Phyto PAM

Phytoplankton Analyzer
PHYTO-PAM
and
Phyto-Win
Software V 1.45
System Components
and
Principles of Operation
2.130 / 01.99
2. Edition: July 2003
phyto_4e.doc
 Heinz Walz GmbH, 2003
Heinz Walz GmbH • Eichenring 6 • 91090 Effeltrich • Germany

Phone +49-(0)9133/7765-0 • Telefax +49-(0)9133/5395
Email info@walz.com • Internet www.walz.com
Printed in Germany
NOTES
Note regarding the US-SQS:

The manual refers to the US-SQS, which is discontinued since June 2003. It
is replaced by the Spherical Micro Quantum US-SQS/B consisting of 3.7
mm diffusing sphere coupled to integrated PAR-sensor via 2 mm fiber.
The US-SQS/B differs by the following features:
The diffusing sphere is slightly greater.

The fiberoptics between diffusing sphere and PAR-sensor is short and rigid.
The sensor is connected to the amplifier with a 3 m koax cable.
The comments in the manual in regard to bending the fiberoptics do not

apply to the US-SQS/B. The way of connecting the sensor to the Power-
and-Control Unit PHYTO-C is the same.
Note regarding the wavelengths of the Measuring Light:

The excitation wavelengths of the measuring light have changed. The
information on the excitation wavelengths is stored in the file
CHANNEL.DAT. When the program is started, this information is loaded
and the PHYTO-PAM specific wavelengths are imported into the program
and displayed. Therefore the displayed wavelengths might differ from those
in the manual.
Note regarding the actinic and saturation pulse intensities of the

PHYTO-EDF:
The actinic light intensity reaches 1300 µmol quanta m-2 s-1 instead of
1800 µmol quanta m-2 s-1 (as mentioned in the technical specifications
chapter 5.4.1) and the saturation pulse light intensity reaches 2600 µmol
quanta m-2 s-1 instead of 3600 µmol quanta m-2 s-1.
It should be considered, that the absoption in the red light is higher
compared to white light. Therefore the light intensities are approx. 20 %
more effective.
I
CONTENTS
1 Safety instructions ........................................................................ 1

1.1 General safety instructions .......................................................... 1
1.2 Special safety instructions........................................................... 2
2 Introduction .................................................................................. 3
3 Components of the PHYTO-PAM Fluorometer........................ 6
3.1 Standard System I with Optical Unit ED-101US/MP ................. 6
3.1.1 Power-and-Control-Unit PHYTO-C ...................................... 8
3.1.2 Battery Charger MINI-PAM/L .............................................. 9
3.1.3 Optical Unit ED-101US/MP ................................................ 10
3.1.4 Photomultiplier-Detector PM-101P ..................................... 11
3.1.5 Measuring LED-Array-Cone PHYTO-ML.......................... 13
3.1.6 Actinic LED-Array-Cone PHYTO-AL (recommended)...... 13
3.1.7 Miniature Magnetic Stirrer PHYTO-MS (optional)............. 14
3.1.8 Spherical Micro Quantum Sensor US-SQS (optional)......... 15
3.1.9 Temperature Control Unit US-T (optional) ......................... 18
3.2 Steps for setting up the basic PHYTO-PAM System I.............. 18
3.3 System II with Emitter-Detector Unit PHYTO-ED .................. 19
3.3.1 PHYTO-ED.......................................................................... 20
3.3.2 Spherical Micro Quantum Sensor US-SQS (optional)......... 22
3.3.3 Stirring Device WATER-S (optional).................................. 23
3.4 System III with Emitter-Detector-Fiberoptics Unit
PHYTO-EDF............................................................................. 24
3.4.1 PHYTO-EDF........................................................................ 25
3.5 Installation of the PhytoWin-Software...................................... 31
3.6 First measurements with the PHYTO-PAM.............................. 33
3.6.1 4-channels excitation mode.................................................. 36
3.6.2 Principle of distinguishing between different groups of
phytoplankton....................................................................... 41
I
CONTENTS
3.6.3 How to determine chlorophyll concentration....................... 43

3.6.4 How to assess photosynthetic capacity ................................ 46
4 Features of the Windows-Software PhytoWin......................... 47
4.1 User surface of PhytoWin-Software.......................................... 49
4.2 Channels-window...................................................................... 54
4.2.1 Zero Offset and noise N(t) ................................................... 55
4.2.2 Measurement of F, Fm, dF and Yield .................................. 56
4.3 Algae-window ........................................................................... 59
4.3.1 Chlorophyll concentration.................................................... 61
4.3.2 Apparent electron transport rate ETR .................................. 62
4.4 Report-window.......................................................................... 64
4.5 Light Curve-window ................................................................. 68
4.5.1 Edit Light Curves ................................................................. 73
4.5.2 Light Curve Fit-parameters .................................................. 76
4.6 Settings-window........................................................................ 79
4.7 Reference-window and deconvolution of main groups of
phytoplankton............................................................................ 82
4.7.1 Reference Spectra for F and dF............................................ 83
4.7.2 Transformation of Reference Spectra into 4-point Excitation
Spectra and vice versa .......................................................... 90
4.8 Delta F-window......................................................................... 93
4.9 Chlorophyll calibration and determination................................ 97
4.9.1 Chl (MF)-mode .................................................................... 97
4.9.2 Active Chlorophyll in Delta F-mode.................................. 104
4.10 Light Calibration of Internal PAR-list .......................... 105
4.11 VIEW-mode .................................................................. 107
5 Technical Specifications........................................................... 116
5.1 General environmental conditions........................................... 116
II
CONTENTS
5.2 Standard System I with Optical Unit ED-101US/MP ............. 117

5.2.1 Basic System ...................................................................... 117
5.2.2 Accessories......................................................................... 120
5.3 System II with Emitter-Detector Unit PHYTO-ED ................ 121
5.3.1 Basic System ...................................................................... 121
5.3.2 Accessories......................................................................... 122
PHYTO-EDF........................................................................... 123
5.4.1 Basic System ...................................................................... 123
6 Rechargeable battery ............................................................... 125
7 Warranty conditions ................................................................ 126
III
CHAPTER 1 SAFETY INSTRUCTIONS
1 Safety instructions
1.1 General safety instructions

1. Read the safety instructions and the operating instructions first.
2. Pay attention to all the safety warnings.
3. Keep the device away from water or high moisture areas.
4. Keep the device away from dust, sand and dirt.
5. Always ensure there is sufficient ventilation.
6. Do not put the device anywhere near sources of heat.
7. Connect the device only to the power source indicated in the
operating instructions or on the device.
8. Clean the device only according to the manufacturer’s
recommendations.
9. If the device is not in use, remove the mains plug from the
socket.
10. Ensure that no liquids or other foreign bodies can find their way
inside the device.
11. The device should only be repaired by qualified personnel.
1
CHAPTER 1 SAFETY INSTRUCTIONS
1.2 Special safety instructions

1. The PHYTO-PAM Phytoplankton Analyzer is a highly sensitive
research instrument which should be used only for research purposes,
as specified in this manual. Please follow the instructions of this
manual in order to avoid potential harm to the user and damage to
the instrument.
2. The PHYTO-PAM employs high intensity LED-array light
sources which may cause damage to the eye. Avoid looking directly
into these light sources during continuous illumination or saturation
pulses.
2
CHAPTER 2 INTRODUCTION
2 Introduction
The pulse-amplitude-modulation (PAM) measuring principle is
based on selective amplification of a fluorescence signal which is
measured with the help of intense, but very short pulses of measuring
light. In the PHYTO-PAM Phytoplankton Analyzer µsec measuring
light pulses are generated by an array of light-emitting diodes (LED)
featuring 4 different colors: blue (470 nm), green (520 nm), light red
(645 nm) and dark red (665 nm). The differently colored measuring
light pulses are applied alternatingly at a high frequency, such that
quasi-simultaneous information on chlorophyll (Chl) fluorescence
excited at the 4 different wavelengths is obtained. This feature is
very useful for distinguishing algae with different types of light
harvesting pigment antenna. For example, in green algae Chl
fluorescence is much more effectively excited by blue and red light
(470, 645 and 665 nm) than by green light (520 nm). In the case of
cyanobacteria, almost no Chl fluorescence is excited by blue light
(470 nm), while excitation at 645 nm is particularly strong due to
phycocyanin and allophycocyanin absorption. On the other hand, in
diatoms and dinoflagellates excitation by blue (470 nm) and green
(520 nm) is relatively high due to strong absorption by fucoxanthin,
Chl c and carotenoids. While this multi-excitation approach opens
new ways in basic research, it also has considerable potential for
practical applications. Phytoplankton in natural surface waters
displays dynamic heterogeneities, depending on time, location and a
number of natural and man-made environmental factors. The
fluorescence signals measured by the 4-wavelengths excitation
method carry the information to differentiate between the
contributions of the main types of phytoplankton with different
pigment systems. Furthermore, following proper calibration, also the
Chl content of the various types can be estimated. And, last but not
least, being a PAM-Fluorometer, the PHYTO-PAM also offers the
3
possibility to assess photosynthetic activity of the various types of

phytoplankton with the help of saturation pulse quenching analysis.
During the past 15 years there has been considerable progress in
the quantification of Chl fluorescence information in terms of
photosynthetic activity. This progress has been closely linked with
the development of PAM-fluorimetry and the saturation pulse
method. This method takes advantage of the quantitative relationship
between Chl fluorescence and the efficiency of photosynthetic
energy conversion. The fundamental character of this relationship is
due to the fact that fluorescence originates from the same excited
states, created by light absorption, which alternatively can be
photochemically converted or also dissipated into heat. Hence, the
relationship between fluorescence and photosynthesis is just a
consequence of the first law of thermodynamics and simple calculus:
fluorescence + photochemistry + heat = 1
This is an equation with 3 unknowns, 2 of which (fluorescence
and heat) can be determined as relative values by two fluorescence
measurements, such that the third unknown, photochemistry, is
obtained. In practice, the two fluorescence measurements take place
shortly before and during a pulse of saturating light, i.e. within less
than a second
Numerous studies, have shown that the fluorescence method
really works, provided the experimental conditions are carefully
controlled. For example, a close correspondence between
photosynthesis measurements via Chl fluorescence and oxygen
evolution was reported by Gilbert, Wilhelm and Richter (Bio-optical
modelling of oxygen evolution using in vivo fluorescence:
Comparison of measured and calculated photosynthesis/irradiance
(P-I) curves in four representative phytoplankton species. J Plant
Physiol 157: 307-314). Of course, as with all methods, there are also
pitfalls that should be avoided. It is a major purpose of this
4
Handbook to point out potential problems and to help the user to

