analySIS

isp
Image
Sequence
Processing
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 ride

Image Sequence Processing 2

isp
isp and mFIP ........................................................................2
Microscope Hardware Requirements ..................................2
Time-lapse experiments ......................................................3

Menu Description 3

DEFINE… ..................................................................................4
General buttons ...................................................................5
Sequence .............................................................................6
Info .......................................................................................7
Flow .....................................................................................7
Acquisition Modes ................................................................9
Settings ..............................................................................12
Macro .................................................................................13
ANIMATE… .............................................................................14
Sequence and database selection .........................16
Defining a time range .............................................17
Playback controls ...................................................18
EXPORT TO AVI… .................................................................19
Eisp0703
 ISP • Image Sequence Processing

ISP

Image Sequence Processing

Use the ISP add-in to make time-lapse measurements.

The Image Sequence Processing add-in enables you to

• acquire a series of single images, stacks or mFIP images in predefined
intervals. If you are appropriately equipped, it is possible to automati-
cally operate the entire procedure.
• store these series in a database or a directory on the hard disk. All data
with regards to the structure of image sequences are saved as well.
• playback these series in an animated form, view a number of them si-
multaneously and at the same time to observe them in detailed zoom.
• export the series in the form of AVI videos, thus making them accessi-
ble to users who do not have access to software required for the cre-
ation of their own image sequences.

isp and mFIP

isp displays special strengths in cooperation with the mFIP add-in for fluorescent microscopy.

The mFIP add-in enables you to make acquisitions using multiple colored
samples. A single image is created for each color. The single images can
then be individually processed and superimposed. isp expands the spec-
trum of possibilities with regards to time sequences.

Microscope Hardware Requirements

The possibilities which isp offers you depend on your system's microscope hardware equipment.

Stage A motorized stage is required for automatic mobilization. Stages which are
able to move in X and Y directions enable you to make automatic acquisi-
tions on various positions of the sample. The controlling of the stage as well
2

as the definition of positions and paths can be done via the stage manager
add-in. The stage manager also enables you to interactively define complex
stage paths. These stage paths can be saved and then used by isp. Expla-
nations and descriptions of the stage manager can be found in the separate
documentation provided with that add-in.
Z Drive An automatic Z drive expands the possibilities of isp. Firstly, the stage man-
ager enables you to make corrections on non-exact horizontal specimen
surfaces. Secondly, you have the possibility of acquiring a stack in Z direc-
tion and automatically focusing on single images. Z corrections for the indi-
vidual fluorescences are possible within the scope of the mFIP add-in.
Motorized Microscope When using a motorized microscope, isp can take over the control of the mi-
croscope.
 Time-lapse experiments

Time-lapse experiments
Time-lapse acquisition isp enables you to carry out time-lapse acquisition of image sequences. The
number of frames in a sequence and the time lapses between them can be
defined at will. Various camera settings and input-channel settings can be
separately utilized.
Process Control isp offers an automatic process control. All process times are clearly shown
in a window. A memory check ensures that you are warned if there is inad-
equate memory storage space available.
Stage Control When connected to an X/Y(/Z)-motorized stage, isp is able to go to various
positions and acquire image sequences in cycles. Hence, user-definable im-
age sequences can be done of various points on the specimen and can be
repeated based on intervals which can be preset. Various camera and mo-
torized stage settings can be selected.
Motorized Microscopes isp can also communicate with the microscope via diverse remote interfac-
es. While doing this, each image sequence can use different illumination
methods and filter or objective settings.
Fluorescent Acquisition isp reads the data from the analySIS add-in mFIP. Hence, image sequenc-
es can be recorded which then can be viewed and analyzed as a composi-
tion of fluorescent and bright field images.
Animation All sequences can be saved and queried within a database and subsequent-
ly animated. The user is provided with an animation studio for playing and
editing sequences. Acquisition times are shown in the overlay. Views can be
duplicated and sequences can be observed simultaneously.
AVI-Export The individual sequences can be exported as AVI videos and thus can be
observed outside of isp. isp does this by offering all compression procedures
installed on the computer for exporting.

