integration Method
Click on the Set Integration Areas button and select an appropriate method as
well as the frequency limits as described in the integration chapter of this
manual.
Figure 186: Defining the Integration Method
In addition, you have the possibility to define a reference peak by placing a

mark in the Use Reference Peak check box. Select an integration method and
frequency region for this peak as you would for any other peak. Be sure to
indicate Reference Peak in the drop-down list. This reference peak will be used
to normalize the spectrum.

As the final step you must define the type of calibration function you would like
to fit to your calibration set. While a linear function is suitable for samples
which obey Beer’s law, deviations can be taken into account by choosing a
quadratic or cubic function.
Figure 187: Choose Calibration a Method
After you have set up your Quant 1 method you will be asked to save the
method to disk. Usually, Quant methods will be saved in the “Quant”
subdirectory of the OPUS folder. Then the computation of the calibration
function starts. Depending on the number of calibration spectra, this may take
up to a few seconds or longer.
Click on Next to display the results of the calibration. Each component has its
own tab. The first column lists the file names of the calibration set. The true
value (i.e. the known amount of the substance) and the value calculated by the
fit are given in the next two columns. The difference between these values, the
error of the calculated value and the peak size “X” calculated from the spectra
are also shown.

Evaluate
Figure 188: Calibration Results
You can switch between the result pages for each component using the arrow
button. Toggle between the tabular view and a report view of the results by
selecting the Calibration Report check box. The report view will give you a
printable version of the report. Clicking on Next will get a graph of the
calibration result. The graph allows one to easily recognize data with poor
correlations (for example incorrect values caused by typographical errors during
data entry).

Figure 189: Graphic Display of Calibration Results – Fit vs. True
Below the graphics, The method file, the correlation coefficient and the
calibration equation are stated.
Using the pull-down menu at the bottom of the graph you can switch between
different representations of the calibration result: “Fit vs True” displays the
values obtained by the fit against the known (true) values of the component.
Other options are “Difference vs. True” or “True vs. X”.

Evaluate
Figure 190: Graphic Display of Calibration Results – Difference vs. True

Figure 191: Graphic Display of Calibration Results – True vs X
You can print the results, the figures as well as the data tables, using the Print
button. A report of the results including the calibration equation is stored
together with the method file. Exit the program by clicking on Finish.
9.3.2 Quantitative Analysis 1

After you have created a calibration set you can now start to analyze your
samples. Keep in mind that the concentration of the samples should fall within
the concentration interval covered by the calibration set. Furthermore, the
spectrum of the unknown sample must be acquired using the same parameters
as for the spectra of the calibration set.

Evaluate
Figure 192: Quantitative Analysis
Select the spectra you wish to analyze and load the appropriate Quant 1 method.
If a method had been created or loaded before, it will automatically be available
for the analysis.
Click on Analyze to start the analysis. The result will be saved in a Quant 1 data
block together with the analyzed spectrum and the spectra will be marked as
modified in the browser.
Figure 193: Quant Info Block
Like every other report, you can read Quant reports by opening a report
window. Open the header of the report by right-clicking on the report window.
The header contains the name of the Quant method used for the analysis and the
date the method was created. The report lists the component names, their
predicted concentration together with their units, the correlation coefficient
sigma and the results of the peak integration.

Signal-to-Noise Ratio
Figure 194: Quant 1 Report
You can apply more than one Quant method to analyze a spectrum; the resulting
reports are saved in the same report data block. They appear as entries in the
tree of the report window. Switch between reports by clicking on the report
name of the tree.
Theory:
The functions used for the calibration will be saved in the calibration record as
Y = f(X); where the Y are the values obtained by the fit and X is the peak size
obtained from the spectra. Sigma is a parameter representing the difference
between predicted and true value. Keep in mind that the true values are also
prone to statistical errors, depending on how carefully they have been
determined. An indication for the quality of the calibration is the correlation
coefficient r:
∑ ( ( Zi – Zm ) ( Yi – Ym ) )
r = --------------------------------------------------------------------
∑ ( Zi – Zm ) 2 ∑ ( Yi – Ym ) 2
Here, Z stands for the true concentrations of the components, while m is the
respective average value. The correlation coefficient should be close to 1.0.
The error in analyzing samples of unknown concentration can be estimated by

σ. There is an approximately 68% probability that the concentration of the
unknown sample falls within an interval of the predicted value plus or minus σ:
1
σ = ------------ ∑ ( Z i – Y i ) 2
M–f
M: number of calibration samples

f: degree of freedom (linear 2, quadratic 3, cubic 4)
Z: true concentration
Y: predicted concentration
9.4 Signal-to-Noise Ratio
This command calculates the Signal-to-Noise ratio (SNR) of a spectrum over a

given spectral range. The results may be stored with the spectrum.

Evaluate
Two S/N values are calculated: RMS (Root Mean Square) and PP (Peak to
Peak). In both cases a function is fitted to the spectrum in the region of interest.
This command is either a straight line or (optionally) a quadratic parabola. This
curve defines the (nominal) signal. RMS is calculated as the root of the mean
square of deviations (i.e., the standard deviation). PP noise is the peak to peak
excursions (maximum - minimum) in the y-direction.
Some spectra types (e.g. Absorption, Emission) have base lines near zero.
Specifying a Signal-to-Noise ratio makes no sense in these cases.
The (mean) nominal signal is divided by the newly calculated noise values and
yields the SNR. The result for the PP SNR is always smaller (“worse”) than that
for the RMS value.
Figure 195: Signal-To-Noise Ratio
You can choose the parabolic fit function by checking the Fit Parabola box,
otherwise a linear function is automatically fit to the data. Click on Show to
display the results of the fit. If desired, you can save the fit in combination with
the spectrum.

Signal-to-Noise Ratio
Figure 196: Select a Frequency Range from the Pull-down Menu
The frequency range is entered on the second tab; in addition to manual input,
pre-defined spectral ranges are provided.
Figure 197: Signal To Noise Evaluation
Minimum and Maximum gives the extrema of the ordinate values over the
evaluated range. To locate the results of a SNR calculation, open a new report
window by right-clicking on the “Display” icon in the Browser. Drop the file of
interest into the report window and open the “Data Parameters AB” branch
(alternatively, right-click directly on the file name and choose Show
Parameters).

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Figure 198: Report Window Showing Data Parameters AB Branch
9.5 Peak Picking
The Peak Picking command helps you to identify peaks in spectra. The
command offers high flexibility and allows to adjust and fine tune the search
parameters.
Select the Peak Picking command and drag & drop the spectra from the OPUS
browser window into the File(s) to peak picking selection field. Define the
frequency range by clicking on the Frequency Range tab. Specify the Sensitivity
on the Select Files tab, which is the most important parameter for the
identification.

Peak Picking
Figure 199: Peak Picking – Select Files tab
To work in interactive mode click on the Start interactive mode button.

According to the threshold value set by the slider the number of identified peaks
changes (see figure 200).

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Figure 200: Peak Picking – Interactive Mode
In some applications very small bands may be neglected, and in other cases
high-intensity peaks are normal and thus the low-intensity peaks may be crucial.
Therefore, specify the intensity range to be considered for the peak picking on
the Y-limits tab.

Peak Picking
Figure 201: Peak Picking – Y-Limits
The relative peak height (A in figure 201) allows to define a maximum peak
intensity in relation to the surroundings of the peak and the baseline. It is also
possible to define an absolute peak height in absorption units, i.e. to specify the
limits as absolute absorption values (B in figure 201).
In case of absorbance spectra usually the maxima are of interest, whereas for
transmittance or reflectance spectra the minima are the important features. This
can be accounted for by selecting the appropriate peak picking mode on the
Mode tab. The Automatic mode uses the spectrum type information stored in the
data block to determine if maxima or minima are picked.
Not very often (e.g. when subtracting photoacoustic spectra) is it necessary to

specify whether the algorithm should pick for minima (i.e. transmittance
spectra) or maxima (i.e. absorbance spectra).

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Figure 202: Peak Picking – Mode tab
To be independent of the baseline, the second derivative algorithm is typically

used, since the first derivative does not isolate peaks sufficiently well in case of
weak shoulders. The Savitzky-Golay algorithm is actually used to obtain the
derivative.
The number of smoothing points used can be adjusted to suppress the effect of
noise. As a rule of thumb, the number of smoothing points should not be greater
than the full width at half maximum of the smallest peak of interest. This value
is ignored when using the standard method.
An additional peak picking method is the calculation of the center of gravity.

This algorithm calculates, from a certain fraction of peak height, the centroid of
an area. The position of this centroid determines the peak position. Specify
which portion of band area (in %) has to be considered to calculate the gravity,
in the Fraction of peak height entry field. You can only enter integers between 1
and 99.
The center of gravity method yields the same results in case of symmetric
bands. In case of antisymmetric bands the band position is moved towards the
broader edge. This interacts with the size of the peak height used for the

Peak Picking
calculation. If the fraction of peak height is too small, the band will not be listed
on band list. Too small a fraction of peak height would decrease the number of
measuring points, used to calculate the band position, to less than 3.
The band position is calculated as follows:
Based on the band maximum Y max, X max , which is usually not the maximum of
the measuring values, the measuring points are consecutively numbered to the
left and right. The numbering starts from 0 for both sides, while the y- value of
each measuring point must be greater than Yi ≥ Ymax – ( Ymax – Ymin ) ⋅ Fraction , with
Y i being the measurement values, and the Fraction term being the percentage
value defined for the peak height. This yields to the following sums:
SumY = ∑ ( Y right ( i ) – Y Fraction ) + ∑ ( Y left ( i ) – Y Fraction )

i=0 i=0
SumYX = ∑ ( Y right ( i ) – Y Fraction ) ⋅ ( i + 0 ,5 ) – ∑ ( Y left ( i ) – Y Fraction ) ⋅ ( i + 0 ,5 )

i=0 i=0
Thus, the band position yields
PeakPos COG = [ x max ] + 0, 5 + SumYX

------------------
SumY
whereas [ x max ] represents the next smaller integer of the x-value for the band
maximum.
The band position in wave number units is:
PeakPos COG ( v ) = PeakPos COG ⋅ ∆v + v min and ∆v being the wave number distance
between two measuring points and v min being wave number of the first data
point.

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Xmax, Ymax
30%
100%
Xmin, Ymin
Figure 203: Band edge
If you use the Peak Picking command on a spectrum that already has a peak
table appended, you can either overwrite the previous table by the new one, or
append the new table to the existing one.
Theory:
The standard method is used for peaks with small or no overlap in spectra of
low or average spectral resolution (0.5cm-1 or above).
The x-position is the x-value of the interpolated maximum or minimum, with

intensity being the y-value of this point. To determine the relative intensity an
internal local baseline between two lateral minima (or maxima) is drawn. The
relative intensity is then the y-axis distance between this baseline and the
maximum (or minimum).

Peak Picking
Full Width at Half

Maximum
Relative Intensity
Local Baseline
Figure 204: Spectrum with Line width, Relative Intensity and Baseline Indicated
The lateral extremes are determined by going outwards from the x-position of
the line, until another line at least as strong is found (or the end of the spectrum
is reached). The lowest point in this interval is then used as a lateral minimum
(or maximum).
To find the line width, a line parallel to the local baseline is drawn which
intersects the middle of a vertical line connecting the maximum (or minimum)
of the band and the local baseline.
Peaks will be included in the peak pick table if their relative intensity falls
within the interval defined on the Y-Limits tab. This interval was normalized
such that the difference between maxima and minima corresponds to 100%.
The definition of the upper limit is optional and can be used to mask, for
example, large water bands.

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Figure 205: Calculation with Baseline Reference
The peak search using the second derivative method is recommended for high
resolution spectra only.
Figure 206: Absorption Spectrum and Second Derivative
The x-positions are the x-values of the minima (or maxima) of the smoothed,
second derivative spectrum. This is particularly useful for seriously overlapping
bands because in this case an extremity of the spectrum is frequently not shifted
with respect to the true band position. Weak shoulders can also be recognized
using the second derivative method.
In order to calculate the relative intensities and the width of the peak, the zero-
points and the minima of the second derivative are computed. These points are
significant for the peaks that make up the envelope:

Peak Picking
[ν-1, 0] (zero-point)
[ν0, I"0] (minimum)
[ν1, 0] (zero-point)
In figure 207 two Lorentzian curves are superimposed. The zero-points and the
minima of both signals are almost identical (both for the derivatives of the
isolated signals as well as for their superposition). The maxima of the
overlapped signals are shifted and therefore misleading.
If a strong signal overlaps a weak signal, a maximum could be found where a

zero-point should be. If a maximum is found prior to a zero-point, during the
search for a minimum of the second derivative, the position of the maximum
has to be used instead. This points to the limitations of the method.
Apparent Peak Positions
True Peak Positions
Apparent Peak Positions
True Peak Positions
Figure 207: Apparent and True Peak Position

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To access the Peak Table, right-click on the Peak Pick report block and select
the Show Peak List command from the pop-up menu. A table created using the
standard method for low resolution spectra and relative intensities of higher
than 10% (accuracy to 4 decimal points) could look like the following:
Figure 208: Result of a Peak Search
9.6 Quick Identity Test
The Quick Identity Test offers a user friendly method to judge the similarity of
two spectra. This method requires a reference spectrum of the substance of
interest. The test determines the Euclidean distance between the test and
reference spectrum.

Quick Identity Test
Figure 209: Quick Identity Test – Selected Files
Enter the reference spectrum in the field Principal File for Quick Identity Test,
and the files to be tested in the field Files for Quick Ident.
You can define several frequency regions on the Frequency Ranges tab. The
data of the regions indicated will be compared, only. You can also compare the
frequency range common to all spectra by activating the Use File Limits check
box. Switch between regions by using the arrow key. Delete a region by
clicking on the Clear button.

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Figure 210: Quick Identity Test – Frequency Ranges
Select a data preprocessing method, the derivative or the vector normalization.

A vector normalization causes the Euclidean distance to fall within an interval
of 0 and 2.
On the third tab you can define the data preprocessing method. It is possible to
perform a spectrum derivative and vector normalization. The latter has to be
selected to be able to set the scale level of the spectral distances to a value range
between 0 and 2.

Quick Identity Test
Figure 211: Quick Identity Test - Data Preprocessing
A report block will be appended to every spectrum which was compared to the
reference spectrum. This Report of Correlation Search lists the spectrum name
and sample name (as taken from the spectrum parameter block), the number of
the spectrum, the Hit Quality and the file name. The hit quality should
preferably be a small number, with zero being an absolute match.
In addition, a new file QIDNT.0 will be created that summarizes the reports of
all test spectra. The report headers of this report are identical with the headers of
the respective test spectra reports.

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Figure 212: Quick Identity Test Report
The report is structured similar to an OPUS/IDENT report. In this report you

can vary between several parameters which are defined in the Quick Identity
Test.
The following information is important when using the Quick Identity Test:
• Method file
File name of the method used for the test
• Expected Reference
The principal file used
• Vector normalized spectra
Indicates that vector normalization has been was used.
• X-Ranges
Number of frequency ranges.
• Order of Internal Derivation
Specifies the order of the derivative used
• Smoothing Points for Internal Derivation
Specifies the number of smoothing points
9.7 Quality-Test
The quality assessment of spectra measured using the Quality-Test command is

an integral part of spectral analysis and should always be carried out before the
actual evaluation.

Quality-Test
This test assesses the quality of spectra measured with regard to absorbance
values, signal-to-noise ratio and intensity of the water vapor lines. Spectra that
exceed certain limit values should not be considered for analysis.
Select the Quality-Test command from the Evaluate menu. The following
dialog box (see figure 213) opens:
Figure 213: Quality Test - Select Files
The Select Files tab includes the spectrum to be tested. You can drag and drop
the file icon from the browser window into the File(s) for Quality-Test field.
Note that the spectrum to be evaluated needs to be an absorbance spectrum.
Click on the Quality-Test button to perform the test using the parameters of the
method currently loaded. To load or save a method, click on the Load/Save
Method tab of the Quality-Test dialog box.

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Figure 214: Quality Test - Load/Save Method
The quality test results are stored in the Quality-Test Report data block ( )
which is added to the evaluated spectral file. Double click on the QTEST block
in the OPUS browser window to open the Quality-Test Report window. Figure
215 shows an example of a Quality-Test Report.
Figure 215: Quality Test Report
The first line of the report indicates the test result. A value of 1 means passed,
whereas 0 means failed. Do not use spectra that failed for further analysis. The
second line includes the file path of the test method used. The lower window
shows all parameters and their limit values (min. and max.) as well as their
measured values. These parameters can be defined if you click on the
Parameters tab.

Quality-Test
Figure 216: Quality Test - Parameters
Parameters
Some parameters and their limit values are explained in the following:
x-Range 1
The range defined in the first column (2100 - 1600cm-1) calculates the
maximum and minimum absorbance values of the original spectrum ([AB] data
block). The difference between these two values has to be higher than the one
indicated in the Delta y min entry field and lower than the limit defined in the
Delta y max entry field (0.345 to 1.245 absorbance units).
x-Range 2
The range defined has to represent a characteristic band of the sample (Amide I
at 1700 - 1600cm-1). The first derivative is calculated and the maximum and
minimum absorbance values are determined. The difference between these two
values results in S1, a parameter which approximately corresponds to the
intensity of the band defined.
S1 is used to calculate the signal-to-noise ratio, i.e. S1 is divided by the noise

determined from the first derivative within a spectral range which shows no
absorbance bands (as defined in the x-Range 4). The minimum S1/Noise-ratio
value is indicated in the Signal/Noise entry field (value: 200).
S1 is also divided by the water vapor signal determined in the x-Range 5. The
minimum S1/WaterVapor-ratio value is indicated in the Signal/Water entry
field (value: 100).

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x-Range 3
The range defined has to represent a second characteristic sample band (sugar-
ring vibration at 960 - 1260cm-1). The first derivative is calculated and the
maximum and minimum values are determined. The difference between these
two values results in S2, a parameter which approximately corresponds to the
intensity of the band defined.
S2 is used to calculate the signal-to-noise ratio, i.e. S2 is divided by the noise

determined within a spectral range which shows no absorbance bands (as
defined in x-Range 4). The minimum S2/Noise-ratio value is indicated in the
Signal/Noise entry field (value: 40).
S2 is also divided by the water vapor signal determined in the x-Range 5. The
minimum S2/WaterVapor-ratio value is indicated in the Signal/Water entry
field (value: 20).
x-Range 4
The spectrum noise is calculated within a spectral range that shows no

absorbance bands of the sample (range: 2000 - 2100cm-1).
In this range the first derivative is calculated and the maximum and minimum
values are determined. The difference between these two values is termed noise
and should not exceed the maximum value defined in the Noise max entry field
(value: 0.00015, i.e. 1.5 x 10-4).
x-Range 5
The water vapor intensity is calculated in a spectral range which indicates

strong water vapor absorbance but no sample absorbance (range:
1847 - 1837cm-1). The first derivative is calculated and the maximum and
minimum values are determined within the range defined. The difference
between these two values causes this strong water absorbance. The value should
not exceed the maximum value defined in the Water max entry field (value:
0.0003).
x-Range 6
The frequency range is determined if the spectrum shows interferences

(fringes). The defined frequency range has to be free of any sample absorbance
(range: 2200 - 2000cm-1). The maximal difference between the highest and
lowest value of the first derivative is defined in the Fringes table line (value:
5 x10-5).

Multi Evaluation
9.8 Multi Evaluation
The Multi Evaluation function is the automated evaluation of NIR spectra for
qualitative or quantitative analysis. It combines IDENT, QUANT and
conformity test methods with the results being displayed in one single report.
The advantage of multi evaluation is, e.g., if you want to identify an unknown
product, you can first perform an IDENT analysis. Based on the results obtained
you can continue with a QUANT analysis. Sometimes it is advisable to perform
a preliminary test to see whether the product to be used for a quantitative
analysis has been measured at all. The combination of an IDENT analysis and
conformity test may similarly be appropriate.
Multi evaluation parameters are stored in a special method file with the
extension *.ME. Before you can start a multi evaluation you have to create a
multi evaluation method. If you want to edit the multi evaluation path of this
method, make sure that you have the right to change parameters. To verify the
user rights select the User Settings command in the Setup menu, and click on
the 21CFR11 Rights tab. For further details, see chapter 14.10.
9.8.1 Multi Evaluation Setup

To start the multi evaluation analysis you have to set up a method or load a
method which has been previously created. Click on the Multi Evaluation Setup
command to open the following dialog:

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Figure 217: Multi Evaluation Setup - Load Method tab
To load an existing method click on the Load Multi Evaluation Method button
and select the particular method from the dialog that opens.
Depending on the kind of evaluation you want to perform on the original

spectrum or spectra set up a new method by means of the other evaluation
option tabs available. The evaluation options correlate with each other, i.e. the
sequence of product analysis shall be as follows:
1) IDENT (no further test)
2) IDENT → Conformity Test
3) IDENT → Conformity Test → QUANT
4) IDENT → QUANT
5) Conformity Test → (no further test)
6) Conformity Test → QUANT
7) QUANT (no further test)
The sequences 2 and 4 allow to identify the product in a first step by using the
No Reference defined IDENT test option.
If you use the IDENT Evaluation with several substance groups, and the multi
evaluation test result shows that some of these groups may apply to the product
to be evaluated, any further test would not be reasonable. This result, however,

Multi Evaluation
will only be generated if the basic IDENT library had not been validated
properly and overlappings had not been eliminated either.
Otherwise, if only one substance group applies, you can continue by performing
the Conformity Test and/or QUANT Evaluation. This test depends on the
substance group selected for the IDENT Evaluation.
It is also possible to perform the multi evaluation analysis by the Conformity

Test only. If one conformity test method turns out to be successful, you can
continue with the QUANT Evaluation.
As soon as you close the Multi Evaluation Setup command without saving the
changes made the following dialog pops up:
Figure 218: Multi Evaluation Setup - Pop-up dialog
This dialog pops up even if you have not made any changes on the method at
all, but clicked on one of the IDENT, Conformity Test or QUANT Multi
Evaluation tabs.

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9.8.1.1 IDENT Evaluation
Figure 219: Multi Evaluation Setup - IDENT Evaluation tab
The Active check box is deactivated by default and thus all functions and
controls are disabled and grayed. Activate the Active check box. If you activate
the Change IDENT Method check box, you can select the appropriate IDENT
method from the drop-down list.
Note: All IDENT, Conformity Test and QUANT methods used for multi
evaluation have first to be copied to the sub-directories of the multi evaluation
root directory. The following default setting applies:
...\OPUS\MultiEvaluation
\Conformity Test Method
\IDENT Method
\QUANT Method
These paths will be created in OPUS not until the Multi Evaluation Setup
command has been selected for the very first time.
Confirm the choice by clicking on the Accept Method Change button. The name
of the IDENT method file with the extension *.FAA will be displayed in the
upper selection field (see A in figure 220).