make optimal use of the PHYTO-PAM. Routine measurements with
this instrument are rather simple and can be carried out by mouse-
click via comfortable Windows-software. Hence, in principle a lot of
results may be obtained within short time, even by unexperienced
users. However, before such routine measurements can be carried
out, some time should be invested by an experienced researcher for
working out suitable protocols for calibration and experiments.
While the PHYTO-PAM has outstanding sensitivity and offers a
number of exceptional new features, it also has clear-cut limits. The
range of conditions within which it can provide reliable information,
has to be defined for each practical application by basic research and
suitable controls. In particular dealing with mixed phytoplankton
samples, the reliability of data increases with the amount of
background information on the investigated sample. This information
must be collected by the user and fed into the PhytoWin-program
that does the deconvolution analysis and calculations. In particular,
for longer term monitoring of a particular type of natural surface
water it will pay off to prepare pure cultures of the major types of
phytoplankton known to be present and to store their Reference
Excitation Spectra (see 4.7) and Chlorophyll Calibration Factors (see
4.9).
The PHYTO-PAM is new tool in phytoplankton research,
opening the way to numerous applications in basic and applied
studies. This undoubtedly will lead to new insights that may also call
for modifications of the PHYTO-PAM, particularly of the PhytoWin-
Software. We are grateful for all suggestions concerning such
modifications and also for pointing out possible software errors.
Updated software-versions will be distributed free of charge.
5
CHAPTER 3 COMPONENTS OF THE PHYTO-PAM
3 Components of the PHYTO-PAM Fluorometer

Presently (i.e. July 2003) three different versions of the
PHYTO-PAM Phytoplankton Analyzer are manufactured featuring
different emitter-detector units: The standard System I for laboratory
applications, System II for field applications and the fiberoptics
version System III for periphyton/microphytobenthos studies. All
three systems are based on the same Power-and-Control-Unit and the
same PhytoWin-software.
3.1 Standard System I with Optical Unit ED-101US/MP
4 3
1
Fig. 1 PHYTO-PAM Standard System I Components
The basic operational system of the PHYTO-PAM Fluorometer

in its standard version consists of:
6
1) the Power-and-Control-Unit PHYTO-C

2) the Optical Unit (ED-101US/MP with standard 10x10 mm
quartz-cuvette) which mounts on the Stand with Base Plate
(ST-101)
3) the Measuring LED-Array-Cone (PHYTO-ML), for
fluorescence excitation with blue (470 nm), green (520 nm), light
red (645 nm) and dark red light (665 nm); with additional red
LEDs (655 nm) for actinic illumination (up to 550 µE m-2s-1); to
be attached to the Optical Unit
4) the Photomultiplier-Detector (PM-101P) with filter box and
special Detector-Filterset; to be attached to the Optical Unit at
right angle with respect to Measuring LED-Array-Cone
5) the Battery Charger (MINI-PAM/L) to charge the internal
battery of the Power-and-Control-Unit
6) PC with Pentium processor and special Windows Software
PhytoWin running under Windows 98/Me/2000/XP; to be
connected via RS 232 interface cable to Power-and-Control-
Unit; serving for operation of PHYTO-PAM, data acquisition and
analysis.
The system can be extended by a number of recommended and
optional components:
7) the Actinic LED-Array-Cone (PHYTO-AL) for the study of
high light adapted phytoplankton; mounting in the Optical Unit at
180° with respect to Measuring LED-Array-Cone; although not
indispensable for basic operation of the PHYTO-PAM, highly
recommended particularly for the sake of strong saturation pulses
and reliable saturation pulse quenching analysis
7
8) the Miniature Magnetic Stirrer (PHYTO-MS) that can be

introduced via the bottom port of the Optical Unit and connects to
the Power-and-Control-Unit
9) the Spherical Micro Quantum Sensor (US-SQS) that features a
special holder to be mounted on the cuvette in the Optical Unit
and connects to the Power-and-Control-Unit (Aux. Input).
10) the Temperature Control Unit (US-T) featuring a Peltier Heat-
Transfer Rod and a separate Power-and Control Unit.
3.1.1 Power-and-Control-Unit PHYTO-C

The Power-and-Control-Unit of the PHYTO-PAM contains a
large rechargeable sealed lead-acid battery (12V/7.2Ah), such that in
conjunction with a notebook PC the instrument can also be used for
field investigations. For transport, the handle-bar should be moved
into central position facing the front panel, where it can be locked
using the two stops. For changing position, the two stops must be
removed again and, when gently pulled out, the handle can be moved
into the desired position.
All controls and electrical connectors are located on the front
side panel of the PHYTO-PAM
• ML Array socket, to connect Measuring LED-Array-Cone

PHYTO-ML
• AL Array socket, to connect Actinic LED-Array-Cone

PHYTO-AL (particularly recommended). It is important to push
the connector completely into the socket and to fasten the
threaded ring to make sure that the PHYTO-AL is recognized by
the PHYTO-C
8
• Aux. Input socket, to connect auxiliary devices, like the

Spherical Micro Quantum Sensor US-SQS (optional)
• Magnetic Stirrer socket and potentiometer, to connect and

control the stirring rate of the Miniature Magnetic Stirrer
PHYTO-MS (optional)
• Power switch and green indicator lamp, controlling connection

between internal battery and the electronics
• RS 232 socket, to connect RS 232 interface cable for data transfer

between Power-and-Control-Unit and PC
• PM socket, to connect Photomultiplier-Detector PM-101P
• Charge socket, to connect Battery Charger MINI-PAM/L (100 to

240V AC)
• Fuse plug, containing M 1.6A (medium blow) main fuse of

internal power circuit
• Excitation Channel Output sockets, to connect analog device of

signal registration (like chart recorder) for monitoring the orignal
fluorescence signals obtained with four different excitation
wavelengths.
3.1.2 Battery Charger MINI-PAM/L

The Battery Charger MINI-PAM/L is provided for recharging
the internal lead-acid battery (12V/7.2Ah) of the PHYTO-PAM. It is
connected to the Charge-socket on the front panel of the Power-
and-Control-Unit. The charger, which operates at input voltages
between 100 and 240V AC, features overload protection. Full
charging of an empty battery takes ca. 12 hours. During laboratory
operation, the charger may remain permanently connected. Battery
9
voltage is displayed on the Settings-window in conjunction with the

PhytoWin-Software (see 4.6).
3.1.3 Optical Unit ED-101US/MP

The Optical Unit is mounted on the Stand with Base Plate
ST-101. It consists of a solid aluminum holder (black anodized) with
an octagonal body, in the center of which a 10x10x45 mm glass- or
quartz cuvette can be positioned (see 3.6.1 for practical hints). A total
of 5 optical ports is provided at the 4 sides and the bottom for
connection of various optical components. The tube-port featuring a
10x10x100 mm perspex rod serves for mounting of the
Photomultiplier-Detector PM-101P. At right angle, close to the
mounting rod of the Optical Unit, the Measuring LED-Array-Cone
PHYTO-ML is introduced. In this way, optimal optical coupling of
the emission- (port 1) and excitation- (port 2) pathways to the cuvette
is achieved. Furthermore, the amount of excitation light is minimized
which may enter the emission port and cause a background signal at
the detector (e.g. via filter fluorescence). Three 15 mm Ø PVC rods
with a highly reflecting mirror at one side are provided, to be
introduced via the free ports with the mirrored side facing towards
the cuvette and gently pushed against the cuvette walls. They serve
the purpose of fixing the cuvette and at the same time increasing the
signal by reflecting transmitted excitation light back into the cuvette
and also reflecting fluorescence via the emission port to the detector.
If the Actinic LED-Array-Cone PHYTO-AL is available, this
preferentially should be positioned in the port opposite to the
Measuring LED-Array-Cone. The bottom port normally should be
closed by one of the PVC rods (to increase signal and to avoid
disturbance by ambient light). If available, the Miniature Magnetic
Stirrer PHYTO-MS can be mounted in the bottom port.
10
The top of the Optical Unit is covered by a special ring, which

holds the cuvette in central position, and by a hood with injection
hole. During measurements this hood should be applied, as ambient
background light may strongly enhance photomultiplier noise. At
high photomultiplier gain even the injection hole should be covered.
If the Temperature Control Unit US-T is available, after
removing the hood the Peltier Heat-Transfer Rod is set on top of the
Optical Unit, with the tip of the rod penetrating into the quartz-glass
cuvette.
3.1.4 Photomultiplier-Detector PM-101P

The Photomultiplier-Detector consists of a miniature
photomultiplier with high red sensitivity (type H6779-01,
Hamamatsu), a special pulse amplifier and a filter holder
(V-shaped), which accepts filters of variable sizes with total
thickness of up to 15 mm. For standard Chl fluorescence
measurements a special filter set is provided, which consists of a
filter combination (in one frame) with 1 mm blue glass filter (BG3,
Schott), 1 mm long-pass dichroic filter (R65, Balzers) and 2 mm
long-pass red-glass filter (RG9, Schott) and an additional 1 mm RG 9
in a separate frame. The figure below shows the arrangement of the
filters. The additional RG 9 has to be next to the photomultiplier,
then the holder with the special filter combination follows. The
engraving "Cuv. Side" has to face towards the perspex light-guide.
11
Fig. 2 Arrangement of the filters in front of the photomultiplier
1 Additional filter RG 9
2 Special filter combination (consisting of BG 3, R 65 and RG 9)
3 Black anodized aluminum cover
The blue-glass filter BG 3 absorbs scattered measuring light,
while passing most of long-wavelength fluorescence. The dichroic
filter R65 serves the purpose of reflecting scattered excitation light,
thus preventing excitation of fluorescence in the RG9 filter.
Therefore, it is essential that the blue-glass filter and the dichroic
filter are facing towards the perspex light-guide (CUV. SIDE). For
optimal signals, the tube-port of the Optical Unit with the perspex
light guide should be gently pushed into the opening of the filter
housing of the Photomultiplier-Detector until it touches the filter,
pressing it carefully against the wall of the housing. The nylon
screws serve for fixing the position.
12
The Photomultiplier-Detector can be manually switched on/off

by green/red pushbuttons, respectively. When exposed to excessive
light, the unit is automatically switched off and the red indicator
lamp lights up. Then, after the cause of overload has been removed,
it can be manually switched on again.
3.1.5 Measuring LED-Array-Cone PHYTO-ML