Menu Description
After installing the add-in, the Image Sequence Processing submenu locat-
ed in the Images menu is available. It is located below the Image Series
command. The add-in has three commands.

How to... You must execute the following steps in order to activate the add-in if your
current configuration does not offer the commands of the isp add-in:
1) Open the Special menu.
2) Select the Add-In-Manager... command.
" The Add-In-Manager dialog box is opened.
3) Select the Image Sequence Processing check box located in the Avail-
able add-ins list.
4) Click on the Close button.
 ISP • Define…

You can also select two of the isp commands via the ISP button bar:

Define p. 4
Animate p. 14

How to... This is how you show the ISP button bar if it is not being displayed:
1) Open the Special menu.
2) Select the Edit Button Bars... command.
" The Edit Button Bars dialog box is opened.
3) Select the ISP check box located in the Button bars list.
4) Close the dialog box by clicking on OK.

Define…
Use this command to define image sequences and to control acquisition of them.

Process is the term used for a complete unit edited using the isp add-in. An
image sequence is the result of a process. An entire process is in turn divid-
ed up into three types of building blocks: cycle, sequence and acquisition.
Definition Acquisition refers to an acquisition procedure executed within a sequence.
This acquisition process can include the acquisition of a single image, a se-
ries of single images or a stack. If the mFIP add-in is installed as well, the
acquisition procedure may conducted using mFip for acquisition.
Definition A sequence combines the parameters of the acquisition and the settings of
the stage and the microscope. The interplay of acquisition and sequence en-
ables the use of all possible parts of the system which are controlled by the
program for the creation of the image series. A sequence contains an acqui-
sition (see above) and is an integral part of the cycle.
Definition A cycle controls the chronological aspect of acquisition. It contains at least
one sequence. The sequence(s) of a cycle can be started immediately or at
4

a certain point in time and may be conducted once or as often as desired.

The sketch illustrates the
structure of an image se- Cycle 11
Zyklus Cycle 22
Zyklus
quence. The individual cy-
cles are identical.

S1 S2 S3 S1 S2 S3

A1 A2 A3 A1 A2 A3

Cycle The chronological structure of an image series is primarily defined by the cy-
cle. You determine how often a cycle is to run, and if the first cycle is to begin
immediately or at a later defined time.
 General buttons

Define Image Sequence Processing dialog box

The Define Image Se-
quence Processing dialog
box contains 4 tabs and the
Sequence area in which the
individual sequences of a
process are defined.
This area is shown/hidden
via the Details button.
The buttons in the bottom
section of the dialog box re-
main available no matter
what tab you are on.

General buttons
The buttons located in the bottom section of the Define Image Sequence Processing dialog box are lo-
cated on every tab.

OK Click on OK to close the dialog box. If you have entered a name into the Pro-

5
cess field located on the Info tab, the current parameters are saved and are
automatically reloaded the next time the Define… command is used.
File… Click on the File… button to save an ISP process. The ISP save input/output
dialog box is opened. A saved ISP file receives the file name extension .std
and is stored in the isp subdirectory within your analySIS directory. It con-
tains all of the settings of a process.
Use this command to permanently save ISP processes.
Details >> Click on the Details button to show/hide the Sequence group. The Sequence
<< Details group is for the definition and organization of the individual sequences of a
process.
Start Click on the Start button to begin the process with all the current settings.
Available The Start button is available as soon as a name is entered into the Process
field located on the Info tab.
 ISP • Define…

Sequence
You organize the individual sequences of a process in the Sequence group.

Available If the Sequence group does not appear in the Define Image Sequence Pro-
cessing dialog box, make it appear by clicking on the Details >> button.
Sequences are organized using the button bar within this group.
Delete All Sequences,
Add Sequence
Delete Sequence
Preview
Read Device Settings

Delete All Click on the Delete All Sequences button to delete all the entries from the
Sequences Sequence group.
Add Sequence Click on the Add Sequence button to add a new sequence to the list of al-
ready existing sequences. To change the name of a sequence, select the
sequence and press [F2] or click on the sequence again (after a brief
pause).
Delete Click on the Delete Sequence button to delete the selected sequence.
Sequence
Preview Click on the Preview button to test the selected sequence with the settings
you assigned. This function is helpful, for example, to test the camera set-
tings for a sequence.
Read Device Click on the Read Device Settings button to adopt the current settings from
Settings the stage, camera and/or microscope to the selected sequence. The Read
Device Settings dialog box opens after clicking on this button.
6
 Info