Multi Evaluation
Figure 220: Identity Test Method group field
The Change IDENT Method check box and the drop-down list will be
deactivated again.
For the IDENT analysis two alternative evaluation modes are available. The
mode No Reference Defined (see figure 219) works without a pre-defined
reference spectrum and allows the complete analysis of all substances. This,
however, requires the substances to be part of one validated IDENT library, and
further evaluation methods, e.g. QUANT, to be assigned properly.
To work with an expected reference group check the Expected Reference Group
option button. The reference group previously selected will always be set as
default. To change the reference group activate the Change Expected Group
check box and select the particular group from the drop-down list. This list
includes all groups of the current IDENT library.
Figure 221: Evaluation Mode group field
Confirm the choice by clicking on the Accept Group Change button. The name
of the reference group selected will be displayed in the upper selection field (A
in figure 221), and the Change Expected Group check box and the drop-down
list will be deactivated again.
All the settings made on the Conformity Test and QUANT Evaluation tab
correlate with the expected reference defined.

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9.8.1.2 Conformity Test
Figure 222: Multi Evaluation Setup - Conformity Test tab
Activate the Active check box. If you have defined an expected reference group
on the IDENT Evaluation tab, the upper drop-down list includes the name of the
reference group defined and will be deactivated. If no reference group has been
defined, the drop-down list will be activated and you can select a particular
group of the IDENT library (see figure 223).
Figure 223: Select Product for Assignment
Assign an individual conformity test method to the selected IDENT library

group. Activate the Change Conformity Test Method check box and select the
appropriate method from the drop-down list. Confirm the choice by clicking on
the Accept Change button (see figure 224).

Multi Evaluation
Figure 224: Select Conformity Test Method
If the settings are made, click on the Add button (see figure 225). A table will be
displayed including the assignments made, and the name of the conformity test
method. To remove a particular assignment from the list, select the
corresponding line and click on the Delete button.
Figure 225: Method List of Conformity Test

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9.8.1.3 QUANT Evaluation
Figure 226: Multi Evaluation Setup - QUANT Evaluation tab
Activate the Active check box. If you have defined an expected reference group
on the IDENT Evaluation tab, the upper drop-down list includes the name of the
reference group and will be deactivated. If no reference group has been defined,
the drop-down list will be activated and you can select a particular group of the
IDENT library.
Assign an individual QUANT or INTEGRATION method to the selected

IDENT library group. Activate one of the Quantitative Analysis Method option
buttons and select the appropriate method from the drop-down list.
Figure 227: Quantitative Analysis Methods
In case of QUANT 1 and INTEGRATION you can also select between different
data preprocessing methods. The methods include Vector Normalization, 1st
and 2nd Derivative and combinations of both methods. Frequently, the Vector

Multi Evaluation
Normalization method is used to preprocess data. In many cases, however, you

even get better results if you select 1st or 2nd Derivative. For further details on
the preprocessing methods, see chapter 8.
In the Parameters group field you can specify additional values which are set to
0 by default.
Figure 228: Parameters group field
Activate the Correction of Result check box and apply a formula from the drop-
down list. If you want to create a new formula for the correction of analysis
results, click on the Create Formula button. The following dialog pops up:
Figure 229: Correction Formula Calculator
By means of the Load Formula button you can load an existing formula with
the file extension *.for. The string code begins with the Adjusted_Result = term,
and you can add up to 4 different variables:

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• 1 variable for the result predicted by the method

• 3 variables for input values which can be set during spectra
evaluation
If you click on the Add input... button(s) or Predicted result button or on one of
the figure buttons, the string code will be continued according to the entries
made.
Example: Adjusted_Result = Predicted_Result * 3.01/Add_input 1 * Add_input 2/5.2
Always use the Calculator block which includes brackets, decimal point and the
four basic arithmetic operations. To save the new formula click on the Save as...
button. Make sure that you use a valid formula which does not produce any
arithmetic error.
No recommendations can be made for the values to be entered for Target

Concentration or the highest allowable standard deviation in case of several
analysis (Maximum% RSD). The optimum value has to be determined
empirically.
Depending on the test result warning and alarm values can be set in case of the
concentration and average value limit. As soon as the warning value defined
will be exceeded, a warning is given and informs you where the error has
occurred. If all parameters have been set, click on the Add button to have the
method list displayed. The warning and alarm values will be set to 0 again.
Figure 230: Quantitative Analysis Method List
The analysis method list includes all the parameters set. The figure displayed in
the Method column refers to the method selected, i.e.:
0 = QUANT 2
1 = QUANT 1
2 = INTEGRATION
To remove a particular assignment from the list, select the corresponding line
and click on the Delete button.

Multi Evaluation Test
9.8.1.4 Store Method
Figure 231: Load Multi Evaluation Setup - Store tab
To finish the multi evaluation setup procedure click on the Store Method button.
The method will be stored in the OPUS MultiEvaluation directory whose root
path can be defined in the Setup menu by means of the User Settings command,
provided you have the necessary user rights. For the MultiEvaluation directory
the default root path will always be the currently used local OPUS directory.
9.9 Multi Evaluation Test
Start the multi evaluation by clicking on the Multi Evaluation Test command.
The following dialog opens:

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Figure 232: Multi Evaluation Test - Select Files tab
Drag & drop the file(s) to be tested from the OPUS browser window into the
File(s) for Multi Evaluation Test selection field.
Click on the Load Multi Evaluation Method button and load the particular
method. Normally, the path of the method previously used is displayed above
this button.
The Values for Quantitative Analysis tab displays the three input variables
defined by means of the formula calculator (see figure 233).

Multi Evaluation Test
Figure 233: Multi Evaluation Test - Values for Quantitative Analysis tab
Start the multi evaluation analysis and click on the Test button. Each step
performed during multi evaluation will be indicated by the status bar. The multi
evaluation results are stored in an ME data block ( ) and displayed in a
special report (see figure 234).
Figure 234: Multi Evaluation Report
The multi evaluation test report contains the test name and path as well as the
results of the different method tests, e.g. QUANT, IDENT or Conformity Test
(A in figure 234). The Multi Evaluation final test status is indicated by either
ERROR, REGULAR, UNCHECKED, WARNING or ALARM (B in
figure 234).

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If, e.g., in the QUANT evaluation method the upper and lower concentration
limit defined for warning or alarm differs, the final result is checked against
these limits.
The concentration limits are not taken into account if all concentration limits are
set to 0 (default setting). If they are not evaluated, the status is reported as
UNCHECKED unless an ERROR occurs. Any ALARM supersedes a
WARNING. An error occurs if, e.g., a data block type does not correspond to a
method.
If the assignments made on the Conformity Test tab correspond to the ones
made on the QUANT Evaluation tab, the evaluation will be performed.
Otherwise, the evaluation will not performed.
9.10 Quick Compare
The Quick Compare function is an easy quality control tool which can be used
for MIR spectra. Loaded spectra are compared with one reference spectrum or
all spectra files of a directory, and a correlation coefficient (see chapter 9.10.2)
is calculated. To perform the Quick Compare function you have to use spectrum
files which include either an AB (absorption) or TR (transmission) data block.
Quick Compare parameters are stored in a special method file with the
extension *.QCM (Quick Compare Method). To create such a QCM method file
use the Quick Compare Setup command. If you want to edit a QCM method file,
make sure that you have OPUS administrator rights. For further details on this
subject, refer to section 14.10.

Quick Compare
9.10.1 Quick Compare Setup

Before you can start Quick Compare you have to set up a method or load a
method previously created. Click on the Quick Compare Setup command to
open the following dialog:
Figure 235: Quick Compare Setup - Load/Store Method
To load an existing method click on the Load Method button. The General
Method Information group field includes information on the method, e.g. path
and method file name, threshold, data preprocessing etc. As the Use File Limit
check box on the Parameters tab is checked by default, the frequency range
value will be set to 1.
To select the reference file(s), click on the Reference Files tab.

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Figure 236: Quick Compare Setup - Reference Files
You can either select one single spectrum file or all spectra files of a complete
directory. Click on the Select Single File or Select Whole Directory button. In
either case a dialog opens which you use to select the correct OPUS spectrum
file(s).
The current selection will be displayed in the file selection field on the bottom
of the Reference Files tab. It is also possible to drag & drop a spectrum file from
the OPUS browser window to the file selection field.
If you have selected a complete directory, the Take Average as Reference check
box will be enabled. If you activate this check box, an average reference
spectrum will be calculated from all spectra stored in the directory selected. To
perform the comparison with all reference files, define the maximum number of
entries to be included in the hit list. Up to 5 entries are possible.
To set up additional Quick Compare parameters click on the Parameters tab.

Quick Compare
Figure 237: Quick Compare Setup - Parameters
The Comment entry field can be used to enter any kind of text, e.g. details about
the method created such as Two spectral regions, No data preprocessing etc.
As the Use File Limit check box is activated by default, the wave number range
is based on the first, and possibly only, reference spectrum. If you deactivate
this check box, the Interactive Regions Selection and Clear Selected Regions
buttons as well as the Spectral Regions table will be enabled.
To select the spectral regions you can either type in the limits manually into the
Spectral Regions table or select them interactively. In the latter case click on the
Interactive Region Selection button. Move the borders of the frequency region
accordingly, or right click into the frequency region and select one of the
options from the pop-up menu.
If you want to delete one or more spectral region(s), select the respective line(s)
on the Spectral Regions table and click on the Clear Selected Regions button.
To delete the spectral regions when working in interactive mode right click on
the region and delete it by the Remove pop-up menu.

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Use the slider to determine the threshold which influences the Quick Compare
result. If the result is OK, the correlation coefficient is greater than the threshold
selected. The result is not OK if the correlation coefficient is less than the
threshold selected. You can also enter the exact threshold value between 0 and
100%, manually into the corresponding entry field.
Optionally, you can select between three different data preprocessing methods.
If you check the First or Second Derivative option button, the Smoothing Point
selection box will be enabled. The optimal number of smoothing points set for
the specific preprocessing methods has to be determined empirically.
The Exclude CO2 Region check box allows to exclude CO2 bands from the
calculation. If you activate this check box, the wave number regions of
660 to 680cm-1 and 2,275 to 2,400cm-1 are excluded when calculating the
correlation coefficient (see chapter 9.10.2).
If you have set all parameters, return to the Load/Store Method tab and click on
the Store Method button to store the new method. This button is only enabled if
you have specified a reference file and a wave number range.
9.10.2 Quick Compare Theory

The comparison between sample and reference spectrum will be performed by
calculating the correlation coefficient.
The correlation coefficient r of the two functions y 1 ( k ) and y 2 ( k ) is calculated

as ratio from the covariance and product of the two standard deviations
σ y1 and σ y2 :
Cov ( y 1 ( k ), y 2 ( k ) )
r = ---------------------------------------------
-
σ y1 ⋅ σ y2
The value of r ranges between -1 (inverted spectra) and +1 (identical spectra).

This correlation coefficient r will be calculated into a percentage and reflects
the similarity of the two spectra. The – 1 ≤ r < 0 range is mapped to 0%, and the
0 < r ≤ 1 range is mapped linearly to 0% ...100%.
9.10.3 Quick Compare

Start the comparison by clicking on the Quick Compare command. The
following dialog opens:

Quick Compare
Figure 238: Quick Compare - Select File
Drag & drop the file(s) to be compared from the OPUS browser window into
the File(s) for Quick Compare selection field. Make sure that the data blocks for
the sample and reference files are of the same spectra type, i.e. AB (absorption)
or TR (transmission). Besides, the wave number range of the sample spectrum
has to be at least as large as the range defined for the reference spectra. You can
also load 3D files as sample files to perform a Quick Compare. However, 3D
files cannot be loaded as reference files.
Click on the Load Method button and load the particular method. Normally, the
path of the method previously used is always displayed above the Load Method
button.
The settings in the Result Presentation group field will be stored as OPUS
parameters and are set by default if you start the Quick Compare command the
next time. The same applies to the method selected. If you activate the Show
Results Immediately check box and click on the Compare button, the Quick
Compare results will be displayed in the QC Results-Display, see figure 239 et
seq.
In case of 3D-files the Show Results Immediately and Print Results

Automatically check boxes will be disabled. The Quick Compare results in case
of 3D-files will be stored in a TRC data block ( ) of the sample file and
displayed in a specific report view.

Evaluate
Figure 239: QC Results-Display - Result Not OK
The QC Results-Display consists of a sample and reference spectrum window.

In the lower part of the display the Quick Compare result is indicated. A red
cross and the description NOT OK would indicate that the comparison has
failed. In this case the correlation value calculated is less than the threshold
value defined in the method. A green check mark and the description OK would
indicate that the comparison has passed. In this case the correlation value
calculated is greater than the threshold value defined in the method.
Figure 240: QC Results-Display - Result OK
Figure 240 shows a QC Results-Display which was based on a Quick Compare

between a sample spectrum and several single spectra files of a complete
directory.

Quick Compare
Figure 241: QC Results-Display - Several Single Spectra
If a sample spectrum is compared with the average value of several reference

spectra, the QC Results-Display can be as follows:
Figure 242: QC Results-Display - Average As Reference
As soon as you have activated the Show Results Immediately check box, the
Print Results Automatically check box will be enabled. If you activate this
check box, the comparison results will automatically be printed after the
calculation has been terminated. The layout of the print is similar to the QC
Results-Display.
To start Quick Compare click on the Compare button. The evaluation results are
stored in a QC data block ( ). This data block includes the parameter values
used and the result calculated which can range between 0 and 100% (0% = no
correlation, 100%=full correlation), see figure 243.

Evaluate
Figure 243: Quick Compare Report
9.11 Spectrum Search
OPUS offers several library search commands. For details, e.g. Library Editor
see the OPUS Search Manual which supplied with the OPUS Search package.
The aim of spectrum search is to identify unknown substances. To perform a

search you need a library which is in line with your needs. BRUKER offers a
variety of commercial libraries which allow to solve many analytical problems.
You will find a free demo library on your OPUS CD containing 350 entries.
9.11.1 Starting a Spectrum Search

Select the Spectrum Search command in the Evaluate menu and specify the
spectrum files. To do this click on the Spectrum Search tab. If you activate the
Show Search Report immediately check box, a report window displaying the
results opens automatically after the search run has finished. You can also limit
the search to an existing search report. In this case only the substances listed in
the report will be compared to the test spectrum.

Spectrum Search
Figure 244: Spectrum Search
On the Search Parameter tab you define the desired search parameters.

Evaluate
Figure 245: Spectrum Search – Search Parameters
• Algorithm: BRUKER search algorithm uses a peak table together

with the experimental data (spectra). A temporary peak table is auto-
matically generated during a search using the Standard algorithm.
The second algorithm, Use existing Peak Table employs existing
peak tables, allowing one to suppress, for example, solvent peaks.
• Search Sensitivity: Using Search Sensitivity you can control the result
of your search. It is difficult to give a general recommendation for
the sensitivity value, because the search result depends highly on the
type of recorded spectra. For spectra taken from KBr pellets with a
typical Signal-to-Noise ratio, a sensitivity setting of 6 to 10 would be
reasonable. The best is, however, to learn about different sensitivity
settings by doing test runs applied to known substances. As a rule of
thumb, values higher than 15 rarely yield a significant result.
• Maximum Number of Hits: The number of hits that are to be saved in
the search report can be specified. Depending on the value set in the
Minimum Hit Quality field, the resulting number of hits can be lower
than this value.
• Minimum Hit Quality: This field is used to enter the minimum value
to qualify of a hit in the search. A value of 1000 would be a perfect
match, whereas a value of 0 is obtained in the case of no correlation
at all. In reality the search algorithm gives a value higher than 0 even
if no (or negligible) similarities exist between spectra. Therefore,
one restricts the number of hits included in the search report to a
lower limit (default settings 300). This value also depends on the

Spectrum Search
sample type and should be evaluated by measuring representative

samples. Only if a search yields no hits, should the Minimum Hit
Quality be set to a lower value.
You can limit the search to certain frequency regions of the spectrum instead of
comparing the whole recorded frequency range of the spectrum to the library
spectra. Enter either the frequency ranges manually in the table cells or use the
Interactive Range Selection button to directly select a frequency range in the
spectrum. Once you defined a list of regions to exclude you can save them
(Save Ranges as) for future use. Clear ranges clears the table and the Restore
last Ranges button automatically calls up the last range definition you used.
Figure 246: Spectrum Search – Exclude Frequency Regions
On the Select Library tab you select at least one library to apply for the search.
A search can involve either one or more libraries, but creates only one search
report.

Evaluate
Figure 247: Spectrum Search – Select Library
Use the Add Libraries and Remove Libraries buttons to include or exclude
libraries in the list. The library selection field shows only one single file for
each library to ensure a clear structure. You can select several libraries from the
selection field.
To remove libraries from the selection field, select them first and click on the
Remove Library or Remove all Libraries button. Save a library created by
means of the Save Library List button. To modify a library click on the Change
List button. The library previously used will be set by default the next time
when using the Spectrum Search function.
You can also test the integrity of a library file by the Check Library command.
This command also updates the number of file entries. If a file passes the test, it
will be checked by a green mark.
Problematic files are indicated by a red “x”. This can also be caused by the fact,
that OPUS cannot locate the library file (e.g. after you moved the file to a
different directory).
9.11.2 Search Report

The result of a spectrum search will be saved in a report; you can read through
the report by opening a report window. The report will automatically be
displayed if you have checked the Show Search Report immediately box.

NeuroDeveloper Classification
Otherwise, open the report by double-clicking on the report block.
The report window consists of four areas, which can be adjusted in size by
moving the window bars. The list at the bottom of the window contains all
spectra matching the search criteria. The hits are numbered consecutively (first
column) and sorted by hit quality. The first spectrum is selected (red square)
and automatically displayed in the display area above. The spectrum will only
be displayed if the box before the spectrum name is checked. To display the
substance information and the structure, the spectrum must be selected. The hit
quality is marked before the name of the substance, followed by the entry
number of the spectrum in the library.
Figure 248: Search Report – Results
Display the query spectrum by clicking on the Show Query Spectrum button.
Close the report window by clicking on Exit.
9.12 NeuroDeveloper Classification
For information on the NeuroDeveloper program, refer to the extensive online

documentation.

Evaluate

Forward, Back
10 Display
The commands within this pull-down menu are for manipulating the display of
the active spectrum window. They allow you to zoom in on a detail of the
display, and go back to the original display size. Some of the commands are not
always available, depending on the preceding steps performed. For example,
the Forward and Back commands are only active if you switched the display
magnification.
Figure 249: Display Menu
10.1 Forward, Back

Back allows you to restore the original display size on your screen after you
have zoomed in on a detail of the displayed curve. Forward will display the
zoomed in area again.
10.2 Stacked
If you loaded more than one spectrum into the same spectrum window you have
the option of a stacked display i.e. the spectra will not overlap. The preview
window is not affected by this command.

Display
Figure 250: Spectrum Window Containing Two Spectra – Normal and Stacked View
The ordinate will be duplicated when displaying two spectra in the stacked
mode. You can separate both spectra by displaying another abscissa, using the
Axis command of the spectrum window pop-up menu (accessible by right-
clicking on the spectrum window). If you expand a part of one stacked
spectrum, the other spectrum will automatically be enlarged.
10.3 Scale All, Scale Y

You can fit a spectrum to the size of the spectrum window using the Scale All
command. If you only want to scale the ordinate, you can achieve that with the
Scale Y command.
10.4 Page Forward, Page Backward

If you have displayed only part of a spectrum you will see this part shown on a
white background in the preview window, while the rest of the spectrum which
is not shown appears on a gray background. You can move the displayed region
along the frequency axis using the Page Forward and Page Backward
commands. In this case you can browse a spectrum while keeping the displayed
frequency region the same.
10.5 Zoom In
The Zoom option allows you to choose the magnification. Use the left mouse
button to draw a frame around the region you would like to expand. After a
second mouse click the crosshair cursor disappears and instead you can
reposition the frame. Now left-click again and the area marked by the frame will
be resized to the spectrum window.

Installing Default Printer
11 Print
The Print menu includes printing spectra functions and allows to create new
printing templates or layouts and load existing ones. It is also possible to use
templates which have been created by former OPUS versions, e.g.
OPUS-OS/2. They will automatically be converted.
Figure 251: Print Menu
Before being able to start printing spectra you have to set up a default printer in
Windows first.
11.1 Installing Default Printer
The default printer is automatically addressed by the computer when printing.

To install the printer connect it to the parallel port of your computer or make
sure that a printer is available on the network. For details on the hardware
connection, refer to the printer manual.
Install the printer driver as follows:

1) Click on the Windows Start button, select the Settings command and
click on the Printer option. The Printer dialog opens.
2) Double click on the New Printer icon and follow the on-screen
instructions.
3) If the installation has been successful, a new printer icon appears in the
Printer dialog.
4) To check whether the printer has been defined as default printer double
click on the new printer icon. A menu pops up in which The Default
Printer command has to be checked.

Print
11.2 Print Setup
Use the Print Setup command to define the printer and the print parameters like
paper size and print quality. Clicking on the Properties button opens a different
dialog. The settings shown will depend on the printer configuration.
Figure 252: Print Setup
11.3 Print Spectra
Select the Print Spectra command to directly print spectra. The following
dialog opens:

Print Spectra
Figure 253: Print Spectra
Drag & drop the respective spectrum from the OPUS browser window into the
File(s) to Plot selection field. Click on the Change Layout button to select a plot
layout. If the plot layout selected consists of several frame types, use the Frame
drop-down list to define which spectra have to be printed in each frame.
To display a preview of the plot click on the Preview button. If the plot consists
of several pages you can select between a single and two-page display.
Additionally, you can zoom in or out the spectrum previewed.

Print
Figure 254: Print Preview
Click on the Frequency Range tab and either type in the limit values manually
or define them interactively. If you click on the Get Display Limits button, the
current display limits are automatically set.