The Measuring LED-Array-Cone consists of 25 measuring
light LEDs peaking at 470, 520, 645 and 665 nm, as well as
12 actinic light LEDs peaking at 655 nm. A special perspex light-
guide cone serves for narrowing down the mixed beam to 13 mm Ø.
A short-pass filter (λ < 695 nm) at the cone exit prevents long-
wavelength LED-light to enter the cuvette and to reach the
photodetector. Such stray light would cause a background signal. The
LED-array and the perspex cone are mounted in a tube-shaped black-
anodized aluminum housing, the narrow end of which can be
introduced into the Optical Unit.
3.1.6 Actinic LED-Array-Cone PHYTO-AL (recommended)

The Actinic LED-Array-Cone consists of 37 actinic light LEDs
peaking at 655 nm. A special perspex light-guide-cone serves for
narrowing down the beam to 13 mm Ø. A short-pass filter (λ < 695
nm) at the cone exit prevents long-wavelength LED-light to reach the
cuvette and the photomultiplier. Such stray light would cause an
increase in photomultiplier noise. The LED-array and the perspex
cone are mounted in a tube-shaped black-anodized aluminum
housing, the narrow end of which can be introduced into the Optical
Unit.
13
While not being required for basic operation of the PHYTO-

PAM, the Actinic LED-Array-Cone is strongly recommended,
particularly for the study of samples adapted to high light intensities.
Maximal actinic intensity with the Measuring LED-Array-Cone
alone amounts to ca. 600 µmol quanta m-2s-1 and is increased to ca.
2000 µmol quanta m-2s-1 using the Actinic LED-Array-Cone.
Actinic intensities exceeding 600 µmol quanta m-2s-1 may be required
to reach saturation in light response curves (see 4.5). Furthermore,
and most importantly, fluorescence based quantum yield
measurements rely on very high light intensity during saturation
pulses. Saturation pulse intensity should be particularly high for
quantum yield determinations in light adapted samples. Therefore,
for reliable saturation pulse quenching analysis the PHYTO-AL is
indispensable.
When the PHYTO-AL is connected to the PHYTO-C, this is
recognized by the PhytoWin software and consequently the correct
Internal PAR list is applied (see 4.10).
Note: It is important to push the connector completely into the
socket and to fasten the threaded ring to make sure that the
PHYTO-AL is recognized by the PHYTO-C.
3.1.7 Miniature Magnetic Stirrer PHYTO-MS (optional)

The optional Miniature Magnetic Stirrer is rod-shaped, fitting
the bottom port of the Optical Unit. It is based on a rotating
magnetic field, the strength of which declines with the distance to the
magnetic flea in the cuvette. Therefore, it should be made sure that
the stirrer-rod is all the way pushed into the port. In order to avoid an
increase of background signal and stirring noise, small non-
fluorescing fleas should be used.
14
The Miniature Magnetic Stirrer is connected to the

corresponding socket (Magnetic Stirrer) on the front panel of the
Power-and-Control-Unit, which also features a potentiometer for
control of stirring rate.
3.1.8 Spherical Micro Quantum Sensor US-SQS (optional)

The optional Spherical Micro Quantum Sensor US-SQS is
available for assessment of the photosynthetically active radiation
(PAR) within the cuvette. When connected to the Aux. Input on the
front side of the Power-and-Control-Unit, the PAR-values
displayed on the PC-monitor screen correspond to the momentarily
measured values. When the sensor is not connected the displayed
values are derived from an internal PAR-list that has been previously
obtained with the help of the US-SQS. Such a list is prepared for
each individual instrument at the factory and incorporated in the
PhytoWin-Software (Default-values) which also features a routine
for recalibration of the internal PAR-list with the help of the US-SQS
(see 4.10).
Alternatively, the US-SQS can be also connected to the LI-COR
Light Meter (models LI-189 or LI-250) with the help of a standard
BNC-cable.
The spherical sensor consists of a 3 mm Ø highly scattering
plastic sphere which accepts light from all sides and which on the top
side is connected to a 1 mm Ø plastic fiber which carries the light via
an SMA-fiber connector to a separate Detector Unit with
preamplifier. A blue enhanced silicon photodiode is used as detector
in conjunction with a special filterset selecting the photosynthetically
active radiation between 380 nm and 710 nm.
The US-SQS was calibrated against a LI-COR Quantum Sensor
(Type LI-190) in air. If recalibration is carried out be the user, for
15
optimal results it is recommended to apply the same light source for

calibration that is used for actinic illumination. In the case of the
PHYTO-PAM this is red light (655 nm) emitted by the LED-Array-
Cone PHYTO-AL. As the US-SQS detects light from all directions,
it has to be made sure that it receives only direct radiation from the
calibration light source (no reflected light), just like the planar
calibration sensor. For this purpose, the US-SQS should be placed in
front of a black background. When the calibration is carried out in
air, the PAR read with the US-SQS should be 1.5 times larger than
the PAR read with a standard device (like LI-190). The correction
factor 1.5 is applied in order to obtain proper readings underwater
(immersion effect). At the same quantum flux density the US-SQS
shows a 1.5 times lower signal when immersed in water as compared
to air. Hence, the measured values of PAR are correct only when the
spherical sensor is submersed in water. When used in air, the PAR-
values should be divided by 1.5. A potentiometer is provided on the
Detector Unit for recalibration, if necessary. The Detector Unit
features two outputs, one for connection with the PHYTO-PAM
Power-and-Control-Unit (Aux. Input), the other for connection with
the LI-189 or LI-250 via BNC-cable. The output signal at the BNC-
socket is adjusted to -10 µA/1000 µmol quanta m-2s-1. Hence, when
e.g. connected to the LI-250, a factor of -100 must be entered in this
device.
For reproducible PAR-measurements, the spherical sensor should
be placed into the center of the 10x10x10 mm illuminated space of
the cuvette. This can be visually ascertained after removing one of
the PVC rods from the Optical Unit. The cuvette should be filled
with water in order to assess the PAR relevant for phytoplankton
investigations.
The plastic fiber connecting the Detector Unit with the diffusing
sphere is sensitive to bending. At constant light intensity the PAR-
16
reading decreases with decreasing bending radius. This effect may

become disturbing at bending radius below 10 cm (decrease ca. 5 %).
Therefore, it is recommended to mount the Detector Unit always in
the same way on the same stand, on which also the Optical Unit is
mounted, with the fiber leaving the Detector Unit in horizontal
position and entering the cuvette in vertical position. If mounted in
this way, the bending radius does not exceed 10 cm and errors in
PAR-determination can be minimized.
When fluorescence is measured with high sensitivity, the
spherical sensor will contribute significantly to the signal and, hence,
should be removed from the cuvette. In this case it should be also
disconnected from the Aux. Input of the Power-and-Control-Unit,
such that the internal PAR-list is effective. Otherwise the displayed
PAR does not correspond to the PAR-value in the cuvette. After use,
the sphere should be rinsed with clean water. Organic solvents
should be avoided. An ethanol moistened tissue may be used for
gentle cleaning of the surface of the sphere. Excessive bending of the
fiber should be avoided. When not in use, the delicate connection
between the scattering sphere and the plastic fiber should be
protected by the hood provided with the device.
Whenever the US-SQS is connected to the PHYTO-PAM (via
Aux. Input) or disconnected from it, the PhytoWin Program has to be
quit and the PHYTO-PAM has to be switched off. Then restart the
system in order to assure that the program recognizes the status-
change and correspondingly activates external PAR-reading or the
internal PAR-list, respectively.
17
3.1.9 Temperature Control Unit US-T (optional)

The Temperature Control Unit US-T consists of the Power-and-
Control unit US-T/R, the Peltier Heat-Transfer Rod US-T/S and an
AC Adaptor. A separate manual is provided for this unit.
3.2 Steps for setting up the basic PHYTO-PAM System I

For putting together the various components the following steps
have to be carried out:
(1) Put the Stand with Base Plate together; an appropriate nut key is
provided.
(2) Mount the Optical Unit on the Stand with Base Plate; the
covering ring and hood first may be put aside.
(3) Place the quartz cuvette in the center of the Optical Unit.
(4) Push the perspex light guide rod into the tube-port until it
gently touches the cuvette and lock it in this position using the
nylon screw on top of the octogon ring.
(5) Slide the Measuring LED-Array-Cone into one of the port holes
neighbouring the perspex rod (preferentially close to the
mounting bar of the Optical Unit) until it gently presses against
the cuvette. The cable should point downwards. Fix position by
nylon screw.
(6) Push the two PVC rods into the remaining port holes in the
octogon ring until they touch the cuvette and fill the bottom
port hole with the third PVC rod.
(7) Make sure that the cuvette can be lifted and put back again
without too much friction, if necessary by gentle tilting
movements and exerting some pressure to all sides. A small play
18
of 0.2 - 0.5 mm is alright. Then install covering ring, assure that

all nylon screws are well fixed, and cover cuvette with hood.
(8) Put Detector-Filterset into filter box of Photomultiplier-Detector
with the blue filter facing towards the entrance hole (see Fig. 2)
and then push the tube port with perspex rod of the Optical Unit
into the opening of the Detector Unit such that the filter is
gently pressed against the wall of the housing; cover the filter
box with the light-tight V-shaped hood.
The following steps have to be taken for proper electrical

connections:
(1) Connect Photomultiplier-Detector with Power-and-Control-Unit
(PM socket).
(2) Connect Measuring LED-Array-Cone with Power-and-Control-
Unit (ML Array socket).
(3) Connect PC and Power-and-Control-Unit via RS 232 cable.
(4) Connect Battery Charger with Power-and-Control-Unit (Charge
socket) (not obligatory, but recommended for laboratory
application).
3.3 System II with Emitter-Detector Unit PHYTO-ED