Apply current settings The Apply current settings from group enables you to decide which device
from adjustments are to be adopted for the selected sequence. Only those devic-
es which can be controlled via the application are suggested.
Stage, Camera, Micro- Select one or any combination of the following check boxes - stage, camera
scope or microscope - to adopt the settings of the device in question.
Note If you click on the OK button, the current settings are adopted for the select-
ed sequence without any further inquiry.

Info
Use the Info tab to enter general information for the current process.

Process Enter a name of your choice for the current process in the Process field. If a
process name already exists, ISP automatically saves all of the process pa-
rameters and makes them available the time this command is used.
Note It is necessary to enter a name into the Process field. The Start button is only
available if the Process field has an entry.

Description Enter any description of the process into the Description field.

7
 ISP • Define…

Flow
The Flow tab is for making the main settings for controlling the process and thus control of acquisition as
well.

Start acquisition Determine the process starting time in the Start acquisition group.
Immediately Select the Immediately option to immediately begin acquisition by clicking
on the Start button.
At Select the At option to begin acquisition at a point in time of your choice. En-
ter a time of your choice into the box. isp uses the Windows Timer to deter-
mine the time.
Cycles The Cycles group enables you to determine how often a sequence is to be
carried out and how much time is to be left beween two cycle starts.
Number Enter how often the defined cycle is to be carried out into the Number box.
8

Repeat every Enter how much time there is to be between two cycle starts into the Repeat
every box. The value will generally be limited by the length of the acquisition
processes which are carried out within the cycle. If your defined cycle re-
quires more time than alloted by the entry in the Repeat every box, isp car-
ries out the acquisitions as fast as possible.
Acquisition The Acquisition group enables you to determine which acquisition method
is to be used in the process. The methods at your disposal depend on the
add-in's and settings of your system. Click on the Define… button after hav-
ing selected the desired mode from the picklist.
Mode Select the desired acquisition time from the Mode picklist. An explanation of
each acquisition mode can be found in the Acquisition Modes section see p.
9.
Save image Enter whether or not you want to save the images acquired by isp directly
on the hard disk or if they should be saved to an analySIS database in the
Save image group.
Database Select the Database option to write the acquired image series to an analy-
SIS database.
 Acquisition Modes

Folder Select the Folder option to write the image files directly onto the hard disk
drive.
Click on the … button to either open the Select Database dialog box or the
Select Folder dialog box. Select the database or folder which you want to
use to save the images in this dialog box.

Database fields used with ISP.

ISP uses the database for saving data concerning the process of acquisition
which is unique to ISP acquisitions. This is why ISP uses 12 specific data-
base fields and will create them if they are not available in existing databas-
es. Have a look at the following table for specifics on these fields:
Field Name Field Meaning
Type
ISP Name Text Process Name
ISP Sequence Text Sequence Name
ISP Cycle Integer Sequential Cycle Number
ISP Stage Sample Integer
ISP Stage Cluster Integer Parameter used by isp for organizing in-
dividual images. These values are auto-
ISP Stage Frame Integer matically assigned
ISP Image Frame Integer
ISP Cycle Count Integer Sequential Cycle Number
ISP StagePos Count Integer Parameter used by isp for organizing in-
ISP Frame Count Integer dividual images. These values are auto-
matically assigned
ISP Process ID Text Definite identification of the process. The
ISP Process ID is automatically assigned
by the application.
ISP Stack Count Integer Parameter used by isp for organizing in-
dividual images. The value is automati-
cally assigned.

9
Acquisition Modes
ISP executes at least one acquisition for each sequence. This can be either
a single image, a stack or an mFIP acquisition. Each of these three modes
has its own dialog box for defining acquisition parameters. The respective
dialog box can be accessed by clicking on the appropriate mode in the Mode
field and then clicking on the Define… button.

Frame
Select the Frame mode to acquire cyclical single images or a series of single images.