Print Spectra
Figure 255: Plot Spectra - Frequency Range
On the Options tab you can define the number of peak labels, scaling and
printout format.
Figure 256: Print Spectra – Options
If you activate the Auto scale to all spectra, the x-axis of the spectrum will be
linearly scaled. The Use Compressed Wavenumbers check box allows to plot

Print
the with compressed wave numbers, i.e. the wave numbers above 2000cm-1
will be compressed by a factor of 2.
The printout can both be sent to the printer or the clipboard. It is also possible to
create a bitmap or a PDF file. To save the plot define the file name and path in
the respective entry field, or edit the path by means of the Change Path button.
Click on the Plot button to start printing.
11.4 Quick Print
You can use the Quick Print command to plot the contents of an OPUS view
without specifying a template. A default template suited for the currently
displayed view will be used. You can change this default template by editing it
or saving a different template of your choice as default. The following templates
are available:
Default Template Name Associated Window Type

3D.PLE 3D Window
3D+.PLE 3D+ Window
DEFAULT.PLE Display (spectrum) window
LIBRARY.PLE Library window
LIVE+OVERVIEW.PLE Live video and overview image window
LIVEVIDEO.PLE Live video window
MAP+SPEC.PLE Result window of a MAP acquisition
OLDREPORT.PLE Report window
OVERVIEW.PLE Video overview window
ONLINE.PLE Result window of a CHROM acquisition
REPORT.PLE Report window
SEARCHRESULTS.PLE Search report window
SINGLEREPORT.PLE Report window
STRUCTURE.PLE Structure window
VIDEOPOSTRUN.PLE Video postrun window
The Quick Print command generates a printout which shows the OPUS window
as it is displayed on the screen. If only part of the spectrum is displayed, only
this part will be printed including all labels and annotations.

New Layout – Plot Layout Editor
11.5 New Layout – Plot Layout Editor
Use the Plot Layout Editor (PLE) to create templates used for multiple
printouts. The templates you created can be saved using the Save as command
from the File menu. The PLE enables you to label peaks in a spectrum, plot
details of a spectrum, print parameters and peak tables.
Start the PLE by selecting New Layout from the Print pull-down menu. Now
the PLE tool bar becomes active and a new PLE window will be opened:
The PLE window consists of a black grid and a red frame. This frame represents
the available print area of your printer. Located next to the PLE workspace is
the PLE Browser. To the left of this window you find a column with the title
item.
The PLE window has a PE tab attached. Use this tab to switch between the PLE
and the spectrum window.
Since the available print area depends on your specific printer, its particular
settings must now be configured. If you have already installed a printer for
Windows, then you may skip the next section.

Print
OPUS Browser PLE Browser PLE tool bar PLE workspace Active frame
Figure 257: The PLE User Interface
• Start the PLE with New Layout from the Print pull-down menu.
• From the File menu choose the Print Setup command.
• The printer properties page will be displayed. Select the appropriate
paper size and format.
• Close the dialog box by clicking on OK.
• Now you can start your work with the PLE.
OPUS Browser
The OPUS Browser lists all windows that are open, spectrum windows as well
as PLE windows. The active window is highlighted. You can switch between
windows by clicking on their icon in the Browser, or by clicking on the window
tab.
PLE Browser
The PLE Browser lists all objects that are on the PLE workspace. A frame will
be referred to by the type of object it contains (table, spectrum etc.). The active
frame is indicated by a red arrow in the Browser and bordered by a thick line on

the PLE workspace. You can click on a frame to make it the active frame. This
can be useful, if the item is not visible because it is covered up or is outside of
the visible window area. You can right-click on an item in the Browser to bring
up its properties dialog.
Figure 258: PLE Browser
PLE Workspace
This is a visual representation of the printed page, containing all the frames.
Each frame can be scaled and positioned individually. A read-out below the
workspace gives you the exact position of the activated frame (left side), while
you move it around as well as size of the frame (right side).
Figure 259: Read-out for Frame Size and Position
By clicking on a frame with the right mouse key, you will bring up the
Properties dialog box of this frame. Right-clicking the mouse on the page, in a
portion that does not contain a frame, will bring up the Page Properties dialog.
11.5.1 PLE Tool bar
The tool bar allows quick access to the most frequently used PLE com-
mands. Select a tool by clicking on its icon before using it.
Draw a circle or ellipse on the page.
Draw a line or an arrow on the page.

Print
Draw a frame on the page. A frame can contain spectra, text, a bitmap or a
metafile.
Draw a frame that will contain a table.
The selection tool allows you to use the mouse to select and move items
on the page.
Add or remove a page. This allows you to create sophisticated templates

with more than one page.
Select page number.
Zoom factor (percentage). The zoom factor does not affect the size of the
templates’ printout.
Remove objects from the workspace. These objects have to be selected

before.
Clear a selected frame.
Open the PLE Page Properties dialog.
Anchor an object to its position on the workspace.
Open the PLE Box Properties dialog.
11.5.2 Pop-up Menu

If you right click on a frame, a menu will appear at the point where the mouse is
clicked. This allows access to various actions, that can be performed on the
frame.

Remove deletes this frame from the workspace, while Snap to Grid aligns this
frame exactly on the closest grid lines. Insert Legend is only available to
manipulate spectrum frames and appends a legend to a spectrum frame.
Assign lets you change the content of a frame. You can assign pictures, meta
files, spectra, tables, text files or an OPUS view to a frame.
Copy duplicates the content of a frame or a page to a meta file or to a bitmap.
Figure 260: The PLE Pop-up Menu
Paste inserts a bitmap, a meta file or a text file from the clipboard into the
selected frame.
Edit manipulates the contents of a frame. This command is only available for
text and table frames.
Properties opens the dialog box associated to the selected frame.
Cancel closes the pop-up menu without performing any changes.

Print
11.5.3 PLE Page Properties

Like all other objects the workspace itself has a property sheet associated with
it. Using the PLE Page Properties allows you to define general settings of the
PLE workspace. You call up this dialog box by right-clicking on the empty
space of the PLE page.
(a) (e)
(b)
(f)
(c)
(g)
(d) (h)
Figure 261: PLE Page Properties
General Page Properties

(a) Specify the units that you want to work with (inches or centimeters).
(b) Select the orientation of the pages in the document.
(c) The available area for printing is represented by a dotted red line on the PLE
page. On account of the paper handling machinery of the printer, it cannot print
to the outermost edge of the paper. To determine the corresponding unprintable
area of the paper, check the manual of the printer or use empirical methods.
(d) Select the size of paper that is in the printer.
(e) This is the zoom (magnification) factor to use in viewing the PLE pages
expressed as a percentage. The typical computer screen is not large enough to
allow viewing the entire page at 100% scale. 75% is a good selection for docu-
ments using landscape orientation, while 50% is good for portrait orientation.
(f) This is the default font used in the document. As frames are created, they will
inherit this property. Once a frame contains data, the font can be changed for
that frame independently of this setting. This only determines what font will be
used when a frame is first created.
(g) The background color of the page.
(h) After you assigned the desired view type to the frame, i.e. a structure view, you
can drag & drop a structure data block onto the frame. To save the PLE page as
a template remove the data block again; the frame will retain the view type asso-
ciated to it. If the Interactive Opus view check box is marked, you can access an

object within a frame. You can assign any type of Opus view to a frame. Simply
draw a frame on the PLE page and right-click on it to open its Properties pop-up
menu. Selecting Assign Opus View will enable interactions with 3D spectra, e.g.
rotating the spectrum.
Grid Properties
(a)
(b)
(c)
(d)
(e)
Figure 262: Grid Properties
(a) This controls whether the grid is visible on the page. A grid is useful for align-
ing objects. However, the grid will not be printed.
(b) As objects are created, they can be automatically positioned and sized to line up
with the closest major grid lines.
(c) Usually a grid is displayed only on the screen because it is useful for alignment
during document composition. If you want the grid to also be printed on the
paper, select this option.
(d) This is the size of the grid, in the units that are specified in the Page Properties
page (above). The grid can be further divided by filling in the Minor fields.
(e) The color used to draw the grid.
Header and Footer Properties

The Header and Footer are information that are printed on the top and bottom,
respectively, of every page. The Header and Footer dialogs are identical, so
only the Header dialog is discussed. Everything said about the Header applies
to the Footer also.

Print
(a)
(b)
(c)
Figure 263: Header Properties
(a) The Header (or Footer) can consist of 6 fields: two rows in the left, middle, and
right. The entries in the fields consist of metastrings; you can either type them in
or drag them from the list (c). Of course you can also type plain text which will
be displayed.
(b) The font to use to print the Header (or Footer).
(c) These are special codes that the PLE uses to identify the information that will be
displayed on the page. You can use the mouse to drag the codes from the list to
the field that you want information to be printed in. Or, you can type them into
the fields directly.

Template Properties
Figure 264: Template Properties
You can also save a template to be used as default. When new PLE documents
are created, they will start with all of the properties of this template. The default
template is automatically named “default.ple” and is located in the same
directory as the OPUS executable program. Using the Save As choice on the
File menu, templates can also be saved to any file name and directory. Using
the Open choice on the File menu, they can be recalled for later use.
11.5.4 Loading and displaying a spectrum

A spectrum can be loaded by simply dragging it from the Browser onto the
workspace. Alternatively, draw a frame by first selecting the icon and
then using the left mouse key. Open the frames pop-up menu by clicking on the
frame with the right mouse button, then select Assign and Spectrum. A file
selection box will appear, in which you may choose the spectrum you want to
insert. It will then show up in the frame, along with the axes and notation.

Print
Figure 265: Spectrum Frame
In order to print the parameters of the spectrum, select the icon from the
icon bar and draw a frame as done for the previous frame. This frame will con-
tain a table which has by default two rows and two columns. Again, change the
properties by calling up the Properties dialog (see chapter 11.5.6) with the right
button. The thickness of the dividing lines between the cells and the colors, as
well as the font, can be changed using the properties box. Also, you can assign
titles to the rows and columns.
Using the left mouse button select a parameter from the list on the second page
of the pop-up menu and move it to the cell in the table where you want it to
appear. The parameter will be displayed along with its value.
Figure 266: Table with Parameters Included
Text can be included using text frames, either typed in or by assigning a text file
to a frame. For manual text input draw a frame and open its pop-up menu. Use
the Change command to transform the frame into a text frame. A text field will
appear in which you now can enter the text. You close this field by left-clicking
anywhere outside the field. You can re-size the text frame as usual. By
selecting Change again you can edit the text.
To import a text file start again by drawing a frame. From the Assign command

of the pop-up menu choose Text File. A file selection box opens from which
you can choose the text file to import. Currently, only files with the extension
“.TXT” can be imported. Text formatting is discussed in chapter 11.5.7
11.5.5 PLE Spectral Frame Properties
(a)
(b)
(c)
(d)
(e)
(f)
(g)
Figure 267: Spectral Frame Properties – Item
(a) Change the size and position of the frame by entering the respective values in
the Size fields. The units used here are specified with the PLE Page dialog.
(b) You can select the line thickness used for the frame in pixels.
(c) The Color button lets you specify the color used to draw the frame, both, the
background color as well as the color of the frame. A color chart is displayed
from which you can either pick a color or define your own color.
(d) Normally, the border of the frame is not printed. Check this box if you would
like to have the border of the frame printed.
(e) Check this box to set the frames’ background color to the value chosen with (c).
(f) A name can be assigned to every object. Naming all the objects in your tem-
plate simplifies their identification in complex layouts. You can use these
names to link frames to each other.
(g) This field contains the target of a link operation. You can link table and text
frames to spectrum frames to keep your layout organized. To establish a link,
enter the Item Name of the target frame in the Linked To field.

Print
(d)
(a)
(e)
(b) (f)
(g)
(c)
Figure 268: Spectral Frame Properties – Limits
(a) These are the limits for displaying the spectral data. The units are specified with
the PLE Page dialog.
(b) The style selected determines the presentation of the data in frame. You can
stack one spectra on top of another, or overlay them on top of each other.
(c) To add a Bruker Logo to your printout select this check box.
(d) Set the x limits (a) to the current outer limits of all the data that is in the frame.
(e) Set the y limits (a) to the current outer limits of all the data that is in the frame.
(f) When this option is selected the data is expanded to fill the area of the frame,
such that the axes coincide with the border of the frame.
(g) If this is not selected, only one spectrum at a time can be displayed in the frame.
The tabs for x and y axis are identical except for the Rotate Numbers check box;
this only exist on the y axis page. This function allows you to turn the labels of
the y axis by 90°. The Show axis for stacked spectra and the Compressed Wave
numbers check boxes are only available for the x axis.

(a) (h)
(b) (i)
(c)
(j)
(d)
(k)
(e)
(f) (l)
(m)
(g)
(n)
Figure 269: Spectral Frame Properties – x Axis
(a) Controls whether the axes, tick marks, and labels are displayed.
(b) You can have separate x axes drawn for every spectrum of the stack. Otherwise,
one common axis will be used for all spectra.
(c) The Compressed Wave numbers command displays wave numbers above
2000cm-1 with a smaller linear scale.
(d) If automatic tick mark placement is not selected, this is the interval between the
tick marks.
(e) If automatic tick mark placement is not selected, this is the position of a tick
mark.
(f) If automatic tick mark placement is not selected, this is the number of decimal
places used for the numeric tick mark labels.
(g) The label to display on the axis. This is automatically taken from the data file as
data is loaded, but can then be changed by editing this field.
(h) Selecting this allows the PLE to alternatively determine where the tick marks
are placed.
(i) If you want tick marks on top of the data area, select this.
(j) If you want the tick marks displayed at the bottom of the data frame, check this.
(k) The thickness of the axis line.
(l) The color to use for drawing the axis.
(m) The font to use for the axis label.
(n) The font to use for the tick mark (numeric) labels.

Print
(c)
(a)
(d)
(e)
(b)
(f)
Figure 270: Spectral Frame Properties – Data
(a) As data is added to a spectral frame, it is put into a “slot”, which is just a
positional number. To change the look of the data in the slots, select the slot in
this list box. Then define the properties for that slot, using the rest of the
controls on this dialog: Color, Line Type, and Line Width.
(b) Remove the data that is selected in the list (a) from the frame.
(c) The color to use for displaying the data selected in list (a).
(d) The line style to use for displaying the data selected in list (a).
(e) The line width (in pixels) to use for displaying the data selected in list (a). Sep-
arate widths can be specified for the screen and the paper.
(f) In case you included annotations in your spectrum you can have them printed
with the font selected via the font dialog box (Font.. button) if you place a mark
in the Annotations checkbooks.

(e)
(a)
(f)
(b)
(c) (g)
(d)
(h)
Figure 271: Spectral Frame Properties – Peaks
(a) Similar to the Data page the slot holding the relevant data has to be selected
first.
(b) Select the stroke line thickness in pixels for the display and the printout.
(c) Label Font lets you control the font type used for the stroke labels.
(d) Change the color of the strokes using Stroke Color.
(e) Checking this box ensures extra space between the highest peak and the
spectrum frame for the peak labels resulting from a peak search. The label type
can be chosen from the list (f).
(f) Select the type and position of the labels you want to assign to the peaks.
(g) Specify the number of peaks to be labelled, starting with the highest peak.
(h) Set the number of digits and decimals of the peak labels.
11.5.6 PLE Table Properties

A table is created by choosing the “Table” drawing tool on the PLE tool bar,
and then drawing it on the page using the mouse. Tables are linked to spectrum
frames via the Item Name and Link To fields on the Item tab (discussed above).
By default, a table of two columns and two rows is created. The number of
columns and rows can be changed by right-clicking on the table and opening the
corresponding Properties dialog box.
Cells in a table can also be edited manually, by right-clicking the mouse over
the cell and selecting Edit from the menu that appears. When you are editing
cells, you can navigate between them using the arrow keys. The return (Enter)
key also switches the editing to the next cell in the column.

Print
The first tab of the Table Properties dialog has been already discussed in
chapter 11.5.5.
(a)
(b)
(c)
(d)
Figure 272: Table Properties – Parameters
(a) The available parameters are categorized. Depending on the category selected,
the information displayed in the list box (b) will change.
(b) Available parameters of the type specified in (a) are listed here. To add
information to a table, select an item from this list and then drag it to a cell on
the table, and drop it there. The strings here are metastrings: a three letter code
preceded by a “^” character. When PLE encounters such a code, it interprets it
as an instruction to extract the information from data slot one of the linked
spectral frame and substitutes that information for the code, when the table is
displayed. If you edit the cell (via the Edit choice on the context menu, below),
you will see the actual codes. When the table is displayed, you see the
information that the code symbolizes. If you do not like the default format of the
information, just edit the cell and change it.
(c) Normally, the information extracted by PLE to expand the metastrings is taken
from the spectrum in slot one of the linked spectral frame. By choosing this
option, the parameters can be repeated for each spectra in a frame, up to the
number of rows you have defined on the Format dialog (below).
(d) As new spectra are added to a frame, new rows can be added to the table to dis-
play the parameters for each spectrum. This setting will override the number of
rows that you have set on the Format dialog (below).

(a) (h)
(i)
(b)
(c)
(k)
(d)
(l)
(e)
(f)
(m)
(g)
Figure 273: Table Properties – Format
(a) The number of columns in the table; the default value is two.
(b) The number of rows in the table; the default value is two.
(c) The font to use for row 1 (if the Row 1 has titles option is checked).
(d) A grid can be displayed, which contains each cell in the table.
(e) The thickness of the grid, in pixels.
(f) Cells can be sized automatically to fill the frame that encloses the table.
(g) If Autosize is not selected, this is the height of a cell (in the units specified to the
right (l)).
(h) If this is checked, the text in column 1 is used as a column header, and is
displayed in the font specified using the Title Font button (c).
(i) If this is checked, the text in row 1 is used as a row header, and is displayed in
the font specified using the Title Font button (c).
(j) Assigns different colors to better distinguish the rows.
(k) The font to use for the body of the table. If Column 1 has titles and Row 1 has
titles are both unchecked, this font will be used for every cell in the table.
(l) The color of the grid, if it is to be displayed. After a selection has been made
this button will be displayed in the color of choice.
(m) If Autosize is not selected, this is the width and height of a cell (in the units spec-
ified to the right).
11.5.7 PLE Text Properties

If a frame contains text, its properties can be set here. The text can consist of
metastrings or manually typed characters. The metastrings used for table
parameters (see chapter 11.5.6) can also be typed into a text frame, and they

Print
will be interpreted by PLE using the data from the spectrum frame linked to the
text frame.
The Item and Parameters tabs have already been discussed in the previous
chapter.
(a)
(b)
(c)
Figure 274: Text Properties – Text
(a) Defines the tab stops for the text in the frame. Multiple positions can be used,
separated by spaces, such as “8 12 20 40”. The last tab spacing is used for subse-
quent tabstops, should more be contained in the line.
(b) The font and font size to use for the text.
(c) Centers the text within the frame.
11.6 Open Layout
New Layout calls up the Plot Layout Editor, while Open Layout shows a list of
existing templates. When using this command for the first time after the
installation of OPUS you will have to navigate to the desired directory.
11.7 Print / Print Preview
You can view the result of a printout using the Print Preview command. Print
will start the printing process immediately.

Print Setup
11.8 Print Setup
Paper orientation and the printer (in case you have more than one printer
attached to your computer) are selected using the Print Setup menu.

Print

Script Recorded History
12 Macro
OPUS functions you use routinely, can be automated as a macro. An OPUS
macro is a sequence of OPUS commands that can be executed as one unit.
Besides the regular OPUS commands a set of macro functions exists to control
the macro execution, the interaction with the user and the evaluation of results.
An OPUS macro basically is a text file with the extension .MTX, which can be
edited using any kind of text editor. A detailed description of all macro
functions and the command language is given in the OPUS Programming
manual.
This chapter briefly describes the commands of the Macro pull-down menu. It
also tells you how to include macros in the OPUS tool bar.
Figure 275: Macro Menu
12.1 Script Recorded History
The information stored in the history block of a file can be extracted into a
script. Select the file you want to extract the performed manipulations from and
load it into the upper window. Select a file name for the script and define the
path, where it should be saved to. Include Measurement includes the
measurement parameters as well.
Once the script has been saved, it can then be carried out on other files using the
Visual Basic Scipt command from the File menu.

Macro
Figure 276: Macro Menu
12.2 Insert MyInstrument
My Instrument is a standardized programming interface for spectrometers

running in 32-bit Windows environments. The design of this interface makes
the spectrometer and the software module, which controls the spectrometer,
synonymous. However, the interface clearly distinguishes between data
acquisition and data processing.
The software allows to set all hardware parameters and measurement conditions
which are typically useful. Special features like the detector temperature or
alignment can be controlled.
Select the Insert MyInstrument command to create a Visual Basic Script.

Macro Converter
Figure 277: Insert MyInstrument - Select File tab
Enter the name of the registered MyInstrument control into the Select
MyInstrument Control entry field, and define the file name and path for the
resulting Visual Basic Script.
12.3 Macro Converter
Use the Macro Converter to translate macros written under OPUS-OS/2 into the
OPUS format. The conversion may require some changes as a result of the
different macro syntax. See the OPUS Programming manual for details.
12.4 Run Macro
To run a macro use the Run Macro command of the Macro pull-down menu.
The file load box appears through which you can immediately start the macro
you have selected. All further action depends on the macro you have chosen.
12.5 Debug Macro
The term Debugging means a step-by-step execution of a macro program with

the aim of locating program errors. The program execution will continue until a
stop mark is reached. This option greatly facilitates locating and analyzing
errors.

Macro
12.6 Macro Editor
OPUS includes an editor to conveniently generate and edit your own macros.
Start the editor with the Macro Editor command from the Macro pull-down
menu. Either generate a new macro or load an existing one by clicking on the
Open Macro button.
12.7 Compile Macro
Macros are written and stored as text files, which will be converted to
executable binary code during runtime of the macro. The Compile command
performs this step separately and generated executable binary code from a
macro text file. Compiled macros are started faster than macros in text format.
12.8 Add Macro to the Toolbar
Macros which you use regularly can be added to the toolbar. To do this you
have to add an entry to the USERMAC.LST file, to be found in the OPUS
directory. If this file does not exist on your machine it has to be created using a
text editor.
For every macro you want to include in the pull-down menu of the tool bar you
have to add the following information to the USERMAC.LST file:
1) Name and path of the macro file.

2) Number of the menu (see table).
3) Text to be included in the menu.
4) Text for the tool description of the tool bar.
5) Text for the status bar.
Separate the entries by an “@” sign, e.g.:

E:\OPUS\MACRO\IT.MTX@8@Instrument test@IT-Test@Start IT
If you want to include an icon for the macro added to the tool bar you have to
provide a 16*15 pixel bitmap. This bitmap must reside in the same directory as
the macro.
To specify the menu you want to add a macro to, use the number indicated in
the following table.