The Emitter-Detector Unit PHYTO-ED is operated in
conjunction with the same Power-and-Control-Unit PHYTO-C as the
standard System I (see 3.1.1).
19
3.3.1 PHYTO-ED
The PHYTO-ED contains all essential components, which in the
standard System I correspond to the Optical Unit, the Measuring and
Actinic LED-Array-Cone and the Photomultiplier-Detector. It weighs
only 600 g as compared to almost 6 kg of the equivalent components
of the standard version and, hence, is particularly well suited for field
applications.
Fig. 3 Emitter-Detector Unit PHYTO-ED (left) with Stirring Device

WATER-S (right) and Power-and Control-Unit PHYTO-C
The PHYTO-ED is connected via three cables to the

corresponding sockets at the front side of the Power-and-Control-
Unit:
• ML-Array, 4-wavelengths Measuring Light
• AL-Array, red Actinic Light
• PM, Photomultiplier Detector
20
It consists of the following components:
• Water-proof cast aluminium housing from which the external

part of the Measuring Head protrudes. A red and a green LED
shows the status of the internal Photomultiplier Detector. With
the help of the red and green pushbuttons the Photomultiplier
can be manually switched on/off. The photomultiplier
automatically is switched off at excessive light impact.
• Measuring Head with optical port for inserting sample cuvette,

featuring o-ring which seals against housing.
• PVC centering ring with o-ring sealing against the inner wall of
the Measuring Head, serving as a guide for the cuvette and as an
adapter for mounting the optional Miniature Stirring Motor
Water-S and the optional Spherical Micro Quantum Sensor US-
SQS/W.
• Cup-shaped perspex inset sealing against an inner o-ring of the

Measuring Head, thus protecting the opto-electronical
components from spilled water samples.
• Quartz Cuvette with 15 mm outer and 13 mm inner diameter;

height 46 mm.
• Darkening Hood covering the part of the Measuring Head

protruding from the housing.
• Circular LED-Arrays for Measuring Light (470 nm, 520 nm,

645 nm and 665 nm) and Actinic Light (655 nm) mounted in the
bottom part of the Measuring Head; featuring filter-ring with 18
individual short-pass filters (<695 nm).
• Photomultiplier Detector based on Photosensor Module H-

6779-01 (Hamamatsu) with collimating optics and optical filter
set passing wavelengths above 710 nm; optimized for low
21
background signal. The Photomultiplier supply voltage is

automatically switched off when it sees too much light (red
status LED on housing lights up). After the cause of the
excessive illumination is removed, the Photomultiplier has to be
switched on manually using the green pushbutton.
• Printed circuit board with pulse-signal preamplifier and

automatic overload switch-off circuitry.
Measuring and Actinic LEDs are assembled in two circular
arrays, with the beams being focused on the bottom part of a 15 mm
Ø quartz cuvette below which the Photomultiplier Detector is
located. Fluorescence is collected with the help of a spherical lens
and stray excitation light is effectively removed by a special filter
set.
The optical properties of the new PHYTO-ED were optimized
for maximal sensitivity at minimal background signal level. With
respect to the standard Emitter-Detector Unit the PHYTO-ED
displays approximately 2-fold sensitivity at more than 5 times
smaller background signal level. In this way, the detection limit of
active Chl is decreased to values well below 0.5 µg/l. Therefore, the
PHYTO-ED can be particularly recommended for the investigation
of surface waters with rather low Chl content, as e.g. open ocean
water.
3.3.2 Spherical Micro Quantum Sensor US-SQS (optional)

A special adapter is available for mounting the optional Spherical
Micro Quantum Sensor US-SQS on the PHYTO-ED. In this way, an
Internal PAR-list can be defined which applies for the recording of
Light Response Curves. For details on the US-SQS, see section
3.1.8.
22
It should be noted that illumination in the circular cuvette of the

PHYTO-ED is not as homogeneous as in the square cuvette of the
standard Optical Unit (System I). Light intensity drops from the
center, where all LED beams cross, to the periphery of the cuvette.
Therefore, the light intensity measured with the US-SQS at the
center of the cuvette is not representative for the overall sample, the
fluorescence of which is measured. This feature has to be considered
when trying to estimate absolute photosynthetic electron transport
rates or when comparing the measured rates with those measured
with other systems. The effective PAR representative for the overall
sample is approximately 3 times lower than the maximum PAR in
the center of the cuvette.
3.3.3 Stirring Device WATER-S (optional)

A special adapter is provided for mounting the optional Stirring
Device WATER-S on the PHYTO-ED. This can be particularly
useful for dark-adaptation and Fo-measurements of rapidly settling
samples. During actinic illumination, the stirring helps to establish a
quasi-homogenous illumination of the sample.
The WATER-S runs on a long life 3 V Lithium battery (size CR
123A). It features an on/off switch and a potentiometer knob for
stirring rate adjustment. The whole device is placed on top of the
PHYTO-ED, with the top of the 15 mm ∅ quartz cuvette sliding into
the corresponding opening of the WATER-S, in the center of which a
stirring paddle is mounted on the motor axis (via split brass-tube
adater). The disposible paddle can be removed by gentle pulling.
The other way around, a replacement paddle can be mounted by
pushing its cylindrical end all the way into the holder. For
replacement of the battery the housing has to be opened by pulling
the white and grey halves apart. Separation of the two halves is
23
facilitated by forcing gently a thin flat body into the slit (like finger
nail or thin screw driver).
It should be noted that at high photomultiplier gain the paddle of
the WATER-S will cause some increase of noise. This is due to the
fact that some measuring light is reflected from the paddle towards
the photodetector, such that the background signal is approximately
doubled and the electronic noise is correspondingly increased.
Furthermore, there is an increase of sample noise caused by the
movement of cells or cell groups.

PHYTO-EDF
The Emitter-Detector-Fiberoptics Unit PHYTO-EDF is operated
in conjunction with the same Power-and-Control-Unit PHYTO-C as
the standard System I (see 3.1.1) and the Emitter-Detector Unit
PHYTO-ED. It is designed for assessment of fluorescence
parameters of phytoplankton growing on the surface of rocks, sand,
macroalgae, wood etc. It is, hence, well suited for the study of
photosynthetic performance of microphytobenthos and periphyton.
24
3.4.1 PHYTO-EDF
2
3
7
6
4
8 1
Fig. 4 Emitter-Detector-Fiberoptics Unit PHYTO-EDF featuring the

following components described in the text: (1) Emitter-Detector
box; (2) 9-armed Fiberoptics; (3) Fiberoptics/perspex-rod-adapter;
(4) Perspex-rod (or quartz-glass); (5) Stand with Base Plate (ST-
101); (6) Dark-Box; (7) Mounting ring; (8) non-fluorescent black
pad.
The Emitter-Detector-Fiberoptics Unit PHYTO-EDF consists of

the following parts which are illustrated in Fig. 4 (above) and Fig. 5
(below):
• Emitter-Detector box (1), on the top side of which the optical

ports for the 9-armed special fiberoptics (2) are located (SMA
fiber connectors). At the front side, a red and a green LED
show the status of the internal Photomultiplier Detector (red
light, off; green light, on). With the help of the red/green
pushbuttons the photomultiplier can be manually switched
25
off/on. The photomultiplier is automatically switched off upon

incidence of excessive light.
The Emitter-Detector box contains all essential opto-electronical
components. It houses 4 different LED Measuring Light
Sources (470 nm, 520 nm, 645 nm and 665 nm), 4 LED Actinic
Light Sources (660 nm), the Photomultiplier Detector with
special filterset as well as a printed circuit board with pulse-
signal preamplifier and automatic overload switch-off.
All LED Light Sources are equipped with miniature fiber
coupler optics and short-pass filters (λ<700 nm). The fiber
coupler ports at the top side of the Emitter-Detector box are
numbered 1-4 (four differently colored Measuring Light LEDs)
and 5-8 (four Actinic Light LEDs).
In the center of the top side a black PVC-tube features as adapter
for the end piece of the 9th fiber, which carries the fluorescence
to the photomultiplier detector. The detector is protected by a
special long-pass filter set (λ>710 nm) optimized for low
background signal.
The Emitter-Detector box (1) is connected via two cables to the
corresponding sockets at the front side of the Power-and-
Control-Unit: ML-Array, 4-wavelengths Measuring Light, and
AL-Array, red Actinic Light.
• Special 9-armed Fiberoptics (2), with the end pieces of the 9

arms connecting to the corresponding optical ports at the top side
of the Emitter-Detector box (1). The end pieces of the eight arms
connecting to the LED-fiber couplers (fiber ∅ 1 mm) are
numbered 1-8. The fibers 1-4, which are connected to ports 1-4,
carry the Measuring Light wavelengths 470 nm, 520 nm, 645
nm and 665 nm, respectively. Please note that the numbers of the
ports 1-4 and fibers 1-4 correspond to each other. This is
26
important, as the light transmission of the various fibers shows

some variation and, hence, has an influence on the Reference
Spectra on which deconvolution of the various types of
phytoplankton is based. In the case of the Actinic Light this
does not play any role and, hence, the fiber ends 5-8 may be
connected to any of the four ports denoted with 5-8.
The fiberoptics display a joint end with 3.5 mm active ∅

normally mounted in a Fiberoptics/perspex-rod-adapter (3),
with the end tip of the perspex-rod (4) being in contact with the
investigated sample. The rod has an active diameter of 4 mm and
is 50 mm long. It serves for randomizing the measuring/actinic
light and for conducting the fluorescence from the sample
surface to the detector fiber. It is essential that there is no air gap
between the rod and the fibers. The optical contact may be
somewhat improved by a drop of immersion oil. For special
applications (e.g. phytotoxicology) also an optional quartz
glass rod is available upon request.
27
3
9
Fig. 5 Components at the joint end of the 9-armed Fiberoptics: (2)