Define… Click on the Define... button to open the Define Frames dialog box.
 ISP • Define…

Number Enter the desired number of frames per sequence into the Number field. A
number greater than 1 means that a series of that number of images will be
acquired in each sequence.
Time lapse Enter the desired time lapse between the single images into the Time lapse
field. Time lapse is the length of time between consecutive acquisition starts
and thus includes the duration of the acquisition itself. The time lapse's lower
limit is determined by acquisition length - exposure time plus read out time.
Note If the program has not yet read back the camera's set exposure time, you
cannot reduce the time lapse. In this case, close the Define Frames dialog
box and click on the Read Device Settings button located in the Sequence
group. This means that the camera settings will be read and the lowest value
for the possible time lapse is accordingly reduced. Then you will be able to
adjust the Time lapse.
Autofocus Select the Autofocus check box to enable a software autofocus. This auto-
focus is available for every microscope which is equipped with a Z drive
which can be software controlled.
Define Click on the Define button to define the autofocus. The use of the autofocus
depends on both the microscope and the stage used.

mFIP
Select the mFIP mode to use the add-in's multicolor Fluorescence Information Processing (mFIP) acqui-
sition procedure.

Available The mFIP mode is available if the mFIP add-in has been installed.
10

Note In some cases the mFIP add-in is not included in your program package. In
this case, mFIP can be acquired as a separate add-in.

Define… Click on the Define... button to open the Define mFIP dialog box.

Standard The Standard entry appears in both the Configuration 'Acquire' list and the
Configuration 'Merge' list. Standard refers to the settings you made the last
time you used mFIP.
 Acquisition Modes

Configuration 'Acquire' Select an acquisition defined via mFIP from the Configuration 'Acquire' list.
To do this, use the Images > mFIP > Acquire Fluorescent Images… com-
mand to define and save the results as a file.
Configuration 'Merge' Select a merge of fluorescent images created using mFIP from the Config-
uration ’Merge’ list. To do this, use the Images > mFIP > Merge Fluorescent
Images… command to define and save the results as a file.

Stack
Select the Stack mode to create a stack of images acquired at various Z values.

Available The Stack mode is only available if your microscope is equipped with a mo-
torized Z drive which can be software controlled.
Define… Click on the Define... button to open the Define Stack dialog box.

isp offers two procedures for the acquisition of stacks with different applica-
tion areas: the relative and absolute move range.
Move Range Absolute Moving the range absolutely is when a Z range is determined which is valid
for the entire sample and is used for each sequence. The single images in
the stack are acquired at equidistant points within this range.
How to... How to define stacks for the absolute movement method:

11
1) Select the Move range absolute check box.
" The Middle button is now unavailable.
2) Move the stage to the top edge of the desired range.
3) Click on the Top button.
4) Move the stage to the lower edge of the desired range.
5) Click on the Bottom button.
Relative Move When moving the range relatively, only a small Z range based around a ref-
erence point will be travelled through for each sequence. The reference
point corresponds to the Z setting made for that sequence. Starting at the
reference point, a defined distance will be travelled - upwards and down-
wards. The individual acquisitions of the stack are acquired at equidistant
positions within this range. This procedure is suitable for investigating sep-
arate sample areas where similar structures occur at different respective Z
positions.
How to... Here is how you define the stack for moving the range relatively:
1) Clear the Move range absolute check box.
" The Middle button is now available.
 ISP • Define…

2) Now locate an area within the sample where the structure you are look-
ing for occurs.
3) Get the desired structure in focus.
4) Click on the Middle button to define this position as the reference.
5) Move the stage upwards to the upper limit of this structure and click on
the Top button.
6) Move the stage downwards to the lower limit of the structure and click
on the Bottom button.
Number of frames Enter the desired number of frames to be acquired per sequence into the
Number of frames field.

Settings
Define how any connected hardware components are to be used for the sequences on the Settings tab.

isp is able to automatically operate connected hardware components (motor

stage, camera, microscope). This tab is for organizing how these settings
are used and how individual settings are assigned to specific sequences.
12

Stage Assign a specific stage path to a specific process in the Stage group. To de-
fine a stage path, select the Stage > Stage Manager… command.
Path Select a stage path that has already been defined from the Path picklist. The
list contains all stage paths that have been defined and saved via the stage
manager. All positions of the stage path will be loaded and a sequence will
be generated for each position.
 Settings

New… Click on the New… button to define a new stage path. The New Stage Path
dialog box will be opened.