Add Macro to the Toolbar
Menu Number of Menu
Measure 1
Manipulate 2
Evaluate 3
Display 4
Print 5
Macro 6
Edit 7
Validation 8
Settings 9
File 10

Macro

OPUS Validation Program (OVP)
13 Validation
The OPUS Validation Program (OVP) is a supplemental application software
integrated in the OPUS software program. Its primary purpose is to provide an
automated method to validate Performance Qualification (PQ) and Operational
Qualification (OQ) of the spectrometer.
13.1 OPUS Validation Program (OVP)

The OPUS Validation Program (OVP) is part of the OPUS software and
supports the 21 CFR Part 11 regulation in connection with the
OPUS VALIDATION software package.
This chapter is mainly written for the system administrator who is responsible
for the administration and maintenance of the spectrometer system. Details on
the OVP installation, OPV setup for initial and general use by the operator are
described in the following.
OVP is written in a modular, i.e. plug-in format. After installing OVP you have
to configure OPUS to ensure OVP compatibility, and setup OVP to define the
validation process.
OVP works in connection with OPUS as follows:

• As many as twelve test channels can be defined and assigned to OVP
by specifying a unique measurement configuration for each channel.
These configurations are used during the validated measurement
process. Each test channel, e.g. sample compartment, integrating
sphere has individual parameter settings.
• For each test channel a time period is defined which determines when
a Performance Qualification (PQ) or Operational Qualification
(OQ) test will be required. These tests can consist of one or more test
protocols assigned by the system administrator.
• If the time period has expired for a particular channel, a warning will
be displayed in OPUS. In this case the user can run OVP.
• OVP provides a simple Wizard interface which assists the user and
automatically performs the test(s) assigned by the system
administrator. If the test has been completed, a simple pass/fail
interface will be shown with the option to view and/or print a detailed
report.
• If the test has passed, the OPUS warning becomes validated. The
operator can continue using the instrument as this has been properly
validated.

Validation
• An unattended mode is also available which allows to run the test(s)

completely automatically and without any user interaction, e.g. over
night or in the early morning.
13.1.1 OVP Installation
To install OVP insert the installation CD-ROM into the computer primary CD-
ROM drive. After a few moments, the installation program starts automatically.
If the installation program does not start automatically,

• click on the Start button on the Windows toolbar.
• select the Run option.
• type D:\OVP_Install.exe into the text field of the dialog that pops up.
Substitute the proper drive letter for your CD-ROM drive.
• click on the OK button to start the installation.
• alternately use the Browse button to select the installation program
on the CD-ROM.
Once the OVP installation program runs it will determine the current location of
the OPUS program. By default, OVP is installed in the Validation sub-directory
located in the OPUS directory. This path is highly recommended but not
obligatory.
Note: You must have installed OPUS before being able to install OVP.
Select the installation language and click on the Next button to continue. If the
OPUS directory has been located, the installation start dialog appears (see
figure 278). Click on the Next button to continue the installation, or Cancel
button to abort the installation.

OPUS Validation Program (OVP)
Figure 278: OVP Installation Start dialog
The next dialog displays the destination path of the OVP installation. If the
Destination entry field does not indicate the appropriate OPUS sub-directory,
use the Browse button to select the sub-directory. (This may be the case if you
have more than one OPUS version installed).
Note: OVP will only work with OPUS 4.2, build 4.2.37 or greater. If you use an
earlier OPUS version, contact Bruker to get an upgrade. OVP is not compatible
with OPUS versions prior to 4.2.
In case of some operating systems it may be necessary to install the latest

MDAC version. If this component has been installed, the computer will reboot.
Keep the OVP installation CD-ROM in the drive. After the computer has
rebooted, the OVP installation process will start again. Follow the installation
steps described.
13.1.2 Database Installation
Measurement and test parameters are stored in a set of databases. These

databases are delivered on separate instrument-type-specific CDs and have to
be installed separately after the OVP installation. Continue similarly to the OVP
installation steps described.

Validation
The database installation program locates the installation path of the previously
installed OVP. Make sure that you use the same path (.\OPUS\VALIDATION)
for the database installation.
If the databases have been installed completely, OVP is ready to be used.
13.2 OPUS Setup (prior to OVP)

Before running OVP for the first time you have to configure the OPUS
Instrument Test feature to be able to use OVP. Start OPUS and select the User
Settings command from the Setup menu. Click on the Instrument Test 1 tab. For
further details on this subject, refer to chapter 14.10.
13.2.1 Preparing Default Measurement Experiment
This OVP version does not require individual measurement experiments for
each test channel as previous versions did. Instead, a single measurement
experiment is sufficient and essential when working in validated environment.
In that case the measurement experiment must have a valid release signature.
The default measurement experiments for your instrument are in the XPM sub-
directory of the OVP installation directory (.\OPUS\VALIDATION\XPM by
default). The name is derived from the instrument type and must not be
changed, e.g. MPA:XPM for the MPA series, TENSOR_27.XPM for the
TENSOR 27 series etc.
In order to test the experiment validity select the Advanced Measurement, or

Setup Measurement Parameters command if you are working in validated
mode, from the Measure menu and load the measurement experiment(s) for
your instrument.
If no error is indicated on any of the different parameter tabs, you do not have to
change the experiment. If an error is shown, change the parameters which are
marked red and store the modified measurement experiment. Then, sign the
experiment again by a Release signature. For further details on signature setup,
refer to the OPUS VALIDATION manual.
13.2.2 OVP Setup
Before you can setup OVP make sure that you have Administrator rights within
OPUS. You can verify this by the OPUS title bar which has to be as follows:
Figure 279: OPUS title bar

OPUS Setup (prior to OVP)
If the title bar looks different, you only have Operator rights and will not have
access to OVP setup functions.
Assuming you have properly configured OPUS to be used in connection with

OVP (see chapter 14.10) you can now continue in order to access the
Administrative Start dialog of OVP. Left click on the status light ( ) located
in the bottom-right corner of the OPUS user interface. The Instrument Status
dialog opens which contains three rows of status icons for different instrument
components to be tested by OPUS.
Figure 280: Correlation between User Settings and Instrument Status
The second and third row of status icons on the Instrument Status dialog are
designed for the twelve test channels defined on the Instrument Test 1 and
Instrument Test 2 tabs of the User Settings dialog box. Click on the first icon of
the Instrument Status dialog, provided you assigned OVP to the IT test channel
in the User Settings dialog. The following dialog opens, provided you have
assigned OVP to the IT test channel in the User Settings dialog:

Validation
Figure 281: OVP - Instrument Status Message
Click on the Test Now button to open the OVP start dialog.
Figure 282: OVP - Start dialog
If you do not have OPUS Administrator rights, the OVP start dialog will not
include the Setup and Trends buttons, and the validation wizard can directly be
started by clicking on the Measure button.
The About menu option displays a list of version numbers of all main
components used by OVP. Click on the Setup button to access the setup dialog.

Figure 283: OVP - Setup
In the OVP setup dialog the administrator defines which tests will be performed
at what intervals. The setup is the primary step within OVP before the program
can be used.
Figure 283 shows the default setup dialog which is described in the following:
(A)This section displays the name of the spectrometer used. The
instrument type is automatically detected by OVP. Click on the
instrument button ( ) to update the setting if a different
spectrometer had been previously connected.
(B)The IT buttons represent the assigned measurement configurations
used by OVP and are similar to the buttons on the Instrument Test tab
of the User Settings dialog (see chapter 14.10). Click on one of the IT
buttons on the left to select the test assignment position.
(C)This group field defines the test category (PQ or OQ), test interval,
instrument configuration and accessories, if available.
(D)This section includes a dynamic list of available tests that can be
performed. Tests are included as plug-in modules which
automatically are displayed in this section when installed. Activate
the corresponding check boxes to select the appropriate test. The
setup dialog of the selected test will open.

Validation
(E)The status bar displays the current status of the particular setup
dialog. Warnings and reminders are displayed in yellow. During
measurement the status bar is green. If you work in a validated
environment in OPUS, the 21 CFR Part 11 logo on the right will be
marked red.
The following outlines a summary of events performed within the OVP setup
module.
13.2.2.1 Confirming Correct Instrument Type

This first step is to specify the instrument type used. The instrument type is
selected automatically if you start OVP for the first time. The next time you
start OVP the instrument type previously used will be displayed by default. To
update the settings click on the instrument button, see figure 284.
Figure 284: OVP - Selecting instrument type
An update of the settings only needs to be done the first time you use OVP with
a new instrument type. If you delete the user databases, you will not need to
perform an update.
Note: If the instrument type is not displayed, the instrument is not supported by
OVP and you will not be able to use OVP.
13.2.2.2 Adding Measurement Configuration
Figure 285: OPUS User Setting dialog and OVP Setup
As figure 285 shows, the six positions specified on the User Settings dialog
directly correspond to the six positions specified for the OVP experiment
method assignments. The check boxes on the left image have the same
designation as the IT buttons on the right image. This also applies to channels 6
to 12.

A B
Figure 286: Test channel settings
Figure 286 compares the first IT position of each dialog. The first position in
the User Settings dialog (A) correlates to the first icon on the Instrument Status
dialog (B), which correlates to the first position in the OVP setup dialog (C).
For each spectrometer test channel you have to assign a measurement

configuration to be used during actual validation measurement. In general, this
is a valid combination of source, beam splitter, measurement channel and
detector as shown in figure 287.
Measurement Channel Source Beam splitter Detector
Figure 287: Test channel configuration
Note: The test channel must have the same hardware configuration as the
experiments defined in the User Settings dialog to be able to validate the
hardware and optical components used during measurement.
To add an optics configuration for validation, click on the Setup button next to
the position you would like to assign. The Setup the Optics Configuration for a
Test Channel dialog opens as shown in figure 288.

Validation
Figure 288: OVP - Optics Configuration dialog
In general, there are two possibilities to define the proper optics configuration.
You can directly select the particular component from the corresponding drop-
down list which include the optics components available for your instrument.
Figure 289: OVP - Optics configuration by drop-down list
Alternatively, you can use an existing measurement experiment by clicking on

the Get configuration from Measurement Experiment button (see figure 288).
Browse to the location of the measurement experiment file and select it. The
optics configuration is extracted from the experiment and the name and path of
the file will also be displayed, see figure 290.

Figure 290: OVP - Optics configuration by XPM file
If you have selected a wrong experiment which does not fit the instrument
configuration, this will be indicated in the drop-down list (figure 291).
Figure 291: OVP - Wrong XPM file
To assign the configuration click on the Save and Exit button (figure 288). As
soon as an assignment is done the Setup button for this test channel is disabled
(figure 292). If you have to change a configuration, first permanently delete the
assignment by clicking on the scissors icon ( ). Thus, the Setup button is

enabled again and all settings for this assignment are deleted from the
databases.
Figure 292: OVP - Disabled IT test channel
If you click on the particular IT button, the test channel is selected for editing
turns to yellow as a visual reminder of which position is currently selected. The
IT buttons are mutually exclusive, i.e. you can always select only one test
channel. IT buttons which no optics configuration file have been assigned for
are disabled and cannot be clicked on.
After assigning a new optics configuration, a warning will be displayed in the

status bar to remind you to measure the laser wave number for this particular
configuration before assigning any tests.

Validation
13.2.2.3 Measuring Laser Wave Number
Click on the button to perform a test using the optics configuration for
the currently selected IT channel. In OPUS 5 (and higher) it is possible to store
and use individual laser wave number values for each test channel defined.
OPUS 4 uses the measurement channel assigned in the experiment file by the
Setup Measurement Parameters command from the OPUS Measure menu.
Proper handling of test-channel-specific laser wave numbers may require an

update of the instrument firmware as well. In case of doubt contact your local
service department.
The laser wave number is affected by changes in the optical path length. This
can be extremely serious when using optical fibers of different lengths.
Measuring and assigning the laser wave number for each test channel ensures
the accuracy of spectral data.
The test first measures a spectrum of water vapor and uses a specific water band
to determine the optimum laser wave number. To verify the validity of the water
band adjacent water bands are checked as well. In a second step the appropriate
wave number is verified against the bands of the filter material on the internal
validation unit (e.g. polystyrene or BRM 2065). After performing this test a
result dialog pops up.
Figure 293: OVP - Test Result dialog
If the current laser wave number for this channel is within a certain tolerance,
the test has passed and no changes are needed.

Click on the Set button to set the current measurement channel laser wave
number value to the currently computed optimal value. If you do not want to
update the laser wave number, click on the Exit button.
If the water band could not be detected properly as the water vapor
concentration of your instrument is too low, first a warning pops up which will
automatically disappear after one minute.
Figure 294: OVP - Water vapor warning
The result of the laser wave number determination may also indicate a problem.

Validation
Figure 295: OVP - Laser Wave Number Test Results
In this case examine the water vapor spectrum FR_LWN.x (x being a number)
which is located in the OPUS\VALIDATION\TEMP path. If the water vapor
contents are too low, remove the desiccant cartridge for a short period of time to
allow the water vapor concentration in the instrument to increase. Repeat the
measurement until the result is OK.
Note: Changing the laser wave number after assigning tests will invalidate
those tests that require reference measurements (i.e. PQ test).
Important: As of OPUS 5 the laser wave number is stored and used based on
the IT test channel specified in the User Settings dialog. It is not an OVP
component. If you use one experiment to measure the empty sample
compartment, a different experiment is required to measure an accessory placed
in the sample compartment. These two configurations should be setup as
different test channels in OPUS. The laser wave number can be different for
both test channels, even if both configurations use the sample compartment as
measurement channel. In that case it is important to register the measurement
experiments used for measurements with the empty sample compartment, and
for measurements with the accessory, in different test channels.
13.2.2.4 Configuring Test Channel

Once you have assigned an optics configuration to an IT channel, you have to
configure it. Figure 296 shows the section of the OVP setup pertaining to the
channel configuration.

Figure 296: OVP - Channel configuration
You have two basic categories for testing:

• Operational Qualification (OQ)
• Performance Qualification (PQ)
All assignments made by the OQ option refer to the OQ test. Subsequently, all
assignments made by the PQ option refer to the PQ test. Switching between
these two option buttons displays the assignments for the particular test.
You have to define the test interval for both categories. Note that we
recommend running PQ tests as a short-term test on a daily basis (24 hours).
OQ tests should normally run after installation, maintenance or major repair,
e.g. every 6 or 12 months. Type the interval period into the entry field and select
the units from the drop-down list. Available units are hours, days, or months.
The Validation Set Title text field can be used to specify the current setup by a
descriptive name. A default name is always added when a new channel is
configured. The validation set title is used in the reports generated by the
various test protocols.
The Configuration drop-down list includes currently supported hardware

configurations for the particular instrument type. Depending on the instrument
type the configuration is automatically selected based on the optics
configuration set up. Especially, in case of older instruments (e.g. VECTOR 22/
N series), or if a configuration is available with different options (e.g. one with
the standard and another with the high resolution option), the initial
Configuration drop down list may display the Select proper Configuration note.
In such a case select the configuration that best matches the configuration used
for this channel for both OQ and PQ. If your configuration does not match any
included in the drop-down list, contact the Bruker Optics service department.
Depending on the type of instrument and the optics configuration selected an

additional drop-down list for optional accessories can be displayed.

Validation
Figure 297: OVP - Channel configuration
This drop-down list includes a set of accessories which can be used in

combination with the selected optics configuration. Typical accessories for
different configurations can be:
Figure 298: OVP - Accessories for fiber port and sample compartment
If you select None, the basic configuration for that particular channel, e.g.
empty sample compartment is used. In case of combinations during routine
work, e.g. sample compartment with standard sample holder, sample
compartment with an ATR accessory, sample compartment with a diamond cell
you should set up a different test channel for each of these configurations. This
allows you to validate each configuration separately.
The Accessory drop-down list includes Bruker standard accessories. A specific

program allows you to define your own set of accessories. The program will be
described in chapter 13.8.2.
13.2.2.5 Selecting Tests

The test protocols to be performed during validation measurements have to be
defined.
Figure 299: OVP - Test Protocol
All test protocols are plug-ins located in the Plug-ins sub-directory of OVP. The
names of all the tests installed are automatically displayed on the respective
buttons.

If you activate the check box to the left of the button, the test will be activated
and the button color will change to light blue. This indicates that you want to
perform this test for the current test category (OQ or PQ). The initial Setup
dialog automatically shows these test protocols. Some tests require reference
measurements to be created before the test can be used. The setup of the
standard PQ and OQ test protocol will be described in the following.
If you now click on the test button, you will have access to the protocols setup
dialog. Figure 299 shows that the PQ Test Protocol and the (optional)
USP 1119 Test have been selected, but not the OQ Test Protocol.
When selecting tests you should take into account the purpose of the selected
protocol, i.e. select the PQ test for the PQ category and the OQ test for the OQ
category. Selecting the same tests for both PQ and OQ is needlessly redundant.
13.2.2.6 Deleting Optics Configuration from OVP
If you click on the button, the particular test channel will be deleted.
You will be asked to confirm this deletion. Once deleted the settings cannot be
retrieved. If you have accidentally deleted a channel, you have to complete the
entire assignment process again.
13.2.2.7 Menu Options

The Settings menu includes two functions:
Figure 300: OVP Settings menu
The Program Paths function defines the path which is used to store the test
spectra and PDF reports generated during validation measurement. Test spectra
are stored in a structure of sub-directories. The first level uses date
(YYMMDD), the second time information (HHMMSS). Reports are stored in a
separate REPORTS directory. If you click on the Program Paths function, the
following dialog opens:

Validation
Figure 301: OVP Settings menu - Program Paths dialog
The Change Database Password function (figure 300) allows the administrator
to modify the password to be able to access the two user-generated databases:
UserSettings.mdb, and UserData.mdb. If you click on the Change Database
Password function, the following dialog opens:
Figure 302: OVP Settings Menu - User Database Password dialog
To change the password, first enter the old password and then the new one. The
default password for the user databases is Bruker Optics. This allows the
administrator to access the databases from within an external program (MS
Access 2000 format). The default passwords for other databases are secret as
these databases can only be changed by Bruker.
13.2.2.8 Exiting OVP Setup

To exit the OPV Setup dialog click on the Exit menu item. Incomplete
configurations will not be used during a validation measurement.

Validation Measurement
13.3 Validation Measurement

This chapter outlines the sequence of events encountered while validating the
spectrometer. This sequence pertains to the OPUS user with Operator rights
and is similar the one for users with Administrator rights.
13.3.1 Starting Validation Measurement
The OVP validation process is very simple. Once an IT channel has been
assigned for validation, OPUS will store the expiration time/date.
Each time one of the measurement experiment files defined in the User Settings
dialog is loaded, OPUS checks the stored expiration time of all tests specified
for the particular test channel. The status light in the bottom right corner of the
OPUS interface always indicates the following test status according to the
color:
• Green: all tests are up-to-date and valid
• Yellow: at least one of the tests has expired
• Red: the last validation test has failed or has never run
Click on the status light to display the Instrument Status dialog.
Figure 303: Instrument Status dialog
The first row of icons represent the instrument hardware test status. The second
and third row of icons are reserved for the software tests. In figure 303 OVP has

Validation
been assigned to the first three test channels, therefore three icons are displayed
in the second row.
The icon results show a warning as the test for this channel has expired, a green
check mark as the test for this particular channel has passed and is still valid,
and an error as either the test has failed or no test has been measured for that
channel.
Click one of the icons and a dialog opens indicating the current status of this
particular channel:
Figure 304: Instrument Status message
You can either close the Instrument Status Message dialog without measuring
or click on the Test Now button to starts the OVP measurement wizard.
Figure 305: OVP - Measurement Wizard
Figure 305 shows a typical OVP measurement wizard dialog. To continue

follow the on-screen instructions.
The group field in the middle includes all tests which have been assigned for
this particular IT channel. Tests whose interval has expired are automatically

checked for measurement. Tests whose interval has not expired are not checked,
and their remaining time is listed as a reminder.
For example:
If a test has not expired, but the interval has only two hours left you may wish to
select that test and run it earlier.
If a test has expired, but you are not prepared to perform that test (external
standards are needed), you can deactivate the check box for the corresponding
test.
Note: If you decide not to perform an expired test, the instrument status will still
report a warning (yellow light) after validation testing has completed, if more
than one test is assigned to the particular IT channel.
Click on the Measure button to start the selected validation protocols. If you do
not want to perform the validation measurements, click on the Exit button.
13.3.2 Test Protocol Wizards
Each of the selected tests on the measurement wizard will display an individual
wizard dialog customized for the prevailing test protocol. Figure 306 shows the
wizard dialog for the OQ Test Protocol.
Figure 306: OVP - Measurement Wizard with OQ Test Protocol

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As the test(s) are in progress, the status bar provides feedback about the current
state of the measurement process.
Next to the name of each test is an icon indicating:

Test will be performed
Test in progress
Test complete and passed
Test complete and failed
At any time during measurement you can skip the current test protocol. If,
however, a spectral measurement is in progress within OPUS, you will have to
wait for the test protocol to be completed before being able to continue. To skip
the test, click on the Abort button.
If the measurement wizard has been completed for each test, the Report button
is displayed.
Figure 307: OVP - Measurement Wizard with Report button
Clicking on the Report button opens a preview window with the generated
report for this test protocol (figure 308). From within this preview you can print
and review the results of the test. After completing the review, close the
preview window.

Figure 308: OVP - Test Protocol report preview
All measurement results are stored within a log table stored in the UserData
database. To append a comment to the current log entry click on the log
comment button ( ). A dialog opens and you can type a comment for this
measurement, e.g. Measurement failed due to someone striking the instrument.
Click on the Exit button to exit this protocol wizard dialog.
The next protocol wizard will start immediately, if any has been specified. For
all test protocols the procedure will be the same.
If all the selected test protocols have been completed, the OVP wizard dialog
will be displayed summarizing the results of all tests performed (see
figure 309).

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Figure 309: OVP - Measurement Wizard with summary of test results
Click on the Show Report button to view the final report for all tests performed.
This requires the Adobe Acrobat Reader being installed on your computer. The
Adobe Acrobat Reader is available on the OVP installation CD or on the OPUS
installation CD.
To exit the measurement wizard click on the Exit button and return to OPUS.
The status light will change and indicate the status of the tests.
13.4 PQ Test Protocol Plug-in

The PQ test protocol is a short-term test which verifies that the instrument
performance is suited for daily operation. Most of these tests compare the
measured data to a set of reference data which have been recorded after
installation, major repair or exchange of optical components. The PQ test
protocol is intended to be run on a day-by-day basis to ensure that the
instrument is working properly.
The following single tests can be run during PQ:

• Signal to Noise Test
Verifies that the signal-to-noise ratio is better than a specified limit.
• 100% Line Deviation Test
Verifies that the 100% line does not shift on long term.
• Interferogram Peak Amplitude
Verifies that the interferogram peak amplitude is not below a certain
limit.