Fiberoptics joint end; (3) Fiberoptics/perspex-rod-adapter; (4)
perspex-rod (optionally quartz-glass-rod); (9) Distance ring.
At the common end of the 9-armed fiberoptics, the eight 1 mm

∅ fibers carrying the Measuring and Actinic Light, are
arranged in a circle around a central 1.5 mm ∅ fiber, which
carries the fluorescence to the photomultiplier detector. The 1
mm ∅ fibers are positioned at a small angle with respect to the
axis, such that the 8 light beams cross at ca. 3 mm distance from
the fiberoptics exit plane. In some applications it may be
advantageous to put a sample directly into the focal plane of the
crossing beams. For making use of this possibility, the perspex-
rod-adapter (3) must be removed. A special distance ring (9) is
28
provided which can be mounted on the joint end piece of the

fiberoptics (2) (see Fig. 5). A planar sample can be placed
directly on this ring. Alternatively, a thin glass plate (e.g. cover-
slip) can be put between the ring and a sample (e.g. also a drop of
investigated water). While without perspex-rod the light is less
homogenous, the signal is somewhat higher and the background
signal distinctly lower. Hence, a higher sensitivity is reached. It
should be noted that different Reference Spectra as well as
different Zero Offset values will apply for different optical
geometries.
The end of the central 1.5 mm ∅ detector fiber is stabilized by

a stiff steel wire, which prevents excessive fiber bending. When
connecting the fibers to the Emitter-detector box (1), the detector
fiber has to be mounted first. Please handle the fiberoptics with
care, as any damage will affect the signal quality and may change
the relative intensities of the different measuring wavelengths
and, hence, also the Reference Spectra.
• Stand with Base Plate (ST-101) (5) and Dark Box (6), on
which the fiberoptics (2) are mounted. A special Mounting Ring
(7) is provided, which holds the Fiberoptics/perspex-rod-adapter
(3) (see Fig. 4). At its upper side, this Mounting Ring features a
flat adjustment screw on which the perspex-rod-adapter (3)
rests. By moving this screw up/down, the distance between
sample and exit plane of the perspex rod can be adjusted. This
distance determines signal amplitude and actinic light intensity.
Both parameters are also influenced by the interface between
perspex-rod and sample. A drop of water leads to a substantial
increase of both parameters.
The performance of the PHYTO-PAM with respect to sensitivity
and stability is affected by any modulated and non-modulated
background signals. The former is due to non-chlorophyll
29
fluorescence (e.g. originating from the substrate on which the

investigated organisms are growing). The latter stems from
ambient light. With detached samples, the background
fluorescence can be minimized by placing the sample on a black
non-fluorescent substrate. For this purpose, a self-adhesive
black non-fluorescent pad (8) is delivered with the PHYTO-
EDF, which can be stuck on the base plate of the stand, below the
Fiberoptics/perspex-rod-adapter (3). It is recommended to place a
detached sample in a thin walled petri dish resting on this pad.
For measurements in relatively strong ambient light a Dark-Box
(6) is provided, which is placed on top of the non-fluorescent pad
(8) and held in position by the mounting ring (7) clamped to the
pole of the stand (5) (see Fig. 4).
The samples studied with the fiberoptics version PHYTO-EDF

normally differ from samples investigated with the standard
PHYTO-PAM System I or with the PHYTO-ED (System II). While
in the latter cases highly diluted algae suspensions are investigated,
the PHYTO-EDF is designed for photosynthetic organisms growing
on substrate surfaces and normally reaching relatively high Chl
levels. High Chl concentrations bring about a number of
consequences which are of practical relevance:
1. The fluorescence signal is relatively high and, hence, the effect
of the unavoidable background signal due to optical components
of the PHYTO-EDF (fiberoptics, filters etc.) is relatively small.
2. Due to the pigment flattening effect of absorbance spectra,
differentiation of different algal groups is more difficult at high
than at low Chl content. Generally, the "fitting noise" is
increased.
30
3. At high Chl content the measuring light is already absorbed in

the top layer and also Chl fluorescence is reabsorbed. In this
case, the standard procedures of calibration and measurement of
Chl content, as outlined in sections 4.3.1 and 4.9 are not valid.
3.5 Installation of the PhytoWin-Software

Together with your instrument you receive a CD with the
PhytoWin-program (identical for all instruments) and a
Configuration-disc with the files that are specific for your particular
instrument. On the CD there is also a copy of this User Manual in
form of a pdf-file. The PhytoWin-program must be installed on the
PC that is going to be used in conjunction with your PHYTO-PAM.
At the end of the guided installation procedure a Phyto-PAM folder
is created on your PC with Data-directories of the three different
types of Phyto-PAM Measuring Heads (Phyto-ED, Phyto-EDF and
Phyto-US). Into these directories all measured data will be written.
When the installation of the PhytoWin-program is finished, the
Configuration-files have to be manually transferred into the
directory of the relevant Measuring Head.
Please note that for proper display of the PhytoWin user surface
on the PC screen, on your PC the screen resolution should be set
under Windows to 1024x768 dots and the DPI-setting should be 96
dpi (normal size, small letter size).
Important note:
If a PhytoWin-version 1.06 and below is already installed on
your PC, the existing PhytoPAM folder as well as the existing
Phyto.exe should be renamed (e.g. PhytPAMold and Phytoold.exe).
Once the new PhytoPAM folder is created, previously recorded data
as well as the required Configuration-files can be transferred into the
corresponding directories.
31
If a PhytoWin-version higher than 1.06 is already installed on

your PC, it is recommended to first make for safety's sake a back-up
copy (not move or rename) of the already existing PhytoPAM
folder. Then the PhytoWin software must be deinstalled using the
Windows Deinstaller (System Control/Software registration).
Then the installation of the new software version can begin, as
described below, by which the previously stored data in the existing
PhytoPAM folder should not be affected. When the installation is
completed and the user has convinced himself that the old data and
Configuration-files are unaffected, the back-up file can be deleted
again. The old data can be copied into the relevant sub-directories
(e.g. Data_US).
Steps of the PhytoWin installation
• Put CD into drive D of your PC

• Call up "My Computer" and select drive D
• Double click the file Setup.exe
After start of Setup.exe the Install Wizzard is

called up, which guides you through the
installation, at the end of which the PhytoPAM
folder will be installed on your PC (normally on
drive C), with links to PhytoPAM Folder and to
PhytoWin.exe put on the desktop. Directly after
program installation and creation of the PhytoPAM
32
Folder, this contains the

three Data-directories and
the Phyto.exe file. Later,
after definition of the used
Measuring Head, the
Phyto.cfg file will be
automatically added.
Steps for installation of the Configuration-files
• Put disk into drive A of your PC

• Call up "My Computer" and select drive A
• The directory of drive A shows the Configuration-files:
BlueMF32.ref2, GreenMF32.ref2, BrownMF32.ref2,
Channel.dat, Phyto.pmc, Phyto.pmd, Default.cal and Config.txt.
In addition it also contains a copy of this section of the User
Manual describing the PhytoWin installation (readme.txt).
All Configuration-files have to be copied and transferred
manually into the relevant Data-directory (e.g. Data-US) within the
PhytoPAM folder.
Now the PhytoPAM is ready for measurements. In the course of
the measurements additional files will be created automatically by
the program (e.g. the Report.RPT), which are written into the Data-
directories of the applied Measuring Head. After definition of a
particular Measuring Head, this information is stored in the file
Phyto.cfg (main directory in PhytoPAM folder).
3.6 First measurements with the PHYTO-PAM

The PhytoWin program is started via Phyto.exe (in PhytoPAM
folder) by clicking the PhytoWin icon on the desktop. The Start-
33
window is displayed, showing the number of the current PhytoWin

version.
When the program is for the first time started on a particular PC,
the user is asked which communication port (Com Port) is going to
be used:
One of the Com 1-Com 8 ports
can be selected. The same
query also appears when no
instrument is connected via the
RS 232 interface cable, as the
user may just start the program
for viewing stored data. In this
case, the View mode button has
to be pressed.
Once a Com Port was defined, this information is stored and used
for further program starts, as it is assumed that the same Com-port is
also used in the future. If for some reason the communication with
the selected Com-Port does not work or if the instrument (Power-
and-Control-Unit) is switched off, there is a warning:
34
When this warning occurs, please

check whether the instrument is
switched on, the RS-232 cable is
connected and whether the selected
Com Port is occupied by another
application. Then try to start the program again.
When the instrument is switched on and the communication with
the PC works, the program asks for definition of the applied
measuring head. In principle, the user has the choice between the
standard Optical Unit (Phyto US), the Phyto ED and the fiberoptics
version Phyto EDF.
Definition of the applied measuring head is
essential, as each measuring head features
individual parameters (e.g. relating to
photomultiplier sensitivity) that are stored in
separate Data directories for each
measuring head. They are essential for
correct storage and analysis of the measured
data. After definition of the measuring head
the actual program is started with the 4-
channels excitation window being displayed.
While the features of the PhytoWin user software described in
the following sections apply to all measuring heads, in the
description of some details it is generally assumed that the standard
measuring head Phyto US is used.
35
3.6.1 4-channels excitation mode
Fig. 6 Channels-Window, as displayed after program start
The 4-channels excitation mode is the standard mode of

operation of the PHYTO-PAM. After start of the program, on the PC
monitor screen the "Channels"-window is displayed. This shows
the current Chl fluorescence yield, Ft, measured continuously with 4
different excitation wavelengths (470 nm, 520 nm, 645 nm and 665
nm) at default settings. In addition, also the mean value of the 4
fluorescence signals is displayed. Normally, after program start the
displayed Ft-values are close to zero, as the Gain (photomultiplier
voltage) is set to a low setting by default, in order to avoid
unintended damage. As indicated by the status of the ML-switch
(bottom, left), the measuring light is switched on upon program start.
It is applied in LED-pulses with a width of 12 µsec at low frequency
(default setting 2 corresponding to approximately 25 Hz), such that
its actinic effect is relatively weak. This means that no electrons
36
accumulate at the acceptor side of PSII and, hence, the minimal