Name Enter any name of your choice for the stage path you are defining into the
Name field.
Available stage paths The Available stage paths contains all stage paths that have been defined
via the stage manager. Use the Available stage paths list to select a stage
path, generate a copy of that stage path and then alter it. To be able to do
this, the Copy selected stage path check box has to be selected.
Copy selected stage Select the Copy selected stage path check box to use an existing stage path
path as the basis for the new stage path you are defining. isp will make a copy of
the stage path selected in the Available stage paths list. The copy will have
the stage path's new name.
How to... How to define a new stage path:
1) Enter a name for the new stage path you are defining into the Name
field.
2) Disable the Copy selected stage path check box.
3) Click on the OK button.
" Any sequences that may be present will be deleted.
4) Click on the Add Sequence button.
" A new sequence will be added to the Sequence list and appear se-

13
lected.
5) Move the stage to the desired area of the sample, focus the image and
set the correct exposure time.
" Now all the parameters of this sequence have been defined.
6) Click on the Read Device Settings button.
" The Read Device Settings dialog box is opened.
7) Select the Stage check box in the Apply current settings from group.
" The current stage settings will now be used for the newly generated
sequence.
" You may choose to use the same camera and microscope settings
in this step as well.
8) Repeat steps 4 through 7 until you have defined the remaining posi-
tions of the stage path.
" The newly defined stage path will be saved under the name you've
given it. And the next time you use the Image > Image Sequence
Processing > Define… command, this stage path will appear as the
default.
 ISP • Define…

Control microscope Select the Control microscope illumination check box to have the illumina-
illumination tion of an automated microscope controlled. Having microscope illumination
controlled via isp keeps the illumination the sample is exposed to, to a min-
imum. A halogen lamp hooked up to the system will be switched off following
each sequence. It will be switched back on again just before the next se-
quence.

Macro
Use the Macro tab to define preprocessing and postprocessing steps which are to be executed before or
after each sequence, cycle or process.

Alongside the actual image acquisition, you may also define other automa-
tion steps for isp to conduct while it carries out a process.

Apply preprocessing Select the Apply preprocessing check box in the Process, Cycle and/or Se-
14

quence groups to activate preprocessing for the respective unit.

Apply postprocessing Select the Apply postprocessing check box in the Process, Cycle and/or Se-
quence groups to activate preprocessing for the respective unit.
Define Click on the Define… button to define the respective processing steps. The
Define Pre/Postprocessing dialog box will open.
 Animate…

Preprocessing steps / Enter the macro commands that you wish to have executed at this point in
Postprocessing steps the process into the Preprocessing steps or Postprocessing steps fields.
Execute Click on the Execute button to have a test run of the steps shown.
Delete Click on the Delete button to delete all steps defined until now.

Animate…
Use this command for viewing image series saved in a database.

When acquiring image series, the main point of interest is what activity takes
place within the sample - or within a specific area of the sample - over time.
The Animate… command within isp enables you to view this activity in mo-
tion. Image series are shown in action.
Select the Image > Image Sequence Processing > Animate… command to
open the Animate Image Sequence dialog box.

The Animate Image Sequence dialog box

The Animate Image Sequence dialog box has three sections containing dif-

15
ferent options.
 ISP • Animate…

Adjusting the Use the arrow buttons along the right border of the Animate Image Se-
dialog box quence dialog box to make adjustments to the appearance of the dialog box.
Clicking on buttons with an upwards-pointing arrow hides lower sections of
the dialog box. To show these sections once again, click on a button with a
downwards-pointing arrow.