PQ Test Protocol Plug-in
• Energy Test
Verifies that the deviation of the energy distribution of a single-
channel spectrum does exceed a specified limit.
• X-Axis Frequency Calibration Test
Verifies that the frequency calibration of the instrument is correct.
• Y-Axis Reproducibility Tests
Verifies that the photometric accuracy is within specified limits.
13.4.1 PQ Test Protocol Setup
To set up tests for the PQ test protocol, start OVP and open the OVP setup
dialog (see figure 283). Select the test channel for which you want to activate
the test and make sure that the laser wave number for this channel has already
been measured and set. Check the PQ option button and activate the PQ Test
Protocol check box.
Figure 310: OVP - PQ Test Protocol check box
The PQ Test Protocol Setup dialog opens.
Figure 311: OVP - PQ Test Protocol Setup

Validation
The Test Selection and Setup group field includes the different tests which are
part of the PQ test protocol (A in figure 311). Tests which are not available for
the selected instrument are disabled. Tests which should not run can be
cancelled by deactivating the corresponding check box. The first four tests are
grouped as Energy Tests as these tests are all based on one spectrum.
If you start the PQ test protocol setup for the first time, the flashing Measure
button (B in figure 311) indicates that no reference spectra have been measured.
These reference data are essential to be able to run the PQ test. Click on this
button to start the reference measurements. While the measurements are
running the Measure button turns blue and shows a small animation. When the
reference measurements have been finished a message dialog pops up.
Figure 312: OVP - PQ Test Protocol message
If you confirm this message, the Measure button becomes green. The date and
time of the last reference measurement is indicated above the Measure button.
Figure 313: OVP - PQ Test Protocol reference measurements
Click on the Exit button. The active state of the test is indicated in the OVP
Setup dialog by a blue PQ Test Protocol button and a check mark. If the
reference data have not been measured in the PQ protocol setup, the test will not
be activated.
Figure 314: OVP - PQ test activated

13.4.2 Menu Options
The reference data are not stored on disk to avoid accidental deleting or
overwriting. They are stored in the user database. Whenever used the reference
data are temporarily extracted and afterwards removed again.
In some cases it may be necessary to have a look at the reference data, e.g. if the
PQ tests fails immediately. For that purpose you can use the Extract References
command from the Options menu from the PQ Test Protocol Setup dialog.
Select the path where the reference data should be stored.
Figure 315: OVP - Options menu
The file names are ENERGY_REF.0 for the energy spectrum and GFA_REF.0
or GFB_REF.0 for glass filter spectra.
13.4.3 PQ Tests Description
Signal to Noise (S/N Ratio) Ratio Test:
The signal-to-noise ratio test determines the sensitivity of the spectrometer by

calculating the average signal-to-noise ratio of a 100% line.
The S/N ratio is determined by collecting and analyzing a 100% line. A 100%
line is the ratio of two consecutive single-channel spectra with no sample in the
beam. The ratio of these two single-channel spectra is used to generate a
transmission spectrum.
The S/N ratio is determined by measuring the maximum deviation from 100%
transmittance, and calculated by the OPUS Signal-to-Noise Ratio command in
the Evaluate menu using peak-to-peak by means of the quadratic parabola fit
option. In order to get a reliable result 10 spectra are measured (reference and
sample). The S/N ratio is calculated separately for each of the spectra, using the
mean value of all 10 results. The region to measure the S/N ratio will vary for
systems used in the MIR and NIR region.
Figure 316 shows a peak-to-peak noise of 0.1% from 100% transmittance in

MIR region. To calculate the S/N ratio take the reciprocal value multiplied by
100 (1 / 0.1 * 100). Figure 317 shows a 100% line in NIR region.

Validation
Figure 316: MIR 100% line
Figure 317: NIR 100% line
100% Line Deviation Test:
The 100% line deviation test is a long-term stability test which compares the
minimum of the absorbance value of a 100% line to that of the stored reference
spectrum.
The test is based on the spectrum generated from the S/N ratio test.

Interferogram Peak Amplitude:
The interferogram peak amplitude test is a long-term stability test which

compares the amplitude of a measured interferogram to that of a stored
reference interferogram.
An interferogram and a single-channel spectrum are measured and stored as

reference data. For the purpose of this test only the interferogram data block
needs to be considered.
The amplitude of the reference interferogram is set to 100%. In the instrument

test the same measurement is repeated and the interferogram amplitude
(minimum-maximum value) of this test spectrum is compared to the
interferogram amplitude of the reference interferogram. The amplitude of the
test interferogram is indicated in the instrument test report relative to this value.
Figure 318 shows an interferogram, which has been generated by the Double
Sided, Forward-Backward mode.
Figure 318: Double-sided interferogram
Energy Test (Single-Channel Spectrum):
The energy test is a long-term stability test which compares the amplitude of a
measured single-channel spectra to that of a stored reference single channel.
Figure 319 and 320 show the single-channel spectra of the reference file and the
test measurement in MIR and NIR region. The integral over the total reference
single-channel spectrum is set to 100%. In the PQ test report the area between
the two single-channel spectra is given relative to this value.
If the power of the spectrometer source decreases, e.g., the distance between the
two single-channel spectra will increase. Therefore, this test can be used to
detect changes in the source power. Like the previous test, this is a long-term

Validation
stability test. Test spectra are compared to a reference spectrum, which may
have been measured several months before.
A new reference file has to be measured if the instrument has been realigned, or
the source changed.
Figure 319: MIR reference and test single-channel spectra
Figure 320: NIR reference and test single-channel spectra
X-Axis Frequency Calibration Test (Wave number accuracy):
The x-axis frequency calibration test ensures that the frequency calibration of
the instrument is within the specified limits, if e.g. water vapor has been used to
calibrate the wave number. Water vapor has the advantage of having an
extremely narrow band(s) and the wavelength position can be measured to a
very high degree of accuracy. To ensure that the water vapor band is completely

resolved the instrument uses a high-resolution setting. The NIR region uses the
band at 7306.74cm-1 for calibration, and the MIR region at 1554.353cm-1.
Figure 321 and 322 show a typical water vapor spectrum in the MIR and NIR
region.
Figure 321: MIR water vapor spectrum
Figure 322: NIR water vapor spectrum
In addition to the water vapor test the frequency calibration is verified by

measuring either a polystyrene standard sample or a glass filter with a mixture
of rare earth oxides (BRM 2065) whose composition is identical to the NIST
standard SRM 2065. The standard (either PS or BRM 2065) is mounted on the
internal validation unit. Thus, no manual interaction is required for this test.

Validation
If the water vapor concentration is too low or the water band is beyond the
frequency range of the instrument, the result of the polystyrene or BRM 2065
measurement is used instead.
Note: If your instrument is equipped with a Germanium diode, you have to use
water for the X-Axis Frequency Calibration test as there is no suitable
polystyrene peak in the frequency range of this detector type.
Y-Axis Reproducibility Tests (Photometric Accuracy):
The y-axis reproducibility test is a long-term stability test which compares the
overall intensity values of glass filter spectra to the reference spectra.
A glass filter transmission spectrum is used to test the precision of the y-axis. In
the setup of the PQ qualification protocol a reference spectrum is measured. The
daily filter test spectra are compared to the reference spectrum. In figure 323
and 324 the glass filter reference spectra are plotted. During the instrument test
the mean difference over a large spectral range is calculated.
Figure 323: Glass filter NIR reference spectra

OQ Test Protocol Plug-in
Figure 324: Glass filter MIR reference spectra
13.5 OQ Test Protocol Plug-in

The OQ test protocol is a test which checks the instrument performance and
compares it to the instrument specifications. The OQ test protocol is generally
run during final testing before an instrument is shipped to the customer, and
after the instrument has been installed at the customer's site to demonstrate that
the instrument performs as properly as before shipment. The OQ test should
also be performed after each major repair, exchange of optical components
which may influence the instrument performance, and on a regular yearly or
semi-yearly basis after maintenance.
The following individual tests can be run during OQ:

• Resolution Test
Verifies the spectral resolution achieved by the instrument.
• Sensitivity Test
Verifies whether the instrument reaches the specified signal-to-noise
ratio.
• Energy Distribution Test
Verifies the spectrum of an empty channel, and shows the specified
energy distribution over the completely achievable spectral range.
• Wavenumber Accuracy Test
Verifies the absolute x-axis accuracy of the instrument.
• Absorbance Accuracy Test
Verifies the detector linearity (for MIR only).

Validation
• Scan Time Test

Verifies the mechanical properties of the interferometer and the
controlling electronics.
• Water Vapor Test
Verifies that the water vapor concentration does not exceed a
specified value.
• Alignment Test
• Verifies that the interferogram centerburst position is within the
specified range.
• Linearity Test
Verifies that the detector linearity is below detector cutoff.
• Reproducibility Test
Verifies the proper function of all mechanical parts which change the
instrument beam path.
The individual tests depend on the type of instrument. In general, not all tests
will be run for a specific instrument series. For example, the linearity test is
only relevant for MCT detectors, while the absorbance accuracy test is only
necessary for MID IR instruments, like TENSOR.
13.5.1 OQ Test Protocol Setup
To setup the tests for the OQ test protocol, start OVP and open the OVP setup
dialog (see figure 283). Select the test channel for which you want to activate
the test and make sure that the laser wave number for this channel has already
been measured and set. Check the OQ option button and activate the OQ Test
Protocol check box.
Figure 325: OVP - OQ Test Protocol check box
The OQ Test Protocol Setup dialog opens.

Figure 326: OVP - OQ Test Protocol Setup
Tests which are not available for the selected instrument type are disabled, all
the other tests are activated. If you want to skip a test, deactivate the respective
check box.
The Generate Spectral Plots with Reports check box will generate a multi-page
report with a comprehensive test result page and subsequent pages for each test
where all the test spectra are displayed. If you deactivate this check box, the
report will just show the comprehensive test result page.
The Options menu includes the Service Mode command which you can use to
have a measure button displayed for each test. If you click on one of these
measure buttons, the particular test will run and the result will be displayed
either as simple message or as full report. The output report format can be
selected from the Service Mode Options menu.

Validation
Figure 327: OVP - OQ Service Mode Options menu
If you click on the Measure All Selected Tests button, all tests which have been
activated will run. Test spectra generated in service mode are not stored in the
DATA sub-directory but in a temporary sub-directory which can be changed by
means of the Service Mode Options menu. The results of the tests are temporary
and will not be recorded in the user database.
Figure 328: OVP - OQ Test Protocol Setup with service mode enabled
If all options and tests have been set, click on the Exit button. The OQ Test
Protocol button in the OVP Setup dialog is now checked and light blue which
indicates that the test has been successfully activated.

Figure 329: OVP - OQ test activated
To open the setup dialog for this test click on the Bruker OQ (AT) Test Protocol
button. If you deactivate the check box, the OQ test will not run.
13.5.2 OQ Test Description
Resolution Test:
The resolution test verifies the achievable spectrometer resolution and records a
single-channel (single-beam) spectrum of water vapor with an instrument-
specific resolution. This means for most instrument types: 1cm-1 for MIR and
2cm-1 for NIR, see figure 330. The full width at half maximum (FWHM) is
determined and the results are compared to the acceptance criteria of the
instrument.
Figure 330: Water vapor band at 1553.353cm-1
Sensitivity Test:
The sensitivity test determines the sensitivity of the spectrometer by calculating

the average S/N ratio of a 100% line. A 100% line is the ratio of two
consecutive single-channel spectra with no sample in the beam. The ration of
these two single-channel spectra is used to generate a transmission spectrum.
The S/N ratio is determined by measuring the maximum deviation from 100%
transmittance, and calculated by the OPUS Signal-to-Noise Ratio command in
the Evaluate menu using peak-to-peak by means of the quadratic parabola fit

Validation
option. In order to get a reproducible result 10 spectra are measured (each with
separate reference and sample measurements). The S/N ratio is calculated
separately for each of the spectra, using the mean value of all 10 results. The
region to measure the S/N ratio will vary for systems used in the MIR and NIR
region, and in case of different detectors.
The spectrum shown in figure 331 has a peak-to-peak noise of 0.1% from 100%
transmittance in the MIR region. To calculate the S/N ratio take the reciprocal
value multiplied by 100 (1 / 0.1 * 100). Figure 332 shows a 100% line in the
NIR region.
Figure 331: MIR 100% line
Figure 332: NIR 100% line

Energy Distribution Test:
The energy distribution test verifies the achievable spectral range high and low
wave number limits, and the energy at the position of the maximum.
The test involves recording a single-channel (single beam) spectrum. The

absolute values of energy measured at different wave number positions are
determined, see figure 333. These values are divided by the maximum wave
number value and compared to acceptance criteria expressed as a percentage.
The spectral range limits can be affected by the combination of optical

components (e.g. detector, source and beam splitter) as well as the sampling
accessory.
In the MIR region this test measures the energy values at 7,500cm-1 and
370cm-1, and compares the measured results to the acceptance criteria of 0.10%
and 0.2%, respectively.
Figure 333: Single-channel spectrum
Wavenumber Accuracy Test (X-axis):
The wave number accuracy test verifies whether the frequency scale of the
spectrometer is accurate. To test the wave number accuracy water vapor is used.
Water vapor has the advantage of having extremely narrow bands, and the
wavelength position can be measured to a very high degree of accuracy. To
ensure that the water vapor band is completely resolved the test is performed by
a high-resolution setting. The NIR region uses the band at 7306.74cm-1 for
calibration, and the MIR region at 1554.353cm-1.
Figure 334 and 335 show a typical water vapor spectrum in the MIR and NIR
region.

Validation
Figure 334: MIR water vapor spectrum
Figure 335: NIR water vapor spectrum
Absorbance Accuracy Test (Y-axis):
The absorbance accuracy test verifies whether the y-axis of a measured

spectrum is accurate.
The test uses transmission spectrum of polystyrene which shows total

absorption in several regions (see figure 336). At these positions the theoretical
transmission of the spectrum should be 0. The absolute minimum value of the
spectrum is determined and has to be smaller than the specified maximum
value.

Figure 336: Polystyrene spectrum for MIR
Scan Time Test:
The scan time test is used to test the interferometer performance.
A single-channel spectrum is measured with 10 scans at the highest velocity.

The time needed to measure the spectrum is determined and compared to the
limit.
Water Vapor Test:
The water vapor test determines the concentration of water vapor in the
instrument.
A single-channel spectrum is measured to determine the peak height of a water

band within a small frequency region, i.e. 1660 - 1643cm-1 for MIR
(figure 337) and 7315 - 7297cm-1 for NIR (figure 338).

Validation
Figure 337: MIR water band, 1660 - 1643cm-1
Figure 338: NIR water band, 7315 - 7297cm-1
The water vapor concentration is calculated from the measured data as follows:
Water vapor concentration = 100 - ((YMin * 100)/ YMax)
The limit is compared to the maximum value allowed.

Alignment Test:
The alignment test verifies whether the absolute peak position of the
interferogram is within the range specified.
A single-channel spectrum is measured and the absolute peak position is read

from the measurement parameters stored.
Linearity Test:
The linearity test determines the energy contribution of certain detectors below
the detector cutoff frequency.
A single-channel spectrum is measured down to 0cm-1 (figure 339). The energy

contribution in the region below the detector cutoff frequency is analyzed and
compared to the energy value of the single-channel spectrum at the maximum.
Figure 339: Single-channel spectrum around detector cutoff frequency
The following formula is used to calculate the linearity value:
Linearity Value = ((Abs(YMaxCutoff + YMinCutoff) / 2) / YMaxSpectrum) * 100
The linearity value must not exceed a maximum limit.
Reproducibility Test:
The reproducibility test confirms that all moving parts (mirrors etc.) of a multi-
channel instrument are in the correct and reproducible position.
A 100% spectrum is measured for a specific channel and used as reference

spectrum. After measuring the reference spectrum all moving parts relevant for
the specific channel are moved and a new 100% transmittance spectrum is
recorded in the channel position. This procedure is repeated 10 times. The

Validation
deviation of each of the ten 100% spectra from the reference spectrum is
computed. The greatest deviation must not exceed a maximum value.
13.6 OVP Trends Module

The trends module is a long-term diagnostic tool which visualizes the test
results in graphical form. Performance changes of the instrument can be
detected long before the instrument does not match the required criteria. The
trends module can only be accessed from the main OVP program by users with
Administrator rights in OPUS.
Figure 340: OVP - Trends Module
Select the instrument configuration from the Configuration drop-down list (A),
and the test results to be shown from the Test Results Table drop-down list (B).
Check the corresponding test category option (C). The Values tab (see
figure 341) lists all individual tests specified for the test category. If you click
on any of the tests, the test will be marked red and shown in the chart on the
right side.

OVP Trends Module
Figure 341: OVP - Values and Parms tab with tests specified
To compare the measured values with the expected values click on the Parms
tab and select the limit for the same test which will also be shown in the chart.
Multiple results and limits can be displayed in the same chart. Due to the
different y-ranges, however, this might not be useful at all.
Several control options allow to customize the chart. By means of the Chart
Options group field (figure 342) you can have the chart displayed in different
views and colors.
Figure 342: OVP - Chart Options buttons
The toolbar on top allows to scale and shift the x and y-axis ( ), zoom in
and out the display ( ), read out values of individual data points ( ),
zoom in a particular region of the chart ( ), set time marks ( ) and copy,
save or print the chart ( ).

Validation
13.7 Running OVP in an Unattended Mode

The internal validation unit (IVU) which is integrated into the spectrometers
allows to run, with very few exceptions, the OQ and PQ tests without any user
interaction required.
In general, there are two methods to run OVP in an unattended mode.
13.7.1 Running OVP via OPUS macro
When installing OVP the OVP.MTX macro is installed into the VALIDATION
sub-directory. If you run this macro, the OVP Auto Loop dialog opens which
you can use to define several options.
Figure 343: OVP - Auto Loop dialog
(A)Specify the number of measurement channels which you want to test.

This number must not exceed the number of channels you have
specified for OVP.

Running OVP in an Unattended Mode
(B)Activate the check boxes if you want to run the OQ and/or PQ test. If
a test has expired and not been activated, it will run in any case
regardless of the settings made.
(C)If you have specified more than one channel but you do not want to
run the test for all channels, you can specify the channel to start with.
As the channel number is incremented automatically for the net
channel you can only measure subsequent channels from the list.
Click on the Continue button to start the test. The same OVP dialogs are
displayed which you can see when running the test manually. However, you do
not need to click on any of the buttons.
13.7.2 Running AUTOOVP VB-Script
Instead of the macro which can be used for a one-off run of all tests you can use
a VB Script which is also integrated in OVP. This script can be used to run
selected tests for any of the test channels at a specified time.
A B
E F
Figure 344: OVP - Auto OVP dialog
(A)Select the test channel by activating the appropriate check box.

(B)Select the tests to be run from the drop down list. You can select
either PQ, OQ or both tests.

Validation
(C)If you want to run the tests on a daily basis, activate the Perform
selected Tests daily check box.
(D)Enter the start time for the first test to be started in the entry field.
(E)If you have to define further commands, e.g. switching an external
source ON and OFF, you can activate one or both check boxes in the
Pre/Post Sequence Direct Command group field.
(F)Specify the direct command line in the entry field which shall be
executed before and/or after the test measurements have been
completed.
(G)Start the script by clicking on the Start button.
(H)If you have activated the Perform selected Test daily check box, the
time remaining before the first test run will be indicated in the
selection field below the selected test channels.
13.8 OVP Accessory Manager

Accessories are defined as additional optical components which can optionally
be attached to the instruments standard configuration. Examples of accessories
can be:
• A unit for special sampling technique like an ATR accessory which
can be mounted in the sample compartment.
• Different types of fibre probes with different fibre lengths, e.g. a 2m
liquids probe.
An accessory changes some of the basic instrument optical properties and thus
the overall instrument performance. While the basic PQ and OQ tests just verify
the performance and properties of the basic instrument configuration (e.g.
empty sample compartment) it is obvious that these tests cannot be used to
verify the performance of the same instrument if, e.g., an ATR unit is mounted
in the sample compartment.
It is, however, essential to test not only the basic configuration but also
instrument combinations with a built-in accessory, to be able to detect problems
caused by the accessory.
Standard accessories delivered by Bruker are normally included in the separate

accessory databases used by OVP. To be able to run OVP tests in case of
accessories from different suppliers OVP is supported by a separate program
which allows to configure test parameters for these types of accessories.
Accessory data are stored in two different sets of databases, i.e. the standard
accessory databases supported by Bruker and an identical set for user-specific
accessories. These databases are identified by the User prefix and are protected
by the same password as the user databases for the test settings and results
mentioned earlier. Thus, a database update will not have any impact on the
contents of the user accessory data. An empty set of user accessory databases is

OVP Accessory Manager
installed during OVP installation. The Accessory Manager will only modify the
contents of these user-specific databases.
13.8.1 Accessories Influence on Tests
Accessories will change certain test results, e.g. the S/N ratio, or limit the
frequency range of an instrument. In most cases these influences do not depend
on the instrument type used. Therefore, the accessory properties can be
specified as follows:
• Factors - influencing test limits
• Offsets for frequency limits
Depending on the type of accessory a few measurement parameters may also

need to be changed compared to the basic instrument configuration. These
parameters are instrument-type specific and may be:
• Number of scans, reference and sample spectrum (NSS, NSR)
• Preamplifier gain (PGN)
• Aperture setting (APT)
13.8.2 Running Accessory Manager
The OVPACCESSORYMGR.EXE accessory manager is located in the

VALIDATION sub-directory and can be run from the Windows explorer.
Note: Do not move the accessory manager to a different sub-directory as it

expects the user database to be in the VALIDATION sub-directory
DATABASES.

Validation
E
B
F
G C
Figure 345: OVP Accessory Manager - Accessory Database Management dialog
After starting the accessory manager make sure that the Configurations tab (A)
is selected. The following step-by-step instruction describes how to add a new
accessory configuration to the database. In this example we will add the
configuration for a 100m fiber liquid probe.
1) Enter the accessory name, e.g. 100m Liquid Probe, into the New
Configuration Name entry field (B).
2) Select the type of accessory from the Select Accessory Type drop-down
list (C).
Figure 346: OVP Accessory Manager - Accessory type
The accessory type information is used to distinguish accessories which

can either be mounted into the sample compartment, connected to a fiber
port or mounted at an external port of the instrument. In our example
select Fibre.
3) Make sure that the Blank Configuration option button (B) is selected and
click on the Create Configuration button. The new configuration will be
added to the Accessory List (E) and the accessory type is shown in (F).