fluorescence yield, Fo, of a dark-adapted sample is assessed. You can
have a look at the four colors of measuring light at the exit of the
Measuring LED-Array-Cone after pulling this out of its port (not
possible with System II and III). You will notice that there are also
several LEDs in the array which do not emit light. These are the
"actinic LEDs", which will light-up only when the AL-switch is
activated. Actually, when AL is turned on, also the intensity of the
ML-LEDs is increased. This is due to an automatic increase of the
frequency of ML-pulses during actinic illumination. In this way, the
signal/noise ratio is increased and the fluorescence changes induced
by the actinic light are assessed at high time resolution. At the same
time the ML at high frequency contributes to overall actinic intensity,
which is displayed in the PAR-field in units of µmol quanta m-2s-1
(photosynthetically active radiation). A third type of illumination is
triggered by the "Sat-Pulse" button. But, please avoid looking
directly into the LED-array source, as this light is very strong and
may harm your eyes. Point the source on a piece of paper (not
possible with Systems II and III) and press the SAT-Pulse button.
You will see a short pulse (0.2 sec) of very bright red light (655 nm).
This so-called "saturation pulse" can cause complete reduction of
the PSII acceptor pool and, hence, induce an increase of fluorescence
yield (dF) from its current level (F = Ft) to its maximal value (Fm).
Based on such measurements, the effective quantum yield of
photosynthetic energy conversion in PSII can be determined, using
the simple relationship:
Yield = (Fm-F)/Fm = dF/Fm
It should be noted that for reliable full reduction of the PS II
acceptor side of a light adapted sample the saturation pulse intensity
provided by the Measuring LED-Array-Cone alone may not be
37
sufficient. Therefore, the additional use of the Actinic LED-Array-

Cone is strongly recommended for quantitative work.
Let us now start doing some fluorescence measurements. For this
purpose, reinstall the Measuring LED-Array-Cone in the Optical
Unit, fill the cuvette with a sample (which first may be pure water)
and make sure that the Photomultiplier-Detector is switched on
(green indicator LED on the top side of the housing lighting up). At
the right hand side of the Channels-window there is the Gain control
box, showing setting 5 of photomultiplier gain upon program start.
This gain is by far too low to show any fluorescence signal with a
pure water sample. After clicking the Gain-button the Gain-setting is
automatically increased until the channel with the largest signal
shows ca. 400 units (Auto-Gain function). Even pure water samples
will show a fluorescence signal, if the Gain is sufficiently high (ca.
setting 20 by Automatic Gain control). This unavoidable
"background signal" is due to stray fluorescence originating from
various system components like the LED-array, cuvette and filters. It
is minimal when the cuvette is properly placed into the Optical Unit.
Please convince yourself about the importance of this aspect by
inserting first an empty cuvette and lifting it up by 1-2 mm from the
all-down position; then this test should be repeated with a cuvette
filled up with water. You will find that an empty cuvette gives a
much larger background signal than a cuvette filled with pure water.
You will further find that the background signal is minimal when the
cuvette is all the way down. The unavoidable background signal can
be digitally suppressed by the automatic Zero-offset function (Zoff).
But, please note that it will always cause a decrease in the
signal/noise ratio.
In practice, natural surface waters often contain (besides
phytoplankton) other fluorescing substances (like humic acids) in
solution. In order to get rid of this contribution, together with the
38
small background signal caused by system fluorescence, it is

recommended to proceed as follows:
− Make sure that the cuvette is clean, e.g. by washing with

ethanol and rinsing with water.
− Make sure that the cuvette is placed correctly into the

Measuring Head (see above). If the cuvette is not all the way
down, this will cause an increased background signal.
− Fill the cuvette with ca. 2 ml of the sample to be investigated

and apply Auto-Gain to define the Gain-setting at which the
measurements will be carried out.
− Prepare a filtrate of the sample using a 0.2 µm millipore filter

that will retain all phytoplankton.
− Exchange the sample in the cuvette by ca. 2 ml of the filtrate

and measure its fluorescence using the same Gain-setting as
found appropriate for the unfiltered sample. Before adding the
filtrate, make sure that the cuvette is washed free of any
remaining sample with pure water. By giving a saturation pulse,
you may convince yourself that the signal displayed by the
filtrate really is not originating from active Chl. The dFt- and
Yield-values will be zero or close to zero. Please note the little
indicator lamp below the PAR-box, which lights up red as long
as the signal is unstable. All measurements, including Zoff-
determination, should be preferentially carried out after this
lamp lights up green. After Zoff-determination, the signals of
the 4 channels are close to zero. Fluctuating values of up to ca.
2 units may occur due to digital noise and are of no concern.
After Zoff-determination the filtrate is substituted by the sample
and now the proper fluorescence measurements can start, as the
fluorescence yields displayed for the 4 channels now are only due to
the phytoplankton. The most fundamental measurement is the
39
assessment of the quantum yield of photochemical energy

conversion in PSII by application of a saturation pulse. With an
active sample, the 4 channels will show values of maximal PSII
quantum yield (Yield under quasi-dark adapted conditions) in the
order of 0.5 - 0.8. You may have a look at the polyphasic rise
kinetics of fluorescence yield during the saturation pulse (View
Pulse check-box). For appropriate Yield-determination, it is
important that the maximal fluorescence yield is reached during the
saturation pulse, which is the case when a distinct plateau is observed
(see 4.2.2).
Another fundamental measurement is the recording of the
fluorescence changes upon transition from darkness to continuous
light. Just switch on the actinic light (AL-button) and follow the
changes of fluorescence yield with time, Ft. You will observe that
fluorescence yield first rises to a peak level and then slowly declines
towards a steady state level. This is the famous Kautsky-effect,
which reflects the dark-light induction kinetics of photosynthesis. If
a chart-recorder is at hand, you may connect this to any of the
Excitation Channel Outputs at the Power-and-Control-Unit and
record the induction kinetics.
When a saturation pulse is applied during actinic illumination,
the observed Yield-values are distinctly lower than after dark-
adaptation. This reflects a decrease in the efficiency of energy
transformation at PSII reaction centers due to two major factors: first,
partial reaction center closure (primary acceptor QA reduced) and,
second, increase of nonradiative energy dissipation.
The fluorescence information obtained with each saturation pulse
is not lost, even if no chart recorder is connected. It is stored in the
so-called Report-file which can be accessed by clicking the
corresponding "register card" (Report) (see 4.4). All data stored in
the Report-file can be also recalled on the Channels- and Algae-
40
windows for further inspection with the help of the VIEW-mode

(see 4.11). In order to continue with measurements, the user must
return to the MEASURE-mode.
3.6.2 Principle of distinguishing between different groups of

phytoplankton
In the first orienting measurements outlined above, the emphasis
was on basic fluorescence measurements. Reliable assessment of
fluorescence parameters using a number of different excitation
wavelengths is the basis for distinction and characterization of
different groups of phytoplankton. In the Channels-mode of
operation, the PHYTO-PAM is equivalent to 4 separate PAM-
Fluorometers using 4 different excitation wavelengths that are
chosen for optimal differentiation between cyanobacteria, green
algae and diatoms/dinoflagellates, which differ substantially in the
absorbance spectra of their antenna pigments. This aspect can be
most readily visualized by measurements with pure cultures of
cyanobacteria, green algae and diatoms/dinoflagellates. For example,
with a sample of cyanobacteria you will see almost no signal in the
470 nm Channel (no Chl b), whereas a large signal is seen in the 645
nm Channel (due to allophycocyanin absorption). A green algae
sample shows a large signal with 470 nm excitation (Chl b) and a
low signal with 520 nm excitation. In the contrary, diatoms display
strong signals not only with 470, but also with 520 nm excitation,
due to absorption by Chl c, fucoxanthin and carotenoids. On the
basis of these differences, it is possible to separate the contributions
of differently pigmented phytoplankton in natural water samples.
An essential prerequisite for the differentiation between various
types of phytoplankton is that the 4-channels fluorescence responses
of the pure cultures are known. While the measurements of such
"Reference Excitation Spectra" are automized and, hence, quite
41
simple to be performed with the PHYTO-PAM, some basic

understanding is required for proper choice of the conditions for
these measurements (see 4.7). By clicking the "Reference" register
card, you can open a window showing typical "Reference Excitation
Spectra" measured at the factory with your specific PHYTO-PAM
using pure cultures of cyanobacteria (Anacystis) (BlueMF32.ref2),
green algae (Ankistrodesmus) (GreenMF32.ref2) and diatoms
(Phaeodactylum) (BrownMF32.ref2). The MF32 refers to the
Measuring Light Frequency at which these References were
measured (see 4.7). Please note, that the References are not identical
to four-point excitation spectra, as the intensities of the four
excitation beams are not equal. Hence, these Reference Spectra do
not only reflect the wavelength-dependent fluorescence excitation
properties of the phytoplankton, but also the specific intensities of
the 4 different excitation sources in the applied measuring head.
The References delivered with the instrument may help the user
to become acquainted with the method. However, for more detailed
scientific investigations, additional (new) References should be
measured by the user, preferentially for the very species of
phytoplankton known to be present in the investigated water
samples.
Based on the "Reference Spectra" the PhytoWin-program
deconvolutes the original 4-channels signals into the contributions of
the corresponding algal classes, for display of which a special
window is provided (opened by clicking the "Algae" register card).
It should be emphasized that contrary to the unbiased fluorescence
information displayed in the "Channels"-window, the information on
the "Algae"-window is strongly biased by the information contained
in the applied References. Hence, the quality of the obtained results
depends on previous work invested by the user into the measurement
of the References. Such work will profit from background
42
knowledge on the likely presence of particular phytoplankton species

in the investigated water sample. In this sense, the success of
practical applications to a considerable extent depends on close
interaction with basic research, not only using Chl fluorescence, but
also alternative methods, like microscopy, flow cytometry and
pigment analysis by HPLC.
While the content of the three main phytoplankton group is
deconvoluted from fluorescence measurements, the obtained results
often are compared with data obtained from Chl determination and
pigment analysis. In this context, it has to be considered that
fluorescence intensity is not only determined by the Chl content, but
by the content of all pigments which absorb the measuring light and
transfer the absorbed excitation energy to the fluorescent Chl (mainly
associated with photosystem II). In order to determine phytoplankton
content and distribution in terms of chlorophyll concentration,
detailed information on the relationship between fluorescence yield
and chlorophyll concentration of the various types of phytoplankton
must be available.
3.6.3 How to determine chlorophyll concentration