Procedure
The Animate Image Sequence command is for displaying one or more se-
lected sequences that have been saved in a database. First of all, select a
database in the lowest section of the dialog box (sequence and database
selection). Then select one or more sequences from this database.
16

Then you may choose to define a specific time range within this sequence
in order to avoid having to look at uninteresting parts of the sequence. De-
fining and selecting a specific time range is done in the middle section of the
dialog box (defining a time range).
Now use the controls in the top section (playback controls) of the dialog box
to control playback of the sequence(s) selected.
 Animate…

In order to provide you with a clearer idea of how to use this Animate Image
Sequence dialog box, a more in-depth description of its three sections now

17
follows - from bottom to top.

Sequence and database selection

 ISP • Animate…

The sequence and database selection section is where you select the se-
quence(s) you wish to view animated. A maximum of 25 sequences may be
shown at one time. Only databases containing images acquired and saved
using isp may be used.
Database Click on the … button in the Database group to open the Select Database
dialog box. This dialog box is where you select the database or directory
where the acquired sequences have been saved to.
Available sequences The Available sequences list shows all sequences available within the data-
base selected. There are three columns for each sequence: the name of the
process in the Process column; the sequence name in the Sequence col-
umn; and then the No. of frames. Please note that the component sequenc-
es are shown and animated, not the superordinated process. If a process is
comprised of multiple sequences these will all be shown in the Available se-
quences list. To select a sequence you wish to view, select the correspond-
ing check box next to it.

Defining a time range

This section of the dialog box is where you select the sequence you wish to
view. You may also restrict what you view to a specific time segment and/or
image segment of the sequence selected.
Sequence picklist The sequence picklist shows all sequences you selected in the Available se-
quences list. In addition, it contains an entry called ’All sequences’. Select
the sequence you wish to view or select the All sequences entry to have all
18

sequences played back at the same time.

What will happen? Once you have selected a single sequence in the sequence picklist, the
Start of sequence and End of sequence groups will show the corresponding
date(s) and time(s). When you select the All sequences option, the Start of
sequence and End of sequence groups will not show any dates. The time
shown in the Start of sequence group will go to 00-00-00. The time in the
End of sequence group corresponds to the greatest length of time between
the first and the last images of the sequence selected. This means that all
sequences will start at 00-00-00 (a point in time). This 00-00-00 point in time
corresponds to the first acquisition made within each respective sequence.
During playback, time will be counted from this point onwards. Playback is
at a constant speed - not according to the specific time differences between
the various images. This means that the acquisition times of the individual
images are essentially just for determining the order in which images are
played back.
Create Detail Click on the Create Detail View button to generate a detailed view within the
View selected sequence. The viewport arrangement will be adjusted such that a
copy of the current image of the selected sequence is shown within the cur-
 Animate…

rent viewport. To create the detail view (also known as "detail zoom") adjust
the zoom level of this image to the desired magnification. A detail view of an
image shows the exact same time as its original image (contained within the
source sequence).
Use the Navigator within the viewport manager to define an image segment
interactively.
Delete All Detail Click on the Delete All Detail Views button to delete an existing detail view.
Views This button is only active when detail views have been created.
Define as Start Clicking on the Define as Start Time button defines the starting point of a
Time specific time segment (of a whole sequence) you wish to view. The acquisi-
tion date and time of the first image of this specific time segment is shown
in the Mark in group.
Define as Stop Click on the Define as Stop Time button to define the ending point of a spe-
Time cific time segment (of a whole sequence) you wish to view. The acquisition
date and time of the last image of this specific time segment is shown in the
Mark out group.
What will happen? As soon as you have defined either a starting point or an ending point of a
particular time segment, the sequence will only be played back within that
defined segment of time. A blue bar displayed behind the slider control rep-
resents the defined time segment. To view parts of the sequence not con-
tained within the defined time segment, use the slider control.
Reset Click on the Reset button to undo the time segment you have defined. Play-
back starting point and ending point will be reset to the first and last images
of the sequence.