4) Select the test protocol from the Test List drop-down list (G). The tests
which are available will be listed in the section below. All tests are ini-
tially marked as being not available (H).
Figure 347: OVP Accessory Manager - Test configuration
5) Double click on those tests which should be made available for the
accessory. The Stop sign will be replaced by a green check mark. Only
those tests activated by a green check mark will later be accessible in the
PQ test setup dialog.
Figure 348: OVP Accessory Manager - Tests activated
6) The Wizard Bitmaps group field allows to select one of the existing
bitmaps, or to add a new one. The bitmaps assigned will later be shown
in the measurement wizard during test run. In our example we select the
pre-defined Liquid Probe bitmap from the drop down list (I in
figure 349).

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Figure 349: OVP Accessory Manager - Assigned bitmap
7) If you want to add a new bitmap for the particular accessory, prepare a
bitmap with the size of 150 (w) x 300 (h) pixels. Click on the Add New
button to open a dialog which allows to add this bitmap to the database,
and assign it to the particular accessory.
Figure 350: OVP - Add bitmap to database
8) In the Custom Message entry field (figure 351) you can enter a test
description which will be shown in the measurement wizard before
running the test measurements. The text should reflect the actions to be
performed. If required, you can also add an optional test to each sample
measurement. Store the current settings by clicking on the Save Changes
button.

Figure 351: OVP Accessory Manager - Custom Message entry field
9) Select the XPM Parameters tab to specify required parameter changes

for the particular accessory.
Figure 352: OVP Accessory Manager - XPM Parameters tab
10) Select the instrument (K) which you will use the accessory with. Specify
only those parameters in the Experiment Parameters list (L), which are
different from the default setting. Keep those parameter fields empty
which do not have to be changed.

Validation
Figure 353: OVP Accessory Manager - Experiment parameters selected
11) Instead of typing parameter values you can load the parameters directly
from OPUS. Load an experiment or set the parameters by the Setup
Measurement Parameters command in the OPUS Measure menu.
Confirm the settings. Return to the accessory manager and use the
Import from OPUS button (O) to read the parameters from OPUS. The
Compare Parameters button (M) can be used to compare any values
entered to the current OPUS setting. The Export to OPUS button (N)
overwrites the current OPUS settings by the parameters manually
entered.
O
Figure 354: OVP Accessory Manager - Measurement parameters options
12) Click on the Store Configuration button (P).
Figure 355: OVP Accessory Manager - Parameter configuration buttons
13) Steps 9 to 12 have to be repeated for each individual test. For both PQ
and OQ tests.
14) If you want to use the accessory with more than one instrument type
click on the Add new Configuration button (Q) and repeat steps 9 to 13
for each new instrument type.
15) Click on the Test Parameters tab which will be empty and has to be
activated by clicking on the Load Parms button (S).

U
S
Figure 356: OVP Accessory Manager - Test Parameters tab
16) Enter appropriate offsets and factors into the parameter section (T).
Offsets are entered in wave number units and will be added to the value
specified for the basic instrument. If an instrument increases, e.g., the
lower frequency limit for the signal-to-noise test by 100cm-1, enter 100
into the appropriate field.
If a limit is decreased, enter the value with a minus sign. Factors are
used to multiply test limits. In most cases the accessory will probably
decrease the achievable S/N ratio of the basic instrument. If it decreases
the value by 50%, enter 0.5 into the appropriate field. If the minimum
S/N ratio limit of the basic instrument configuration is 10000, this limit
will be decreased to 5000 as soon as you use the accessory. Offsets
which are not influenced need to be set to 0, while parameter limit
factors which do not change need to be set to 1.
Figure 357: OVP Accessory Manager - Test parameter settings

Validation
17) Store the settings by clicking on the Save Parms button (U).
18) To generate the settings for the OQ test protocol select OQ Test from the
Test List drop-down list (G in figure 347). The Test Configuration field
will now show all OQ tests. Proceed for the OQ test protocol and follow
the steps as described for the PQ tests.
Once you have generated a complete accessory configuration you can set up
another configuration by copying the existing one.
Figure 358: OVP Accessory Manager- Create new configuration
Enter the name of the new configuration into the New Configuration Name
entry field. Select the accessory type from the drop-down list and activate the
Copy Existing Configuration option button. Select the configuration to be
copied from the Existing Configuration List drop-down list. Click on the Create
Configuration button to make the copy. Instead of defining all parameters you
just need to make the required modifications.
In the OVP setup you will immediately find the accessories listed in the
Accessory drop down list
Figure 359: OVP Setup - Accessory List

Adding New Test Channel
13.9 Adding New Test Channel

This chapter exemplifies step by step a typical first-time use of the OVP setup.
Assuming that the program has been properly installed, make sure that you meet
the following conditions:
• OPUS has been installed in the C:\PROGRAMS\OPUS path.
• OVP has been installed in the OPUS VALIDATION sub-directory.
• Set up a test channel for the MPA spectrometer with a 2m liquid fiber
probe.
13.9.1 OPUS Setup
1) Select the Optic Setup and Service command from the OPUS Measure
menu.
2) Select the Interferometer/AQP tab and make sure that the Channel
Specific Laser Wavenumber check box is activated.
3) Close the dialog.
4) Select the User Settings command from the Setup menu.
5) Select the Instrument Test1 tab.
6) Click on the Path button to locate the OVP installation path.
7) Type \OVP.EXE at the end of the path. The IT entry field should now
read C:\PROGRAMS\OPUS\VALIDATION\OVP.EXE
8) Close the dialog.
9) Select the Advanced Measurement from the Measure menu, or the Setup
Measurement Parameters command when working in validated mode.
10) Load the default measurement experiment located in the XPM sub-
directory of the OVP installation directory. In case of our example this
means: MPA.XPM in C:\PROGRAMS\OPUS\VALIDATION\XPM.
11) Make sure that none of the tabs indicates an error or warning symbol
(e.g. STOP sign).
12) If an error is indicated on any of the parameter tabs, click on this tab,
correct the error and store the experiment using the same file name. Add
a Release signature to the experiment if you are working in validated
mode
13.9.2 OVP Setup
1) Click on the status light on the OPUS interface. The Instrument Status
dialog opens.
2) Click on the first icon in the second row to open the Instrument Status
Message dialog.
3) Click on the Test Now button to open the OVP start screen.
4) Click on the Setup button to open the OVP setup dialog.
5) Check the instrument type and make sure that the correct instrument

Validation
(MPA) is indicated. If the instrument type is not correct or if the

Instrument Type entry field is empty, click on the button to
update the automatic selection. If the entry field still shows the wrong
instrument type, check if the correct instrument is selected in the OPUS
Optics Setup and Service settings in the Measure menu.
If the entry field is still empty, the instrument selected is not supported
by OVP. In this case contact your local service department for more
information. Currently, the following instrument types are supported:
VECTOR, VECTOR 22/N, TENSOR, MATRIX, MPA and VERTEX.
6) Click on the Setup button in the first row (IT1) of the OVP setup dialog
to open the Setup Optics Configuration dialog. Select Source, Beam-
splitter, Measurement Channel and Detector from each of the four drop-
down lists for your configuration. The following settings apply to our
example:
• Source = NIR
• Beam splitter = Quartz
• Measurement Channel = Fibre 1
• Detector = TE-InGaAs [Internal]
7) Close the dialog by clicking on the Save and Exit button.
8) Select the new entry. Click on the IT1 button. The entry field becomes
yellow.
9) Make sure that the Configuration entry field shows the correct
configuration, i.e. Fibre in case of this example. If the configuration is
not automatically selected or wrong, select the correct configuration
from the drop down list. If the drop-down list does not include the
configuration required, contact your local service department for more
information.
10) If the configuration has not been detected automatically, make sure that
the configuration is still the same even after selecting the respective test
category. Activate the appropriate OQ or PQ option button.
11) If the Accessory drop-down list is enabled, select the accessory you want
to use, or the None option if no accessory is used. In case of this
example select the 2 m Liquid Probe accessory.
12) Press the button to measure a new laser wave number (LWN). As
soon as the result is displayed click on the Set button to set the new
LWN value. If the LWN has already been correct, click on the Exit
button.
13) Activate the PQ option button.
14) Define the time interval between the tests. Generally, PQ tests are
performed once every 24 hours.
15) Activate the OQ option button.
16) Define the time interval between the tests. Generally, OQ tests are
performed once every 6 or 12 months.
17) Enter a unique title into the Validation Set Title entry field. This title is
used in reports to help to identify the configuration used, e.g. Liquids
Probe on Chemical Vat #3.

OVP Program Modules and Databases
13.9.3 PQ Test Protocol Setup
1) Activate the test channel by clicking on the ITx button. The entry field
will turn yellow.
2) If the PQ category has not yet been activated, check the PQ option
button.
3) Activate the PQ Test Protocol check box. The PQ Test Protocol Setup
dialog opens.
4) Click on the Measure button and start the reference measurements.
5) If the reference measurements have finished, click on the Exit button.
13.9.4 OQ Test Protocol Setup
1) Activate the test channel by clicking on the ITx button. The entry field
becomes yellow.
2) If the OQ category has not yet been activated, check the OQ option
button.
3) Activate the PQ Test Protocol check box. The PQ Test Protocol Setup
dialog opens.
4) Make sure that all the respective tests are activated.
5) Click on the Exit button.
Repeat all steps for any other channels which you want to be validated.
13.10 OVP Program Modules and Databases

The main programs and databases required for OVP, and their meaning are
outlined in the following:
\VALIDATION Main OVP Directory:

OVP.EXE Main OVP program
OVP.MTX OPUS Macro for OVP Automation
AUTOOVP.OBS OPUS VB-Script for OVP Automation
OVP_MANUAL.PDF This Manual in PDF Format
\VALIDATION\MODULES Directory for OVP Modules:

OVPSETUP.EXE OVP Setup Program
OVPWIZARD.EXE OVP Measurement Wizard
OVPTRENDS.EXE OVP Trends Module
\VALIDATION\PLUGINS Directory for OVP Test Protocol Plug-ins:

IT_BVP.EXE Plug-in for PQ Test Protocol
AT_BVP.EXE Plug-in for OQ Test Protocol

Validation
\VALIDATION\DATABASE Database Directory:

SYSTEMDB.MDB Instrument Configuration Database
IT_DATA.MDB PQ Test Protocol Database
AT_DATA.MDB OQ Test Protocol Database
ACCESSORY.MDB Accessory Configuration Database
PQ_ACCESSORY.MDB PQ Accessories Test Protocol Database
OQ_ACCESSORY.MDB OQ Accessories Test Protocol Database
USERACCESSORY.MDB User-specific Accessory Configuration
Database
USERPQ_ACCESSORY.MDB User-specific PQ Accessories Test
Protocol Database
USEROQ_ACCESSORY.MDB User-specific OQ Accessories Test
Protocol Database
USERSETTINGS.MDB Test Channel Configuration
USERDATA.MDB Test Data
\VALIDATION\XPM Directory for Default Measurement

Experiment
instrument.XPM Instrument-specific Measurement

Experiment
\VALIDATION\DATA Main Data and Report Directory:

\<YYMMDD>\<HHMMSS> Data Sub-Directory named with test date and
time
\REPORTS Reports Sub-Directory
PQ_configuration_Testtype.0 PQ Test spectra named by instrument
configuration and test (e.g.
PQ_MPA_SAMPLE_ COMPARTMENT_
FREQTEST.0)
OQ_configuration_Testtype.0 OQ Test spectra named by instrument
configuration and test (e.g.
OQ_MPA_SPHERE_LINEARITY.0)
PQ_configuration_date_time.pdfPQ Test Report (e.g.
PQ_MPA_FIBRE_040217_124909.pdf)
OQ_configuration_date_time.pdfOQ Test Report (e.g.
OQ_MPA_FIBRE_040216_103545.pdf)
\VALIDATION\TEMP Directory for Temporary Data

Instrument Status Indicators
13.11 Instrument Status Indicators

OPUS has two types of status indicators. The status light located in the bottom
right corner of the OPUS interface, and the icons displayed on the Instrument
Status dialog. To access the Instrument Status dialog click on the status light.
The status light indicates the status of the active channel as defined by the
currently loaded measurement experiment file (XPM).
While the first row of icons on the Instrument Status dialog indicates the state of
the instrument hardware, the second and third row of icons refer to each of the
12 possible active test channels. The program assigned to the channel position
determines the status indicated on the Instrument Status dialog.
These are two important distinctions. The status light indicates the status based
on the measurement experiment loaded. The icons on the Instrument Status
dialog indicate a status returned by a program assigned to that channel position.
13.11.1 Status Light Setup and Operation
Primarily designed for the latest Ethernet-based spectrometers, the status light
indicates the status of the active test channel. This status is stored on the
instrument, not on the PC.
Each time the user loads an experiment file, the corresponding channel is set as
active channel. The status of this new active channel is checked and indicated
by the status light.
The active test channel refers to one of 12 IT channel positions defined on the
Instrument Test tabs of the User Settings command in the Setup menu.

Validation
Figure 360: Instrument Test tab and XPM file assigned
To activate a channel, select a path by clicking on the Path button. You can also
manually enter the path.
If you select a path, OPUS will be informed that you want to assign the
Instrument Test macro (which can be installed during OPUS installation) to a
particular channel. OPUS assumes that the IT.mtx macro is located in this path.
If the macro cannot be found, a Runtime Error in Macro message pops up when
you attempt to run the test.
Entering an executable program file name, e.g. OVP.EXE informs OPUS to run
that program instead of the macro.
If you have entered a path (and exe name, if desired) into the appropriate IT
entry field on the Instrument Test tab, an icon is assigned for that particular
channel on the Instrument Status dialog.
For the status light to operate, you have to assign measurement experiment files
(xpm) by using the XPMs button. Click the XPMs button to the right of the path
assignment. A dialog opens. All experiment files listed in this dialog are
registered for this particular channel. Therefore, you should only select
experiment files that have the same basic configuration of the spectrometer
(source, beam splitter, measurement channel, detector).
If you load an experiment file, OPUS checks all the experiment files registered.
If a match is found, that channel (1 to 12) becomes the active test channel.
OPUS polls the spectrometer to detect the status of that channel. That channel is
set Active in the spectrometer as well. The status light changes its color as
follows:

• GREEN: The active test channel is active, the tests have passed and
not expired.
• YELLOW: The time interval for one or all the tests for the active
test channel has expired.
• RED: One or all the tests for the active test channel have failed.
If you deactivate one of the IT check boxes, that particular channel becomes
inactive. OPUS does not update the status light if that particular channel is
selected as the active channel.
The following summarizes situations which may have an effect on the status
light:
• User loads an experiment file.
• The XPM lists for each channel are scanned for the first position
containing that experiment.
• If a match is found, this match becomes the active test channel.
• The status for the active channel is read from the spectrometer web
server.
• The status light is changed to reflect that status.
13.11.2 Instrument Status Icon Operation
If you click on the status light, the Instrument Test dialog opens. The status light
will change to reflect the state of the active channel icon.
If a path (and exe name, if desired) has been entered into an IT entry field on the
Instrument Test tab, an icon is assigned for that channel position in the second
or third row of icons on the Instrument Status dialog. The first row indicates the
results of the instrument diagnostics test performed when the Instrument Status
dialog opens.
The first row of icons can have three possible status indicators. A green check
mark indicates that the hardware component has passed the diagnostic test. A
yellow warning is displayed if a limit is nearly reached, e.g. source lifetime has
nearly expired. A red error message indicates that the diagnostics have failed.
The second and third row of icons can have three possible status indicators. A
green check mark indicates that the tests have passed and are still valid. A
yellow warning indicates that the tests have passed, but expired. A red error
indicates that a test has failed.
If you click on the first row of icons in the Instrument Status dialog, the
Instrument Status Message dialog pops up and displays the Service Info button.

Validation
Figure 361: OVP - Instrument Status Message with Service Info button
Clicking on the Service Info button opens a window in OPUS indicating the
diagnostics page from the instrument Web server. On non-Ethernet instruments
the Bruker Web page is displayed, provided you are connected to the Internet.
If you click on the second and third row of icons in the Instrument Status dialog,
the Instrument Status Message dialog pops up and displays the Test Now button.
Clicking on the Test Now button tries to run the macro or program assigned to
this particular test channel.
Figure 362: OVP - Instrument Status Message
If you have not assigned any program name, OPUS assumes that you are
running the IT.mtx instrument test macro. The results of this test are stored in
the IT.log text file. This file is located in the IT sub-directory. If OPUS cannot
locate the IT.log file, the Instrument Status Message dialog displays the
message: Test log not found. OPUS reads the IT.log file to determine the status
of the particular channel.
If the file listed is an executable program, OPUS runs the program and transfers
a parameter to the program requiring the status of the current channel. The
program then returns the test channel status.
This program status check is performed for each channel assigned at the time
the Instrument Status dialog is accessed. The results returned are displayed as
icons.
The following summarizes situations which may have an effect on the icons
displayed in the Instrument Status dialog.
• The user clicks on the status light.
• OPUS polls the programs listed for each of the 12 positions, if
assigned.

• The program returns the test status for that channel to OPUS.
• OPUS changes the icon for that channel to reflect the result returned.
• OPUS performs an instrument hardware diagnostics check.
• The user clicks on an icon to run the tests previously assigned.
• If the tests have been completed, the program directly writes the test
results of the active channel to the spectrometer.
13.11.3 Status Indicator for Non-Ethernet Based

Spectrometers
The status light and icons are intended to be used in connection with Bruker
Ethernet-based spectrometers. In case of previous spectrometer types and
research spectrometers the functionality is different.
A command line option must be added to the OPUS icon to specify a time (in
minutes) that OPUS should use to poll the program for the current status of the
active channel. Once during each interval, the program is polled to request the
status and the status light is updated.
Figure 363: OPUS Property dialog
In figure 363 the /DIAGTIMER=10 command polls the status once every 5
minutes.
The status is not updated when loading an experiment file, it is updated if the
time interval has expired and the assigned program polled.

Validation

Logout
14 Setup
Figure 364: Setup Menu
14.1 Logout
To login a new user or to logout and terminate OPUS chose Logout from the
Setup menu.
Figure 365: Logout Screen
To log in, choose the User ID from the combo box. The last user is always
shown. Enter the proper user password. The password is displayed as a series of
“*”. The user type (Operator or Administrator) for the currently selected user is
displayed.
Choose one of the workspaces from the combo box. The contents of the combo
box depends on the selected user. In case of Operators only the assigned

Setup
workspaces are shown while in case of Administrators all workspaces in the

OPUS root directory are shown. Click on the Login button to log in the new
user. Click on Exit from OPUS to cancel the login procedure and leave OPUS.
14.2 Setup JCAMP/OPUS Conversion

Use this command to set the conditions for the conversion of JCAMP files into
OPUS files. The settings made apply to the Convert3dJCAMP command in the
Edit menu as well as to the Load File command in the File menu. To avoid the
loss of information conversion tables are used to correlate JCAMP labels with
OPUS parameters and information lines. These tables are text files and have the
extension .PCT which can be generated using any kind of text editor. In
addition, the file containing the info text definition has to be specified. The
general syntax for each line is as follows:
#Ixx:yyy:LABEL
Ixx defines the number of the line in the info block, xx being a two-digit
number starting with 01
yyy a three character OPUS parameter
LABEL the name of the JCAMP label
It is mandatory to determine the consecutively numbered info line. Each line

need to have two colons. The parameter name and the JCAMP label definition
are optional.
The following example refers to the DEFAULT.PCT file which is stored in the
OPUS Methods directory.
#I01::SNM:TITLE
#I02::MOLFORM
#I03::MW
#I04::CAS REGISTRY NO
#I05::MP
#I06::BP
#I07:SFM:SAMPLING PROCEDURE
#I08::
#I09:CNM:ORIGIN
#I10::CROSS REFERENCE
#I11::CHARGE NO
#I112:HIS:DATA PROCESSING
Use the Setup JCAMP/OPUS Conversion command to define the conversion

table required for the JCAMP file conversion. If you click on the Change
button, you can load the relevant file from the dialog that pops up. Localize the
files which include the conversion tables desired.

User Management
Figure 366: Setup JCAMP - OPUS Conversion
If you activate the Accept Commata instead of Period check box, a comma is
used as decimal separator during conversion.
14.3 User Management

An essential part of quality regulations is the access control to computer
systems and software packages. While the operating system ensures a high level
of access control to the computer system it might be desirable to have further
levels of access control to the different software packages. This allows to
establish access control for one user group within the operating system, and
have individual access control levels in case of application software. Thus,
several users can work simultaneously with the same software and do not have
to reboot the system each time a different user wants to access a certain
software package.
14.3.1 Definitions
• User Database
A database with different user records.
• User Record
An entry in the user database, which includes user ID, user name,
password, user type, workspaces.
• User ID and Password
Required to be able to log into OPUS.
• User Name
The user name is stored in measured spectra and indicated in all audit
trails.

Setup
• User Type
Specifies the access rights of a user.
• Workspace
User environment in OPUS.
• Assigned Workspaces
Workspaces assigned to a certain user.
14.3.2 Default User Database
To allow immediate access to OPUS after the installation a default user

database is available. This default database includes three pre-defined user
records, which allow full access to OPUS and all workspaces. These records
include the following user data:
User ID Default Administrator Labmanager

Password OPUS OPUS OPUS
Operator name Default Administrator Labmanager
User group Administrator Administrator Labmanager
Assigned Work- Unlimited access to all user workspaces
spaces
We recommend not to delete these user records or to change the password to be

able to use the user management features.
14.3.3 Setting up User Records
Make sure that you are logged in to OPUS with administrator rights to be able
to create, modify or delete user records. Otherwise, the User Management
function will not be accessible in OPUS.
Select the User Management command from the Setup menu. The following
dialog opens.

User Management
B
C
D
G
E
F
I J
K L
Fi 36 U M Ad i i
(A)Buttons to go to the previous and next user records.
(B)Enter the user ID for the user. The user ID must have a minimum
length which can be specified on the Global Options tab. It is not
possible to log in to OPUS without any user ID.
(C)Enter the password for the user. The password must have a minimum
length which can be specified on the Global Options tab. The entry in
the Password entry field is indicated as a sequence of "*".
(D)Re-enter the password for verification. The entry in the Password
Verification entry field is indicated as a sequence of “*”.
(E)The user name is stored in newly measured spectra and in the audit
trail of spectra and methods.
(F)The user group can be defined either as Operator, Labmanager or
Administrator. Each user group has the following rights:

Setup
Workspaces User and Signature

Management
Administrator All Yes
Labmanager All No
Operator Only those assigned No
In OPUS 4 and even more previous OPUS versions the access rights had been
as follows:
Workspaces User and Signature
Management
OPUS Administrator and All Yes
operating system admini-
strator (NT, XP...)
OPUS Administrator and All No
user/power user of opera-
ting system (NT, XP...)
OPUS Operator Only those assigned No
If the previous OPUS access rights have to be valid, start OPUS by the
/CHECKWINADMIN=ON option. In this case the OPUS operating system
rights will also be checked.
(G)Password duration (if any). The password duration can be specified
on the Global Options tab.
(H)This selection field includes all workspaces which can be accessed
by the user. The selection field is only visible for users with Operator
rights, as users with Administrator or Labmanager rights both have
unlimited access to all workspaces.
(I) Use this button to add a workspace to the selection field (H).
Workspaces are always stored with the complete directory path. If
you move a workspace to a different directory, you will no longer
have access to this workspace.
(J) Use this button to remove a currently selected workspace from the
selection field (H).
(K)If you activate this check box, the user will be locked. This check
box is automatically activated if a user tries to log in by using a
wrong password several times. The number of login attempts can be
defined on the Global Options tab.
(L)Button to delete the current record.
(M)Activate this check box if you want to force the user to change his
password when logging in the next time.