Over a wide range of Chl contents, Chl fluorescence intensity is
proportional to Chl concentration. Hence, following proper
calibration, the signal amplitude gives direct information on Chl
content. In practice the following points have to be considered:
(1) As already outlined in 3.6.1, the fluorescence signal may
originate not only from Chl, but also from other fluorescing
components, like humic acids and at high Gain-setting even
from components of the measuring system (e.g. cuvette and
optical filters). This aspect can be accounted for by Zoff-
determination using a filtrate (see 3.6.1).
43
(2) At a given Chl concentration the Chl fluorescence yield is not

constant. For example, as outlined above (see 3.6.1)
fluorescence is increased when PSII reaction centers are closed
during illumination, and decreased when the energy capture
efficiency of PSII is lowered (e.g. by increased heat dissipation
or increased energy transfer to the low fluorescent PS I).
Potential errors due to such effects can be minimized by
carrying out the Chl determination at the same light intensity at
which the Chl calibration was carried out. Furthermore,
moderate light intensities should be used, which are unlikely to
induce substantial reaction center closure and stimulation of
heat-dissipation.
(3) At high Chl concentrations, part of the Chl fluorescence is
reabsorbed by the sample thus leading to underestimation of Chl
content. However, with the optical geometry of the PHYTO-
PAM, this effect generally may be ignored at Chl concentrations
below 300 µg Chl/l.
(4) The relationship between fluorescence yield and Chl
concentration differs between different types of phytoplankton.
Therefore, optimal results can be obtained only, if a separate Chl
calibration is carried out for each type of phytoplankton and the
overall fluorescence yield of a sample is deconvoluted into the
contributions of the various types.
(5) When dealing with mixed samples, a prerequisite for proper
deconvolution is the use of appropriate Reference Spectra (see
3.6.2 and 4.7).
(6) At a given intensity of excitation light, Chl fluorescence
intensity does not only depend on the concentration of Chl, but
also on the concentration of the accessory pigments that transfer
excitation energy with high efficiency to Chl. Hence, in contrast
to chemical Chl determinations, the Chl fluorescence method is
44
not specific for Chl (Chl a, Chl b and Chl c), but rather provides
a measure of the concentration of all antenna pigments that
transfer absorbed energy via Chl a to the photosynthetic reaction
centers. This aspect is particularly relevant for assessment of
cyanobacteria, the major light-harvesting antenna of which (the
phycobilisomes) do not contain Chl.
(7) It also has to be considered, that the overall Chl is distributed
between PS I and PS II, and that most of the measured
fluorescence reflects PS II Chl and not PS I Chl. Therefore, any
change in the ratio of Chl (PS I) to Chl (PS II) will affect the
Chl determination via fluorescence, as the Chl/F is changed. For
example, it is known that Chl (PS I)/Chl (PS II) increases in
diatoms with the irradiance level during growth.
At the factory, only a coarse Chl calibration for green algae was
carried out and identical calibration factors for the three main algae
groups were assumed. This is alright for first orienting
measurements, when information on relative Chl concentrations is
essential. For quantitative work, more accurate and algae-specific
calibration is recommended (see 4.9).
The actual Chl determination is very simple, provided the proper
Chl calibration file is selected. It is important that the Measuring
Light Frequency (MF1, MF2, MF4, MF8, MF16, MF32, MF64 or
MF128) used for calibration and for the actual measurements are
matching. The Chl determination is started by pressing the Chl(MF)-
button. Then automatically the deconvoluted fluorescence
amplitudes of the three different groups of phytoplankton are
sampled and the corresponding Chl concentrations are calculated on
the basis of the stored calibration factors. The measured and
calculated values are displayed on the "Algae"-window and also
stored in the Report-file (line starting with cF).
45
3.6.4 How to assess photosynthetic capacity

As already briefly outlined above (see 3.6.1), Chl fluorescence
not only carries information on Chl content, but on the effective
quantum yield of PSII under quasi-dark and light conditions as
well. The product of quantum yield and quantum flux density of
incident photosynthetically active radiation (PAR) provides a relative
measure of electron transport rate (ETR). Plots of quantum yield
and ETR versus PAR (so-called light response curves) give valuable
information on the photosynthetic performance and light saturation
characteristics of a sample.
The PhytoWin-program provides a routine for automated
recording of light response curves. For a first demonstration, open
the "Light Curve"-window and click the "Start"-button. There is
an immediate Yield-determination of the sample adapted to the
Measuring Light (at the given frequency of Measuring Light pulses).
Then light intensity automatically is increased in a first step (see
increase in displayed PAR-value) that extends over a defined time
period, at the end of which Yield again is determined. Further steps
of increased light intensity follow and at the end of each the Yield is
determined, thus resulting in light response curves of Yield and of
the derived ETR. The PAR-values of the various steps, the
illumination time during each step and the total number of steps can
be defined by the user (via Edit, see 4.5.1). The resulting ETR-curve
resembles a P-I curve (Photosynthesis-Irradiance curve), as known
from gas exchange and 14C-fixation measurements. However, it
should be emphasized that the short illumination periods applied
during such ETR-curves do not allow full equilibration of the
photosynthetic apparatus at the individual PAR-values, contrary to
the extended time periods normally applied for P-I curve recordings.
Nevertheless, so-called "Rapid Light Curves" provide relevant
information as outlined in more detail below (see 4.5).
46
CHAPTER 4 FEATURES OF THE SOFTWARE PHYTOWIN
4 Features of the Windows-Software PhytoWin

Operation of the PHYTO-PAM Phytoplankton Analyzer is based
on the PhytoWin-Software in conjunction with a Pentium PC.
Installation of the software was described in 3.5 and some first, basic
measurements using this software were already described in 3.6.
Here the numerous functions supported by this software are
described systematically in some more detail.
The program features seven main "windows" for different modes
of instrument operation, data analysis and display, accessible by the
corresponding register cards:
• Channels: Original, unbiased fluorescence information at

4 different excitation wavelengths
• Algae: Deconvoluted fluorescence information for green algae,

diatoms and cyanobacteria based on previously recorded
reference excitation spectra; user surface for Chl determination
• Report: File in which all measured data and instrument settings

are stored, which can be edited by the user and exported into
other programs
• Light Curve: Graphic display of light response curves; effective

quantum yield and relative electron transport rate (ETR) as a
function of PAR
• Settings: Controls for instrument settings, like measuring pulse

frequency, actinic intensity, saturation pulse width and intensity,
clock interval, damping, number of averages, etc.
• Reference: Display of reference excitation spectra of green algae,

diatoms and cyanobacteria, previously recorded with the same
instrument
47
• Delta F: Special measuring mode restricted to assessment of

variable fluorescence induced by repetitive saturation pulses; for
ultrasensitive measurement of active Chl
For handling of the PhytoWin-Software the standard Windows-
rules apply. For all possible operations "Tooltips" are provided
which are displayed whenever the cursor is moved into the vicinity
of the corresponding switch or button. They give a brief explanation
which in most cases should be sufficient even for an unexperienced
user to find his way through the program. Probably the best way to
become acquainted with the PHYTO-PAM and the PhytoWin-
Software is to read the preceding section 3.6 (First measurements
with the PHYTO-PAM), fill the cuvette with some interesting sample
and start measuring.
In the following sections some background information on the
different windows and instrument functions is provided.
48
4.1 User surface of PhytoWin-Software
Fig. 7 User surface of PhytoWin-Software in MEASURE-mode
Fig. 7 shows the user surface of the PhytoWin-Software in the

MEASURE-mode of operation with the Channels-window being
selected, as seen on the PC-monitor screen. The screen is divided
into 3 sections:
1) The major central part of the screen features the Channels-
window, which represents one out of seven windows that provide
different ways of data output and user surfaces. These seven
windows are described in the following sections 4.2 to 4.8.
2) At the top, the items of the Main Menu are listed (File, Window,
Options and Help). Each item features a pull-down sub-menu.
49
File Window Options Help

Open Report Channels L Curve Details 4 aTooltips
Save Report Algae L Curve Fit Parameters Info
Clear Report Report ETR Parameters
Export Report Light Curve Light Calibration
Open Calibration Settings Reset Light Calibration
Print Report Reference Chlorophyll Calibration
Printer Setup Delta F
Create Trans-file
Exit Transform Ref-file into Exc-file
Transform Exc-file into Ref-file
3) Below and at the right hand side of the central output window a
number of elements for system operation and display of
instrument status are located, which are always accessible and do
not change when various output windows are selected.
These elements will be briefly described starting from the lower
left corner and ending at the upper right corner:
Light:
On/Off switches of Measuring Light
(ML) and Actinic Light (AL),
respectively.
Display of current value of incident photosynthetically

active radiation (quantum flux density) within the cuvette
in units of µmol quanta m-2s-1. The displayed values are
either derived from an internal PAR-list (see 4.10) or measured on-
line with the help of the Spherical Micro Quantum Sensor (see
3.1.8). They depend on the settings of Act. Light Intensity and Meas.
Light Frequency. Different PAR-values apply depending on whether
the Actinic LED-Array-Cone is connected or not (see 3.1.6).
This indicator lamp may light up alternatively green or red.