Playback controls

This section offers you the controls for operating playback of sequence(s). 19
The controls in this section take into consideration all settings you have
made in the other sections of the Animate Image Sequence dialog box.
First Click on the First button to have the first image of the sequence displayed.
No automatic playback of the sequence will be initiated.
Previous Click on the Previous button to have the previous image within a sequence
or segment of the sequence displayed. No automatic playback of the se-
quence will be initiated.
Backward Click on the Backward button to have a sequence or segment of a sequence
played backwards. Playback will continue until you click on the Stop button.
Note Pressing the [Esc] key is not for stopping playback - the entire Animate Im-
age Sequence dialog box will be closed. When this happens, all your set-
tings will be lost.
Stop The Stop button is for ending playback of the sequence or sequence seg-
ment being shown. Playback will stop and the image where the sequence
was halted will continue to be shown.
 ISP • Export to AVI…

Forward Click on the Forward button to play a sequence or segment of a sequence.

Playback will continue until you click on the Stop button.
Note Pressing the [Esc] key is not for stopping playback - the entire Animate Im-
age Sequence dialog box will be closed. When this happens, all your set-
tings will be lost.
Next Click on the Next button to have the next image within a sequence or seg-
ment of the sequence displayed. No automatic playback of the sequence will
be initiated.
Last Click on the Last button to have the last image of a sequence or of a se-
quence segment displayed. No automatic playback of the sequence will be
initiated.
Frame To select from which frame (ie, image) of an image stack playback is to be-
gin, use the Frame field or its slider control.
The term "frame" used here is borrowed from the video/film technology field;
it refers to a single frame (ie, image) within a video or film sequence.
Delay Use the Delay slider control to slow down playback speed of a sequence or
sequence segment. The further to the right you move this slider control, the
slower playback will be; move it back to the left to speed playback up.
Auto reverse Select the Auto reverse check box to have playback automatically continue
in reverse once the end of the sequence or sequence segment is reached.
Disable the Auto reverse check box to have continuous forward playback. In
this case, once the final image of the sequence or sequence segment is
reached, playback will continue at the first image. When you have the se-
quence or sequence segment played in reverse, once the first image is
reached, playback will continue at the last image.

Export to AVI…
Use this command to generate a video file from an image sequence which can be viewed on any com-
puter.

You must have the isp add-in to be able to animate image sequences. The
Export to AVI… command enables you to generate video files that can be
20

viewed by virtually anyone - whether they have isp or not.

Select the Export to AVI… command in the Image > Image Sequence Pro-
cessing menu to open the Export to AVI dialog box.
 Export to AVI…

Database Select the database containing the sequences you wish to export in the Da-
tabase group. When you select the Export to AVI… command, the database
you last worked with will automatically be opened. Click on the … button to
browse for and select another database.
Available sequences The Available sequences list shows all sequences contained by the data-
base selected. Each sequence is listed according to the process name, the
sequence name and the number of frames it is comprised of. Select the
check box next to a sequence to select this sequence to be exported as an
AVI. If you would like to export more than one sequence, select their check
boxes and they will be exported one after the other.
Export… Click on the Export… button to initiate the export process for the se-
quence(s) selected. The Export [sequence] from ’[process]’ dialog box will
be opened.

Write to Enter the directory and file name you wish to save the video file under in the 21
Write to group.
Browse… Click on the Browse... button to open the Save AVI Movie as dialog box. This
dialog box is where you select a directory and enter the desired file name.
Start movie player after Select the Start movie player after writing check box to have the AVI file
writing played once exporting has been completed. To do this, the playback pro-
gram your computer uses for playing AVI files will be started.
Movie speed Select how fast you wish to have the file played in the Movie speed group.
Frames per second Enter the desired speed in frames per second in the Frames per second
field, or simply use the slider control to adjust the value. The range of avail-
able values is from 1 through 32.
Blending between The Blending between images group is where you can soften the transitions
images between single frames of the video file. Blending means that additional im-
age(s) are inserted between the video file's original frames. An additional
blending image - referred to as a blended frame - is calculated based on the
 ISP • Export to AVI…

two surrounding original frames of the video. Blended frame(s) thus serve
to 'soften' the transition between the two original frames. The more blended
frames inserted, the more gradual or 'softer' the transition will be.
Blended frames Enter the desired number of blended frames into the Blended frames field or
simply use the slider control to adjust the value. The range of available val-
ues is from 0 through 32.
Compression The Compression group is where you decide what kind of compression you
wish to use - if any. The current selection is shown in this group.
Change Click on the Change… button to select a different kind of compression. The
Change Compression dialog box will be opened.