User Management
The total number of user records is displayed in the top line of the dialog box.
The number of the current user record is displayed between the and
buttons.
All entry fields which must be filled in are initially marked red. If you start
typing into any of the red entry fields, the color of the entry fields changes to
yellow. The color of the entry fields remains yellow as long as the number of
characters typed in is lower than the number specified for the current field. If
the minimum number of characters is reached, the entry field color changes to
white indicating a valid input.
The default settings for the different fields are:

• User ID: 3 characters
• Password: 4 characters
The default settings can be changed on the Global Options tab. Any changes
made will have an immediate effect on all user records.
The Password Verification entry field will only change to white if the text
entered is identical to the text defined as password. The password can be empty
if the appropriate check box is activated on the Global Options tab. In this case
the Password entry field will be yellow and the Password Verification entry
field white.
Double user IDs are not allowed and will be indicated by red entry fields.
User records cannot be stored, unless all obligatory fields have been filled
in properly. For operators at least one workspace must be displayed in the
workspace selection field.
The user records are stored in the USERDATABASE.DAT file in the

USERDATABASE sub directory of the OPUS directory. The file is encrypted
and cannot be modified externally. Make sure that this file is protected against
accidental deletion using Windows’ security options. Make a backup copy
whenever you modify this file, but you must not set this file to read only.
Click on the Global Options tab to define further user management options.

Setup
Figure 368: User Management - Global Options tab
(A)Minimum length of User ID.

(B)Minimum length of password.
(C)If you activate this check box, empty passwords are allowed. Note
that empty passwords will never expire, regardless of the password
duration set.
(D)This check box either activates or deactivates the password duration
option, i.e. the password never expires or expires after the number of
days defined.
(E)Password duration in days. This entry field is only visible if the
Password never expires check box has been deactivated. The
duration period starts with the date when the user record is created or
modified.
(F)Maximum number of illegal login attempts, i.e. entering a wrong
password during login. The user gets a warning indicating how many
attempts are left. If the last attempt has not been successful either, the
user will be locked and not be able to run OPUS anymore. The

User Management
administrator only can undo this lock by deactivating the Lock user
check box on the Setup Record tab.
(G)Number of passwords previously used by the user, and not allowed
to be used anymore when changing the password. Thus, the user is
forced to use a completely new password if the duration of his
password has expired.
Any changes made have an immediate effect on all user records in the data base.
Therefore, check all user records after changing any of these settings. Illegal
entries will be marked in red.
The Audit Trail tab indicates the audit trail of all actions for each user. The
following actions are recorded:
• Successful login
• Login attempt of a locked user
• Login with password expired
• Password change
For users with Administrator rights the following actions are additionally
recorded:
• Creating or changing a user record
• Deleting user record
• Locking user record
• De-locking user record
• Creating or changing signature record
• Deleting signature record
• Locking signature record
• De-locking signature record
• Exporting audit trail
• Exporting all audit trails
• Deleting one audit trail

Setup
Figure 369: User Management - Audit Trail tab
(A)Buttons to go to the previous or next user record.

(B)Audit trail
(C)Use the Save current button to store the current user data recorded in
the audit trail.
(D)Use the Save all button to store all user data recorded in the audit
trail. If you click on the Save all button, a dialog opens. Define the
file to be used to store the audit trail data and confirm the entry.
Audit trail data are stored in ASCII format.
(E)If you click on the Clear Audit Trail button, the audit trail data of the
current user will be deleted. This button is only enabled if the audit
trail data have been stored.
The Save and Clear Audit Trail actions are recorded in the audit trail of the user
currently logged in.

Change User Password
14.4 Change User Password

Each user can change his password. There are different reasons for changing a
password:
• A new user record has been created. In this case the administrator
defines the initial password which will be changed by the user.
• The Password Expiration option is enabled and the password has
been expired after the period of time defined. In this case the user
cannot log in to OPUS anymore.
• A user assumes that someone else knows his password.
Select the Change User Password command. The following dialog opens:
Figure 370: Change User Password
(A)User name and user group

(B)Entry field for the old password
(C)Entry field for the new password
(D)Entry field to confirm the new password
When defining a new password make sure that it is different from the last ones
previously used. Furthermore, the new password has to have the minimum
length defined on the Global Options tab of the User Management dialog.
If your password has already expired and you attempt to start OPUS, a warning
pops up.

Setup
Figure 371: Warning - Password expired
If you click on the OK button, the OPUS Login dialog opens. Enter the new
password and verify it.
Figure 372: Change Expired Password
Click on the Change Password button. The OPUS Login dialog opens again.
You can now log in to OPUS by using the new password.
14.5 Setup User Macro List

This function can be used to integrate macros or VB-Scripts into OPUS. The
user own macros/scripts are integrated in the menu and can be added to the
toolbars. It is possible to add macros/scripts in different languages.

Setup User Macro List
A
B
D
E
G
I
K
H
L
J
Figure 373: Setup User Macro List
(A)Select the language for the entry. The default language is the
language in which OPUS was started. Only the entries for the
selected language can be edited. When the language is changed the
entries for the newly selected language are accessible.
(B)Shows the total number of entries and the number of entries for the
current language
(C)The navigate buttons allow to scroll between the different entries for
the current language
(D)The menu where the macro/script shall be added to can be selected
from the combo box.
(E)Use the browse button to select the macro/script for the entry. To
prevent errors the path and name of the macro/script cannot be
entered manually.
(F)Three different text fields have to be specified: The text shown in the
menu, the text shown as tooltip and the text displayed in the status
bar
(G)This button deletes the current entry from the list
(H)An entry can be copied into the list for a different language by
clicking on that button. After copying an entry the language can be
changed in A and the entry can then be translated or otherwise
modified.
(I) This combo box specifies the target language for copying. Copying
into the same language as specified in A is not possible.

Setup
(J) This button stores all entries for all languages in the USERMAC.LST
file
(K)Exit from the function without storing any modifications
(L)Shows the online help for this function
Contents of the USERMAC.LST File

The USERMAC.LST file in the OPUS directory is stored as a plain text file.
[ENGLISH]
.\macro\it.mtx@8@Instrument Test@Instrument Test@Run the Instrument Test
[GERMAN]
.\macro\it.mtx@8@Gerätetest@Gerätetest@Gerätetest durchführen
[FRENCH]
.\macro\it.mtx@8@Test d'instrument@Test d'instrument@Lancer le test
d'instrument
The key words in square brackets specify the different language sections.
Within the sections each line represents a macro/script. The different parts of
the lines are separated by the "@" character. The different parts have the
following meanings:
.\macro\it.mtx@8@Instrument Test@Instrument Test@Run the Instrument Test
(1) ( 2) (3) (4) (5)
(1) Path and filename of the macro/script
(2) Menu number
(3) Text for the menu
(4) Text for the tool tip
(5) Text for the status bar
14.6 Register OPUS

After installing OPUS you can test the program for 30 days without registering.
After this trial period you have to register your copy of OPUS. Furthermore,
you can use libraries and additional OPUS packages only after you have
registered your copy. To register you have to obtain the necessary information
(key, serial number etc.) from Bruker. The registration has to be only
performed once and is valid for all users of the system. You must be a
Windows power user to register.

Customize Toolbars
Figure 374: Registration Dialog
The key will be only visible while you type, later on it will be masked. The
serial number of OPUS and the OPUS library consist of numbers only. The key
also includes characters; be sure to type capital letters when required.
After registering OPUS these fields will be grayed out unless the Change
Register Fields check box is marked. When you buy additional OPUS packages
or libraries you may have to re-enter some of the information in order to use
these packages.
14.7 Customize Toolbars

You can personalize your OPUS workspace by configuring the toolbars to suit
your requirements. Open the Customize Tool bars command of the Setup pull-
down menu. Alternatively, right-click on the empty space of a tool bar to obtain
the dialog box.

Setup
Figure 375: Customize Toolbars
You can
• move bars by the mouse.

• generate new bars or load existing bars.
• use the Show Tooltips check box to display help texts.
• turn separators on and off (New Look).
• include descriptions in the icon (Large Buttons).
Add or remove icons to a tool bar using Commands tab of the Customize Tool
bars dialog box.

Customize Menus
Figure 376: Customize Toolbars – Commands
14.8 Customize Menus

Like the tool bars you can also customize the pull-down menus. By default the
Show All Functions check box is marked during the OPUS installation. As a
result the menus include all available OPUS functions. However, you can create
your personal profile (if your rights according to 21CFR11 allows a
customizing of the workspace) by choosing the functions you wish to use.

Setup
Figure 377: Menu Settings
To customize the menus first remove the tick from the Show All Functions
check box which is selected by default. Select the menu you want to configure
from the menu list (A) and then add the functions you would like to include by
selecting them from the Functions selection field. Use the Add Selected button
to include them in the Functions selection field. You can change their order of
appearance in the menu with the Up and Down buttons and add separators to
structure the menu.
Your individual settings will be saved in your user profile. However, you can
only customize your profile when you were granted the necessary rights to do
so.
You also can use the Menu Settings to configure the display pop-up menu. To
do this, deactivate the All Functions check box and choose Display Popup from
the menu drop-down list. Add the functions you would like to include in the
pop-up menu and activate the All Functions check box again.
Shown in figure 378 is the display pop-up menu in which three functions have
been added. To facilitate the identification of these functions they have a small
tag on the left side.

Display Settings
Figure 378: Display Pop-up Menu with Added
14.9 Display Settings

Change the appearance of the spectrum window by calling up its pop-up menu.
This is discussed in chapter 2.3.
14.10 User Settings

Create and manage OPUS user accounts by means of the User Settings
command. Make sure that you have the necessary user rights to do so.

Setup
Figure 379: User Settings – General tab
The General tab indicates the user status as well as the paths for the most
frequently used OPUS directories. If you want to edit the multi evaluation path,
make sure that you have the right to change parameters.
Click on the 21CFR11 Rights tab to assign the rights for the account.
Figure 380: User Settings – 21CFR11 Rights tab

User Settings
Select the user rights by means of the different check boxes and define whether
you want to work in GLP mode or in validated environment. Make sure that at
least one administrator account includes all the user rights which can be
assigned to.
To select the file name incrementation type click on the Preferences tab.
Figure 381: User Settings – Preferences tab
You can either increment the file name or file name extension. Set the number
of decimals for frequencies and intensities to be displayed in the report. The
default decimals for frequencies are 4 and for intensities 3. If you want to have
the number of decimals automatically set, activate the Automatic check box for
both frequencies and intensities.
Click on the Display tab to set the default display limits and define whether the
axes should have legends.

Setup
Figure 382: User Settings –Display tab
To add arrows to the annotations activate the Annotations get arrows check box.
The Same Color for Series of Spectra check box allows to display spectra,
which have the same basic file name, in one specific color during a particular
loading procedure. Usually, the spectral curve colors are automatically assigned
when loading spectra into the OPUS browser window.
If you activate the Same Color for Series of Spectra check box, two additional
option buttons will be displayed.
Figure 383: User Settings - Display tab with additional features
The Whole file name option button indicates that the file name (without
extension) of the spectra series has to be identical to assign spectra colors.
Activate the File Name check box if only a specific number of file name
characters has to be identical. If, for example, a file name has 12 characters and
you enter 1 into the First character entry field and 8 into the Length entry field,
the first 8 characters of any file name will be checked to see whether they are
conform with the file name series.

User Settings
Click on the Spectra Colors... button to assign a color sequence to the spectra.
The following dialog opens:
Figure 384: User Settings - Color Palette
The standard range of colors include 16 colors defined by default, whereby only
those colors checked will be assigned to spectra.
If you have checked a color, use the arrow buttons to move it to the appropriate
position, either upwards or downwards. The color sequence defined on the color
palette correlates with the spectra color displayed in the spectrum window.
Therefore, the first color on the color palette corresponds to the color of the first
spectrum displayed, the second color corresponds to the color of the second
spectrum and so forth. To save the settings click on the Set button.

Setup
Click on the Diagnostics tab and define which warning indications or alarms
you want to set for which spectrometer component:
Figure 385: User Settings – Diagnostics tab
Each of the Instrument Test 1 and Instrument Test 2 tab includes six test
channels. Each of these test channels can assign one program, e.g. OVP (see
chapter 13), to be used from within OPUS for validation purposes, and
correlates with an icon position on the second row of the Instrument Status
dialog, see chapter 7.7. The Instrument Status dialog can be accessed by
clicking on the status light in the bottom right corner of the main OPUS
spectrum window.
The test channels of the Instrument Test 2 tab correlate with the third row of the
Instrument Status dialog. Thus, a total of 12 different test channels can be
assigned, if required.
Note: OPUS 5 and higher versions only allow to configure twelve test channels.
In previous OPUS versions you can only assign a maximum number of six
channels. Thus, these versions only have one Instrument Test tab in the User
Settings dialog.

User Settings
Figure 386: User Settings – Instrument Test 1 tab
First, activate the IT check box which represents the active test channel, and
either enter the path manually or click on the Path button. If you work with
OVP, select the OVP path which is normally located in the Validation sub-
directory of the OPUS directory. Enter the program file name manually,
including the extension.
Example:
Assuming the instrument has both a sample chamber and a fiber optic probe, to
validate both configurations you would assign OVP to two IT channels on the
Instrument Test tab.
Figure 387: Two Configurations Assigned for OVP
In this example we would arbitrarily designate the first position (IT) to be used
for all experiment files that use the sample compartment, assuming that these
experiments use the same detector, beam splitter, etc. All experiment files that
use the fiber optic probe channel will be designated for the second position
(IT2). This only completes the assignments required by OPUS. Further OVP
settings are required. For further details, refer to chapter 13.

Setup
Use the XPMs button to register one or more measurement experiment files to
the validation channel. These are the experiment files you will use for normal
daily measurement. Each time you load one of the registered experiment files
into OPUS, this list is checked. If a match is found, the status for the particular
channel (IT 1-12) is polled. If it is determined to be valid, the status light will be
green.
You can add as many XPM files as you like. It is important that you only select
experiment files which have the same basic spectrometer configuration (source,
beam splitter, measurement channel etc.). Further details on preparing default
measurement experiments can be obtained from chapter 13.2.1.
If you click on the XPMs button the following dialog opens:
Figure 388: Assign XPM file(s)
Click on the Add button to add XPM files from particular directories into the
selection field. By means of the icon bar on the right you can either define a new
XPM file, or cancel existing ones. Use the arrow buttons to scroll up and down
the entries in the list. Confirm the selection by clicking on the OK button. Undo
the selection by clicking on the Cancel button.
14.11 New Workspace

OPUS is able to manage several user profiles which can be password protected.
A profile contains information OPUS about the users rights, his customized
desktop (tool bars, menus), the parameters of all commands as well as the users
name and password. Create a new profile with New Workspace. See
chapter 14.10 for details.

Save Workspace as
14.12 Save Workspace as

If you changed anything concerning the settings saved in your profile, e.g. the
position of the tool bars, your profile will automatically be updated when you
exit OPUS. If you created a new profile OPUS will ask you for the profiles
name.

Setup

Setting the Language
15 Help
Figure 389: OPUS Help Menu
The OPUS Help commands are available either from the Help menu or by
clicking on any Help button of a dialog box. By means of the F1 button on the
PC keyboard you can activate the online help. To be able to use the online help
function you have to install Microsoft Internet Explorer 4.0 (or higher).
If you select the Online Docs command, you all OPUS manuals available are
indicated on a different menu. They are provided as PDF files. In order to read
these PDF files you have to install the Acrobat Reader from the OPUS CD.
The FT-IR Tutorial imparts basic knowledge about FT-IR spectroscopy. Click
on the About OPUS command to learn something about the OPUS version used,
the registered user name and the OPUS packages available. For further details
on this subject, see chapter 1.
15.1 Setting the Language
When installing OPUS you define the OPUS directory and select between three
languages (English, French and German) to be used for the installation dialogs.
The procedure to set the OPUS system language depends on the Windows
version used. Therefore, the following steps described may be different in your
case. Click on the Windows Start button and right click on the OPUS icon.
Select the Properties command and the following dialog will open:

Help
Figure 390: Properties Dialog - Shortcut tab
Depending on your Windows version this dialog may look slightly different.
Add the correct language parameter into the Target entry field on the Shortcut
tab. Make sure that you type the parameter in capital letters. If the parameter is
not recognized, OPUS will use the default language, i.e. English. The following
parameters are possible:
• OPUS/LANGUAGE=ENGLISH starts the English language module
• OPUS/LANGUAGE=FRENCH starts the French language module
• OPUS/LANGUAGE=GERMAN starts the German language module
To confirm the setting click on the OK button. The language setting will be
transferred to OPUS as parameter when starting the program next time.
15.2 Rebooting the AQP
Sometimes it may be necessary to reboot the acquisition processor (AQP). A

simple way to reboot is to change any of the configurations in the Optics Setup
and Service command in the Measure menu. Any change of these parameters
causes the AQP to reboot.

Abort OPUS
15.3 Abort OPUS
If OPUS hangs for quite some time and cannot be closed by the button, you
can abort the program by using the Windows Task Manager. Data not stored
before aborting the program will be lost. This also applies to the workspace
settings made during the program run (e.g. toolbar configuration, directory
name etc.)
To open the Task Manager simultaneously press the ALT, CTRL and DEL keys
on the PC keyboard. The Windows Task Manager will be displayed.
Figure 391: Windows Task Manager
Select OPUS from the Applications tab and click on the End Task button.
OPUS will terminate without saving any data.

Help

Appendix
Data Block Icons
OPUS files can consist of several spectra, data blocks and reports which all will
be stored in OPUS using the same file name.
a b c d e f g h i j
1
The OPUS browser window and some other types of windows display the file
components by small icons. The following table describes the different icons
and their abbreviations which can be used in connection with macros.
1a Single channel spectrum, reference ScRf
1b Report Report
1c Reflectance spectrum Refl
1d Raman spectrum Raman
1e Quant report Quant
1f Quality test QTest
1g Sample, power spectrum PwSm
1h Reference power spectrum PwRf
1i Sample, phase spectrum PhSm
1j Reference, phase spectrum PhRf

2a Unknown block
2b Peak table Peak
2c Photoacoustic spectrum PAS
2d n th derivative n.Der
2e Logarithm of reflectance lgRefl.
2f Kubelka-Munk spectrum KM
2g Integration report Integ
2h Information block Info
2i Sample, interferogram IgSm
2j Reference interferogram IgRf
3a Protocol History
3b Transmittance spectrum TR
3c Video image Graphics
3d General report GenRep
3e Fit report Fit
3f Emission spectrum Emis
3g 3D spectrum 3D
3h Average report AvRep
3i ATR spectrum ATR
3j Arithmetical result, transmittance AriTR
4a Arithmetical result, absorbance AriAB

4b Absorption spectrum AB
4c Trace Trace
4d First derivative 1.Der
4e Second derivative 2.Der
4f Subtraction report Subtract
4g Molecular structure Strc
4h Search result Search
4i Unknown spectra type Spec
4j Single channel spectrum, sample ScSm

5a Annotation ANNO
5b Cluster Analysis Clus
5c Signature Sign
5d Quick Compare QC
5e Quick Compare results for 3D files TRC
5f Multi Evaluation ME
5g Conformity Test CONF
These basic data block icons can also be combined with other types of icons.
Furthermore, modifications of the above icons exist. For example, the R
character represents the real part and the I character the imaginary part of a
complex data block. A data block icon accentuated by a shadow indicates a 3D
data block.
Icons Used For OPUS Commands
The OPUS commands listed are included in the different menus and can be
called up by means of the tool bar. In the following the most common OPUS
commands are described.

New workspace Draw ellipse
Open Draw line
Close workspace Draw rectangel
Send workspace Insert table
Cut Move
Copy New page
Paste Delete page
New spectrum window Delete
New report window Clear frame
New 3D window Page properties
Tile Object properties
Cascade Lock
Quick print Back (frequency range)
Print Forward (frequency range)
About OPUS Scale all
Scale y
Stacked
Page back
Page forward

Baseline correction Integration
Spectrum subtraction Quantitative analysis 1
AB <–> TR conversion Set up Quant 1 method
Straight line generation Signal -to-Noise ratio
Spectrum calculator Peak picking
Cut Quick identity test
Normalization Conformity test
Make compatible Spektum search
Convert spectra Peak search
Smooth Information search
Derivative Structure search
Frequency calibration Initialize library
Raman correction Store spectrum in library
Black body Library editor
Interferogram to spectrum conversion Library browser
Inverse FT Quantitative analysis 2
Post zerofilling Quant 2 analysis / file list
Fourier self-deconvolution Set up Quant 2 method
Symmetric FT Identity test
Kramers-Kronig Transformation Set up Identity test method
Extrapolation Cluster analysis
1/cm <–> µm Carbon Oxygen Analysis
Averaging 2D Correlation
Merging spectra ranges DMA
Atmospheric compensation Quick Compare Setup
Straylight correction Quick Compare
Noise generation Multi Evaluation Setup
Moving mean Multi Evaluation Test
Make monotone

Measurement Edit parameters
Repeated Measurement Information input
Rapid Scan TRS Set up Info mask
Direct command entry Structure import
Optic setup and Service Edit / create structure
Optics diagnostic Attach structure
Temperature control Instrument test
Motorised stage control Load file
Video assisted measurements Unload file
Time resolved step scan Undo changes
Chromatography Save file
Step scan modulation Save file as
Data extraction Send file
Add traces Send file to GRAMS
Assemble GC file Send file to InStep
Assemble Map file Delete data blocks
Print spectra External program
Setup JCAMP/OPUS conversion VisualBasic Script
Macro converter Load data point table
Run macro Scan OPUS files
Debug macro Find OPUS files
Macro editor Clone entry
Compile macro Clone original
Parameters
The main parameters which may be included in the parameter data blocks are
listed
Data Status Block

General
DPF = "Data Point Format"
NPT = "Number of Data Points"
FXV = "Frequency of First Point"
LXV = "Frequency of Last Point"
CSF = "Y - Scaling Factor"
MXY = "Y - Maximum"
MNY = "Y - Minimum"
DXU = "X Units"
DYU = "Y Units"
DER = "Derivative"

QS1 = "Derivative"
SMO = "Smoothing points for der."
QS0 = "Smoothing points"
DAT = "Date of Measurement"
TIM = "Time of Measurement"
XTX = "X - Axis Label"
YTX = "Y - Axis Label"
ZTX = "Z Axis Label"
XAF = "X axis factor"
YAF = "Y axis factor"
ZAF = "Z axis factor"
GSQ = "GS Base Quality"
Mapping
AOX = "Map Origin X"
AOY = "Map Origin Y"
DDX = "Map Delta X"
DDY = "Map Delta Y"
NPX = "Map Points in X"
NPY = "Map Points in Y"
S/N
NF1 = "First S/N Frequency Limit"
NF2 = "Second S/N Frequency Limit"
SN1 = "S/N (RMS)"
SN2 = "S/N (Peak-to-Peak)"
SN3 = "Max. Ordinate in S/N region"
SN4 = "Min. Ordinate in S/N region"
SNF = "S/N Flags"
Frequency calibration
MWC = "Mult. for Freq.Calib"
AWC = "Add for Freq.Calib"
Search
HQU = "Hit Quality"
COM = "Compound Name"
Display
DST = "Display text"
Instrument Block
General
DPH = "Demod. Phase (Degrees)"
MOF = "Modulation Frequency"
NLA = "NL Alpha"
NLB = "NL Beta"
HFL = "High Folding Limit"
LFL = "Low Folding Limit"

DFR = "Digital Filter Reduction"
DFC = "Number of Filter Coef."
HFF = "Digital Filter HFL"
LFF = "Digital Filter LFL"
ASG = "Actual Signal Gain"
ARG = "Actual Ref. Signal Gain"
ALF = "Actual Low Pass Filter"
AHF = "Actual High Pass Filter"
ASS = "Number of Sample Scans"
ARS = "Number of Background Scans"
GFW = "Number of Good FW Scans"
GBW = "Number of Good BW Scans"
BFW = "Number of Bad FW Scans"
BBW = "Number of Bad BW Scans"
DUR = "Scan time (sec)"
RSN = "Running Sample Number"
PKA = "Peak Amplitude"
PKL = "Peak Location"
PRA = "Backward Peak Amplitude"
PRL = "Backward Peak Location"
SSM = "Sample Spacing Multiplicator"
SSP = "Sample Spacing Divisor"
SGP = "Switch Gain Position"
SGW = "Gain Switch Window"
INS = "Instrument Type"
AQP and OPTIC special settings

ITF = "Interface Type for Optic"
SIM = "Simulation Mode"
DEB = "Debug Printer Mode"
LOG = "Logfile for Measurement"
ADR = "AQP Adress"
AD2 = "AQP2 Adress"
RMX = "Resolution Limit"
PLL = "Maximum PLL Setting"
FFT = "Maximum FT Size in K's"
MXD = "Maximum ADC Sate in Hz"
FOC = "Focal Length"
ABP = "Absolute Peak Pos in Laser*2"
ABP = "Absolute Peak Pos"
LWN = "Laser Wavenumber"
RLW = "Raman Laser Wavenumber"
RLP = "Raman Laser Power in mW"
RDY = "Ready Check"
RC0 = "Raman Background Corrected"
RC1 = "Raman Scattering Corrected"
SRT = "Start time (sec)"
ERT = "End time (sec)"
MAX = "X Measurement Position"
MAY = "Y Measurement Position"
AN1 = "Analog Signal 1"
AN2 = "Analog Signal 2"

Acquisition Block
General
CH2 = "Channel 2"
SGN = "Signal Gain, Sample"
SG2 = "Signal Gain, Sample"
RGN = "Signal Gain, Background"
RG2 = "Signal Gain, Background"
GSW = "Gain Switch Window"
GSG = "Gain Switch Gain"
NSS = "Sample Scans"
NSR = "Background Scans"
REP = "Repeat Count"
DLR = "Delay Between Repeats in Sec."
MIN = "Sample Meas. Duration in Min."
MIR = "Background Meas. Duration in Min."
SOS = "Scantime or Scans"
SOT = "Sample Scans or Time"
STR = "BG Scans or Time"
COR = "Correlation Test Mode"
DLY = "Stabilization Delay"
DEL = "Delay Before Measurement"
HFW = "Wanted High Frequency Limit"
LFW = "Wanted Low Frequency Limit"
RES = "Resolution"
RE2 = "Resolution Ch.2"
TDL = "To do list"
PLF = "Result Spectrum"
SPO = "Sample Number"
RPO = "Background Number"
SPO = "Sample Number"
RPO = "Background Number"
Transient Recorder Parameters (nur OPUS-NT)

General
WTR = "Tr.Rec. Resolution"
WAS = "Tr.Rec. Slices"
WRC = "Tr.Rec. Repeat Count"
WTD = "Tr.Rec. trigger Delay in points"
WPD = "Tr.Rec. Stab. Delay after Stepping"
WXP = "Tr.Rec. Trigger Mode"
WSS = "Tr.Rec. Sampling Source"
W2W = "Tr.Rec. Channel 2 Weighting"
WXD = "Tr.Rec. Experiment Delay"
WDV = "Transient Recorder"
WIR = "Tr.Rec. Input Range"
WTH = "Tr.Rec. Weighting Threshold"

TRS
TRR = "TRS Resolution in micro sec"
TRS = "TRS Slices"
TRC = "TRS Repeat Count"
TRD = "TRS Exp Delay in msec"
TRP = "TRS Positioning Delay"
TRM = "TRS Experiment Trigger Mode"
TRX = "TRS Sampling Source"
Interleaved TRS
ITS = "Interleaved Time Slices"
ISP = "Interleave Time Res. æsec"
IDL = "Interleave Trigger Delay æsec"
ITR = "Max. Exp. Trigger Rate Hz"
Step Scan
STD = "Step Scan Pos. Delay in msec"
STC = "Step Scan Coadd Count"
SMX = "Multiplexer positions"
SMD = "Modulation (0=OFF 1=MOD 2=MOD-DEMOD
4=OLD PHASE 8=AMPL )"
SMA = "Scanner Modulation Amplitude"
SMF = "Scanner Modulation Frequency"
AMF = "Ampl. Modulation Frequency"
ADA = "Ampl. Demodulation Angle"
PDA = "Phase Demodulation Angle"
Chrom
CIN = "Chrom Integrate Trace"
CIM = "Chrom Integration Method"
CDT = "Chrom Display Trace"
CDS = "Chrom Display Spectrum"
CTM = "Chrom Start Trigger Mode"
CSV = "Chrom Save Mode"
CSV = "Chrom Save Mode"
CTL = "Chrom Trigger Level"
GSS = "Gram Schmidt Size"
GSO = "Gram Schmidt Offset"
GSP = "Gram Schmidt Points"
CLD = "Limit Run Duration"
CMD = "Max Run Duration"
Map
MLS = "Map XY List"
MPO = "Map Port (com 1...n)"
MSH = "Map Shape (1..6)"

OS/2 Specific
MDV = "Map Device"
MOX = "Map Origin X"
MOY = "Map Origin Y"
MDX = "Map Sample Dim. X"
MDY = "Map Sample Dim. Y"
MSX = "Map Spacing X"
MSY = "Map Spacing Y"
MGX = "Map Gram Schmidt X Base"
MGY = "Map Gram Schmidt Y Base"
NT Specific
NDV = "Map Device"
NOX = "Map Origin X"
NOY = "Map Origin Y"
NSX = "Map Spacing X"
NSY = "Map Spacing Y"
NGX = "Map Gram Schmidt X Base"
NGY = "Map Gram Schmidt Y Base"
MEX = "Map Measurement Experiment"
OS2 and NT
MUN = "Map units"
MPX = "Map # Pos X"
MPY = "Map # Pos Y"
MSS = "Map Save Spectra"
MCI = "Map Compute Integrals"
MIM = "Map Integration Method"
MCM = "Map Macro"
MEM = "Map Evaluation Macro"
MSV = "Map Save Video"
MVM = "Map Video Method"
MRL = "Map Relative Origin"
MGT = "Map Gram Schmidt"
MGS = "Map Gram Schmidt Size"
MGO = "Map Gram Schmidt Offset"
MGP = "Map Gram Schmidt Points"
Display
MXS = "Meas x-Startpoint Display"
MXE = "Meas x-Endpoint Display"
MYS = "Meas y-Minimum Display"
MYE = "Meas y-Maximum Display"
MDM = "Meas Display Mode"
MDP = "Meas Display Product"
Display Channel2
XS2 = "Meas2 x-Startpoint Display"
XE2 = "Meas2 x-Endpoint Display"
YS2 = "Meas2 y-Minimum Display"
YE2 = "Meas2 y-Maximum Display"

FT Parameter
AF2 = "Apodization Function"
HQ2 = "End Frequency Limit for File"
LQ2 = "Start Frequency Limit for File"
PH2 = "Phase Correction Mode"
SP2 = "Stored Phase Mode"
ZF2 = "Zero Filling Factor"
APF = "Apodization Function"
HFQ = "End Frequency Limit for File"
LFQ = "Start Frequency Limit for File"
PHZ = "Phase Correction Mode"
PHR = "Phase Resolution"
NLI = "Non Linearity Correction"
NL2 = "Non Linearity Correction"
DIG = "Digital Filter"
DI2 = "Digital Filter"
SPZ = "Stored Phase Mode"
ZFF = "Zero Filling Factor"
Optic Parameter
IRS = "Iris Aperture (micron)"
UNI = "Command string for UNI"
APT = "Aperture Setting"
AP2 = "Aperture Setting"
AP2 = "Aperture Setting"
BMS = "Beamsplitter Setting"
DTC = "Detector Setting"
DT2 = "Detector Setting"
OPF = "Optical Filter Setting"
OPF = "Optical Filter Setting"
PGN = "Preamplifier Gain"
PGN = "Preamplifier Gain"
CHN = "Measurement Channel"
DMX = "Multiplexed Data"
ADC = "Ext. Analog Signals"
SON = "External Synchronisation"
SRC = "Source Setting"
VEL = "Scanner Velocity"
HPF = "High Pass Filter"
LPF = "Low Pass Filter"
SRL = "Raman Laser Power(mW)"
RFL = "Raman Flags"
POL = "Polarizer"
Sample Origin
SNM = "Sample Name"
SFM = "Sample Form"
CNM = "Operator Name"
HIS = "History of Last Operation"

PTH = "Measurement Path"
EXP = "Experiment"
PAT = "Path of File"
NAM = "Filename"
NA2 = "Ch. 2 Filename"
ATX = "Annotation Text"
XPP = "Experiment Path"
RAT = "TRS Method name"
CPR = "Copyright message"
Additional Information
OPUS Macro Language

For further details on the OPUS macro language, refer to the OPUS
Programming manual.
Additional Commands in the Evaluate Menu

Depending on your requirements you can add additional evalution modules to
OPUS. As these evaluation modules may be very complex they are documented
in separate manuals.
List of File Name Extensions
The following list includes the OPUS file name extensions. This list is by no
means complete and will be permanently extended. File name extensions used
in OPUS-OS/2 are only listed if they are also used in OPUS-NT.
Extension Used Bya Description

.CLA X Cluster analysis
.CLG N Scan/find OPUS file
.CON X Conformity test
.DAT N Pirouette file, used by InStep software
.DX X JCAMP file, also DX1, DX2...
.INT X Integration method
.MAC O Macro file
.MTB N Macro file
.MTD X Library method
.MTX N Macro file

Extension Used Bya Description
.NTI N Optical bench configuration file
.OWS N OPUS workspace
.PCT X Parameter correlation table used for JCAMP-DX
.PLE N Printing template
.PLT O Printing template
.Q1 X QUANT 1 method
.Q2 X QUANT 2 method
.QCM N Quick compare method
.RED N OPUS help file
.S01 X Spectrum library, also S02, S03...
.SPC N GALACTIC spectrum library
.TXD X Information mask
.XPM X Experiment file
.TRS N TRS Experiment
.QT N Quality Test
.0 X OPUS file (any numerical extension)
a. O: used by OPUS-OS/2 N: used by OPUS X: used by both programs

Index Diagnostic Functions 73
Dialog Boxes 5
Display
Menu 253
Numerics Settings 371
21CFR11 Rights 372 Display Settings 14
Drag & Drop 5
A
E
Abort Task 80
Absorbance Spectra 123 Edit
Add Comment 32 Menu 41
Administrator Rights 361 Evaluate
Advanced Measurement 75, 93 Menu 177
Aperture Motor 74 Export Options 72
AQP 97 External Program 28
Rebooting 382
F
Atmospheric Compensation 160
ATR Spectrum 123 File
Attach Structure 50 Creating New Info Block 45
Auto Align 91 Exporting 27
Averaging 155 Finding 30
Format 25
B Load 6
Band Maximum 211 Menu 23
Baseline Correction 106 Saving 24
Interactive Mode 106 Select File Tab 7
Black Body 131 Sending 27
Browser 57 Sending by E-mail 26
Browser Window 8 Undo Changes 24
Unload 24
C Flaps Motor 74
Fourier Transformation 140
Calibration Filter Motor 74 Frequency Calibration 127
Channel Motor 74 Frequency Limits
Check Signal 88 Selecting 18
Clone Entry 10, 31 Frequency Range
Clone Original 10, 31 Add Region 14
Correlation Mode 85
Cut 118 G
D GRAMS 27, 72
Data Block 9, 28 H
Data Blocks 385
Data Point Table 25, 28 H2O/CO2 Compensation 162
Datablock High Pass Filter 84
Quick Compare 245
I
TRC 243
Derivative 126 Icon 63
Detector Motor 74 Information Block
Printing 45 Advanced Settings 81
Information Input 43 Display 86
Text Definition 44 Optics Parameter 82
Information Mask 43, 46 Menu
InStep 27 Configuration 369
Instrument Test Molfile Format 49
Channel Setting 376 Motor Status 74
Integration 185 Moving Mean 173
Interactive Method Setup 191 Multi Evaluation 225
Integration Method 188 Report 237
Interferogram Setup 225
Double Sided 85 Test 235
Fast Return 85
Forward/Backward 85 N
Single Sided 85, 135 New 38
Internal Background 167 Noise Generation 172
Interpolation 121, 212 Normalization 119
Min/Max 120
J Offset Correction 120
JCAMP 25 Vector 120
JCAMP/OPUS Conversion 354 Number of Time Slices 101
K O
Kramers-Kronig Transformation 145 Open 38
Kubelka-Munk 122 Optical Bench 66
Optics
L Setup 65
Library 43 Service 73
Load Background 88 Optics Diagnostic 102
Load Spectrum OQ Test
Parameter 7 Absorbance Accuracy 326
Low Pass Filter 84 Alignment 329
Energy Distribution 325
M Linearity 329
Reproducibility 329
Macro 281 Resolution 323
Conversion 283 Scan Time 327
Debugging 283 Sensitivity 323
Editing 284 Water Vapor 327
Make Compatible 120 Wavenumber Accuracy 325
Reduce Resolution 121 Overview Window 13
Make Monotone 175 OVP
Manipulate Accessory Manager 334, 335
Menu 105 Adding New Test Channels 343
Maximal Compression Factor 152 AUTOOVP VB-Script 333
Maximum Experiment Repeat Rate 101 Database Installation 289
Measure Databases 345
Menu 65 Default Measurment Experiment 290
Measurement General 287
Acquisition Parameters 83
Installation 288 Workspace 263
Instrument Status Indicators 347 Plot Layout Editor 261
Instrument Type 294 Polarizer Motor 74
Laser Wave Number 298 PQ Test
Measurement Configuration 294 100% Line Deviation 314
Non-Ethernet Based Instuments 351 Energy 315
OQ Test Protocol 319, 320 Interferogram Peak Amplitude 315
OQ Test Protocol Setup 345 S/N Ratio 313
OQ Tests 323 X-Axis Frequency Calibration 316
PQ Test Protocol 310, 311 Y-Axis Reproducibility 318
PQ Test Protocol Setup 345 Print 255
PQ Tests 313 Preview 38, 257
Program Modules 345 Setup 39, 279
Setup 290, 291 Spectra 256
Status Light Setup 347
Test Channel Configuration 300 Q
Test Protocol Wizard 307 Quality Test 220
Trends Module 330 QUANT 1 192
Unattended Mode 332 Add Component 193
Validation Measurement 305 Analysis 202
Calibration 192
P Calibration Function 197
Paek Search Calibration Result 198
Mid Between Min./Max. 139 Calibration Set 197
Page Backward 254 Fit vs True 199
Page Forward 254 Remove Selected Spectra 195
Peak Picking 206 Theory 203
Calculate Band Position 211 Quick Compare 238
Center Of Gravity 210 Correlation Coefficient 242
Peak Height 209, 210 Results-Display 244, 245
Sensitivity 206 Setup 239
Theory 212 Theory 242
Peak Search Quick Identity Test 216
Absolute Largest Value 139
Maximum 139 R
Mid Between Largest Two 139 Raman Correction 130
Minimum 139 Reference Spectrum 130
No Peak Search 139 Raman Experiments 70
Take From Stored Phase 139 Raman Measurement 92
Peak to Peak 204 Raman Spectrum 124
Phase Correction 86, 137 Rapid Scan
PLE Comment 98
Browser 261 End Loop 98
Displaying A Spectrum 269 Measure N Scans 99
Properties 270 Measure NSS Scans 99
Spectral Frame Properties 271 Message Box 98
Table Properties 275 Optic Command 98
Text Properties 277 Reset Time Base 98
Toolbar 263 Set Buffer 98
Set Output “High” 99 Converting 113
Set Output “Low” 99 Subtraction 110
Split Double-Sided Interferogram 100 Spectrum Calculator 116
Split Forward/Backward Interferogram Spectrum Conversion
99 Raman Spectrum 124
Start Loop 98 Single-Channel Spectra 124
Use buffer 1 As Background 99 Spectrum Search 246
Wait Input “High” 98 Spectrum Window 12
Wait Input “Low” 99 Add Annotation 14
Waiting 98 Axes 42
Rapid Scan Time-Resolved Measurements Change Color 14
96 Display 253
Reflectance Spectrum 123 Display Limits 15
Registered Window 59 New 16, 59
Repeated Measurements 95 Properties 14
Report Block 17 Remove From Display 14
Report Window 16, 59, 186 Status Bar 57
Root Mean Square 204 Stepper Motor 74, 90
Routine Measurement 75 Stop Task 80
Rubber Band 108 Straylight Correction 166
Structure
S Creating 49
Sample Changer Motor 74 Editing 49
Sample Parameters 41 New Structure File 49
Savitzky-Golay Algorithm 124, 126, 210 Scaling Factor 50
Scattering Correction 108 Subtraction
Search Data Block 113
Add Libraries 250
T
Algorithm 248
Minimum Hit Quality 248 Task Window 80
Remove Libraries 250 Temperature Control 103
Report 250 Extended Commands 104
Select Library 249 Time Resolution 101
Sensitivity 248 Time-Resolved Measurements 96
Setup Toolbar 21, 55
Menu 353 Commands 56
Shortcuts 5 Configuration 367
Signal-to-Noise Ratio 85, 203 Customizing 55
Fit Parabola 204 New 55
Smooth 124 Tooltip 368
smooth Trigger Delay 101
savitzky-Golay 124
Smoothing 210 U
Source Motor 74 User Macro List
Spectra Color Setting 364
Color Palette 375 User Password
Setting 374 Changing 363
Spectrum User Records
Conversion 122 Settings 356
User Settings 371
USERMAC.LST File 366
V
Vector Normalization 218
View
Menu 55
VisualBasic Scripts 28
W
Window
3D 18
Allow Docking 62
Cascading 61, 253
Crosshair 13
Floating In Main Window 62
Hiding 62
Lock 13
Menu 59
Resize 13
Scaling 254
Tile 61
Zooming 13, 253
Workspace 38
X
XPM Files 378
Z
Zerofilling 135, 140
Zooming 254

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Spectroscopic Software

To install OPUS, insert the OPUS installation CD into your CD drive.

Figure 1: Windows start menu

Bruker Optik GmbH OPUS Reference Manual 1

Figure 2: OPUS Login dialog

2 OPUS Reference Manual Bruker Optik GmbH

Click on OK to open the OPUS user interface. The interface appearance

Bruker Optik GmbH OPUS Reference Manual 3

Figure 4: OPUS user interface

4 OPUS Reference Manual Bruker Optik GmbH

Figure 5: Example of a dialog box with two tabs

Bruker Optik GmbH OPUS Reference Manual 5

2.1 Loading and Selecting a File

Load Spectrum Dialog Box

• use the Load File command from the File menu,

(a) (b) (c) (d) (e) (f) (g)

(h) (i) (j) (k)

6 OPUS Reference Manual Bruker Optik GmbH

j) It is also possible to load spectra of different formats, e.g. JCAMP-DX or GRAMS.SPC

Select Files Option

Figure 7: Example of Select Files option

Bruker Optik GmbH OPUS Reference Manual 7

Figure 8: Convert Spectra – parameter mismatch

2.2 OPUS Browser Window

8 OPUS Reference Manual Bruker Optik GmbH

Figure 9: OPUS browser window displayed as drop-down list

(a) (b) (c)

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If you select one file using the left

Additionally selected by using

Figure 11: Select files

If you right click on a file name, a pop-up menu opens.

Figure 12: Pop-Up menu for file manipulation

10 OPUS Reference Manual Bruker Optik GmbH

File has been

Figure 13: Pop-Up menu for spectrum manipulation

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2.3 Spectrum Window

Lock Window Size

Figure 14: Spectrum and overview window showing lock button

12 OPUS Reference Manual Bruker Optik GmbH

Figure 15: Pop-up menu within the spectrum window

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Properties opens the Display Settings dialog box.

Figure 16: Display Settings – Display Limits tab

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Figure 17: Display Settings – Axes tab

Figure 18: Display Settings – General tab

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2.4 Report Window

Figure 19: Report Window

16 OPUS Reference Manual Bruker Optik GmbH

The information included in the report block is displayed in form of a directory

Figure 20: Report Window - View Properties

2.5 Datafile History

A special type of report window is Datafile History. Any manipulation made in

Bruker Optik GmbH OPUS Reference Manual 17

History Datafile history History list

Figure 21: Report Window showing datafile history