Compress images Make sure the Compress images check box is selected so that compression
is activated.
Compressor model Select the desired compression type from the Compressor model list. The
range of compression types available to you on your PC depends upon the
operating system you have installed, among other things. This is why the list
of compression types available to you may differ from those shown here.
See the table below for an overview of the various compression models and
their respective properties.
Compressor model Description Algorithm
22

Cinepack codec by Ra- powerful compression, time consuming; provides vector quantization
dius high-quality results along with small file size;
Microsoft RLE processes 8- and 16-bit images; fast, lossless run-length encoding
compression; however, data amount is generally
not reduced too much;
Microsoft Video moderate compression; quite fast; Use this wide-
spread compressor to export your movie to an-
other computer as this compressor is very com-
mon; Produces 'stairs' in smooth color gradients;
Indeo® Video powerful compression, time consuming; provides discrete wavelet transformation
high-quality results along with small file size;
Settings… Click on the Settings... button to open the Compressor Configuration dialog
box.
Available The Settings command is only available if one of the following compressor
models has been selected: Cinepack codec by Radius, Microsoft Video 1 or
Indeo® Video 5.10.
 Export to AVI…

Compression quality The Compression quality field is where you indicate what level of quality you
desire the generated images to have. Or simply use the slider control here
to define the desired quality level. The available levels of Compression qual-
ity are between 0 (very poor quality) and 100 (very high quality).
Keyframes The Keyframes group is where you define whether or not and how many
keyframes are to be written into the video file. Keyframes are written loss-
lessly into the video file (ie, without being compressed) no matter what com-
pression model was selected. The compression applied following a key-
frame is always applied based on the keyframe. Using keyframes allows you
to prevent loss in quality over the entire duration of a video.
Enable keyframes Select the Enable keyframes check box to have keyframes written into the
AVI file.
Keyframes every … The Keyframes every … frames field is where you define how many frames
frames are to go between the inserted keyframes. The lower this number is, the
higher the quality of the video - but also the lesser the rate of compression.
Movie properties The Movie properties group provides you with an overview of what results
you can expect based on your current settings.
Total number of frames The total number of frames is the sum of the total number of frames in the
sequence (or sequence segment) plus the Blended frames setting.
Movie length The length of the video depends on the total number of frames plus the
Frames per second value selected.
Movie size The movie's size in pixels is dependent on acquisition. You may, however,
alter its size.

23
Change Size… Click on the Change Size… button to alter the framesize of the video. The
Set Movie Size dialog box will be opened.

Use custom size Select the Use custom size check box to be able to adjust the size just as
you like.
 ISP • Export to AVI…

Custom size The Custom size group is where you enter the desired frame size and select
an interpolation method. The Custom size group is only active when the Use
custom size check box has been selected.
Size Use the two Size fields to define the frame size desired. Select the Keep X/
Y ratio check box and when you enter a value for the one Size field, the other
one will automatically be adjusted accordingly.
Interpolation Select an interpolation method from the Interpolation list.
None Select the None entry from the Interpolation list if you do not want any inter-
polation applied in the alteration of frame size.
Bilinear Select the Bilinear entry to have bilinear interpolation used. Bilinear interpo-
lation provides transitional areas that are relatively smooth and does not re-
quire a whole lot of processing power.
Bicubic Select the Bicubic entry to have bicubic interpolation used. Bicubic interpo-
lation results in transitional areas that are very smooth but does require lots
of processing power. Bicubic interpolation is superior to bilinear interpola-
tion especially when frame size is altered significantly.
Keep X/Y ratio Select the Keep X/Y ratio check box to ensure that the proportions of the vid-
eo remain the same when frame size is altered. Keep in mind, that the con-
venient thing is when you select the Keep X/Y ratio check box, you only need
to fill out one of the Size fields.
24
 Index

Acquisition 4
Acquisition Modes 9
Activate Module 3, 11
Activating the module 11, 13

cycle 4

EFI
Activate Module 3
Fade in button bar 4

Frame 9

ISP
Activate Module 11

25
Activating the module 11, 13
Button bar 4

Menu Description 3
mFIP 10

sequence 4
Stack 10