When it lights up green, the system is ready for
50
measurement. This means that a stable reading is reached and the

signal/noise ratio is high. The indicator lamp lights up red after an
abrupt signal change (e.g. after switching on measuring or actinic
light or after changing photomultiplier gain) and whenever the signal
is disturbed by excessive background light. Due to moving average
signal damping and depending on Damping-setting (see 4.6), it takes
some time for the effect of a disturbance to settle down.
Trigger-button for actinic illumination with terminal

application of a saturation pulse for determination of
effective quantum yield (Yield = dF/Fm). This function is active only
when the illumination time is defined (Act. Light Width on
"Settings"-window, see 4.6). Minimal Act. Light Width is 3 s.
Start-button for Yield-determination by a single

saturation pulse or for averaging of n Yield-
determinations by n saturation pulses, as defined under
"Sat. Pulse and Averaging" on the Settings-window
(see 4.6).
Start-button for a Chl determination based on

measurement of fluorescence yield at the Measuring
Light Frequency at which the active Chl calibration
file was measured (Options submenu, see also 4.3). Measuring
Frequency setting 32 (MF32) is recommended in order to avoid a
state of low PS II excitation (pigment state 2), which is approached
in some types of phytoplankton during dark adaptation. All types of
phytoplankton attain a stable pigment state 1 at MF32 (ca. 20 µmol
quanta m-2s-1), characterized by relatively high values of effective PS
II quantum yield. It should be noted that the measured apparent Chl-
51
concentration (just like the fluorescence yield on which it is based)

will be increased by actinic illumination.
Check box for sub-routine to display the polyphasic

fluorescence rise kinetics of the 4 signals during a saturation pulse.
This function is important to ascertain that for a given sample at
the given conditions the settings of Sat. Pulse Int. and width are
appropriate to reach a plateau of maximal fluorescence yield during a
saturation pulse, which is a prerequisite for proper determination of
effective quantum yield (see 4.2.2).
Repetition Clock: When switched on (check

box), the selected command (Clock-item) is
repeated indefinitely until manually switched
off again. The Clock interval (time between
two consecutive measurements) can be set
(default value 20 s). Minimal Clock interval is
3 s. Please note that the Clock items AL and
AL+Y can be activated only when AL Width
has been defined under Settings (see 4.6).
Running the "Avg. n"-Clock requires previous definition of the
number of averages, n, under Settings.
To leave the PhytoWin-program
When the Power-and-Control-Unit is switched on

and connected via the RS 232 cable with the PC,
following start of the PhytoWin-program
automatically the MEASURE-mode is installed. In this mode of
operation, new data can be measured and analyzed on-line. On the
52
other hand, the VIEW-mode is for off-line inspection of previously

stored data (see 4.11).
Manual start of a New Record, which is characterized

by the time and date of the moment at which New
Record was clicked. This time and date are displayed in the Report-
file (see 4.4) in the headline preceding the numbered data-lines. A
New Record automatically is started upon start of the program, when
returning into the MEASURE-mode from the VIEW-mode (see 4.11)
and upon the first new measurement (i.e. application of a saturation
pulse) after a Light Curve recording (see 4.5). It is recommended to
start New Record manually with every new sample or new
experiment, and to write some relevant information into the Report-
file.
Photomultiplier gain, which after start of the

PhytoWin-program by default is at the low setting of
5. When the Gain-button is clicked, automatically the Gain-setting is
adjusted to a value which is suitable for measurements with a given
sample (Auto-Gain function). It should be made sure that the
photomultiplier is switched on. Otherwise Gain will be increased to
settings 26. Maximal Gain is at setting 30. Automatic Gain-
adjustment is such that the maximal signal amounts to ca. 400 units
(Ft-value on Channels-window). At higher signal levels there may be
"Overload" during a saturation pulse, when fluorescence yield is
strongly increased. The Gain can be also manually adjusted using the
arrows.
Remaining illumination time during the course of an

actinic illumination period. The actinic illumination
53
period is defined on the Settings-window (Act. Light Width) (see

4.6). In conjunction with Light Curves (see 4.5), the width of each
actinic step is defined under Light Curves/Edit.
Date and time of the start of the current measuring

session. A new measuring session is not only started
upon start of the PhytoWin-program, but also when
returning to the MEASURE-mode after VIEW-mode operation.
4.2 Channels-window
Fig. 8 Channels-window for display of original fluorescence signals

measured with 4 different excitation wavelengths
The channels-window represents one out of seven windows

which can be selected for different modes of signal display and
analysis, as well as for definition of instrument settings. The current
signals of the four different excitation channels are displayed in the
Ft-line and also by the four indicator-bars. In the absence of actinic
54
illumination the Ft-values are close to the minimal fluorescence

yield, Fo, of a dark-adapted sample. This is particularly true for the
Ft-values measured at low Measuring Light frequency. Besides the
individual Ft-signals, also the Mean (average of the 4 signals) is
depicted.
4.2.1 Zero Offset and noise N(t)

At low Chl content, when high Gain is required, the Ft-signals
are not only due to Chl fluorescence but also to an unavoidable
background signal that originates from various system components.
Furthermore, in natural surface waters fluorescing compounds like
humic acids may be dissolved, which will contribute to the signal.
The contributions of such background signals can be suppressed by
the Zero Offset (Zoff) function.
To determine Zoff, the cuvette is filled either with pure water or with
the filtrate of a natural water sample. By clicking the Zoff button the
4 background signals are measured and substracted from the original
Ft-signals, such that these are suppressed to zero. It is recommended
to determine Zoff at the same Gain as used for the actual
measurements (see also 3.6.1). There is also the possibility to recall
previously determined Zoff-values from the Report-file using the
Copy Zoff command (see 4.4). If it is foreseeable, that with the same
sample measurements at different Gain-settings will take place, a
number of Zoff measurements at various Gain-settings should be
carried out with the same filtrate. Then at any later time at a given
Gain-setting the corresponding Zoff values can be recalled via the
Copy Zoff command. Please note that the Zoff values also are
adjusted automatically to a changed Gain-setting on the basis of the
known Photomultiplier-Gain characteristic. However, the accurracy
55
of this automatic adjustment is low when Zoff was determined at low

Gain and then the Gain is increased.
As an alternative to the display of the Zoff values, also the

momentary noise, N(F), on the individual fluorescence
channels can be shown. For display of N(t), please click
on N(F) in the selection box. When the noise caused by an external
disturbance has settled down (damping by moving average), the
indicator LED (below PAR-box) gives green light for carrying out a
measurement (application of SAT-pulse). Please note that N(t) will
include any time dependent signal change, i.e. also time dependent
fluorescence changes induced by actinic light.
4.2.2 Measurement of F, Fm, dF and Yield

An actual "measurement" with the PHYTO-PAM requires the
application of a saturation pulse (SAT-Pulse). In Fig. 8 the Channels-
window is shown after Zoff-determination with a filtrate, following a
saturation pulse. This measurement involves assessment of the
fluorescence yield briefly before the saturation pulse, F, and of the
maximal fluorescence yield, Fm. While the Ft-values are
continuously changing and not stored, the F- and Fm-values are
saved in the Report-file. The dF-values are calculated from F and
Fm. They represent the increase of fluorescence yields during the
saturation pulse (dF=Fm-F). The quantum yield of photochemical
energy conversion in PSII (Yield) is calculated by the equation:
Yield = dF/Fm (see also 3.6.1)
In the given example, a sample (mixed suspension of
cyanobacteria and green algae) was dark-adapted and, hence, Yield
corresponds to the maximal PSII quantum yield (commonly referred
56
to as Fv/Fm). The Yield-values determined for the four channels are

similar, but not identical (ranging from 0.52 to 0.55). The
differences, which are considerably larger in a pure cyanobacteria
suspension, are systematic and reflect the excitation of different light
harvesting pigments by the four wavelengths.
For Yield-determination the following points are important:
1) Any background signal should be suppressed with the help of the
Zero Offset function (see above).
2) The Yield-determination should be started only (via SAT-Pulse)
when any signal disturbance, N(t), has settled down, i.e. when
the indicator LED gives green light (see above).
3) The signal amplitude should be appropriately adjusted via Gain.
This is achieved automatically via the Auto-Gain function (see
above). When the signal is too low, the accuracy of fluorescence
measurement is limited by digital noise. Then there is a
corresponding warning:
4) The intensity and width of the saturation pulse should be

appropriate for the investigated sample under the given
experimental conditions. It must be assured that the maximal
fluorescence yield, Fm, is measured. The default setting of
saturation pulse intensity is 10 (maximal), as in most practical
cases errors are more likely to be due to the intensity being too
57
low than too high. An intensity which is sufficient to induce Fm

after dark adaptation, when electron transport is slow, may be too
low after light adaptation, when electrons are rapidly transported
out of the plastoquinone pool. While the maximal saturation
pulse width is 500 ms, the default setting is at 200 ms, as in most
samples a stable plateau of Fm is reached within less than 200
ms. Furthermore, in algae the fluorescence decline following the
initial peak can be very fast. As Fm is determined from the
average of data points at the end of the saturation pulse, this may
lead to underestimation of Fm, dF and Yield.
The "View Pulse" function allows to examine the fluorescence
rise kinetics during a saturation pulse. In Fig. 9 the kinetics at the
maximal saturation pulse width of 0.5 s are displayed. In this
particular example, the fluorescence yield not only rises to a plateau
but also declines again at times beyond 0.2 s. Hence, in this case a
saturation pulse width of 0.2 s (default value) would have been
appropriate (for changing settings see 4.6).
58
Fig. 9 View Pulse function for assessment of rise kinetics during

saturation pulse. In the given example, a saturation pulse width of
0.2 s instead of 0.5 s would have been appropriate
4.3 Algae-window
The Algae-window shows the deconvoluted fluorescence
information for cyanobacteria, green algae and
diatoms/dinoflagellates. The deconvolution is based on Reference
Excitation Spectra (see 4.6) that were previously measured with the
same instrument. The principle of distinguishing between different
groups of phytoplankton is outlined in sections 3.6.2. and 4.7.
59
Fig. 10 Algae-window displaying deconvoluted fluorescence information

after application of a saturation pulse (same sample as for Fig. 8)
In analogy to the Channels-window, the deconvoluted

fluorescence parameters Ft, F, Fm, dF and Yield are displayed. In
addition also the deconvoluted Chl concentrations of the three types
of phytoplankton are shown.
In the same data boxes instead of Chl also the relative
electron transport rate, ETR (see 4.3.2), or the current
noise, N(t) (see 4.2.1), can be displayed.
Besides fluorescence yield, the indicator bars can
also show the dF induced by the last saturation
pulse and the Chl concentration. A corresponding
selection box is provided. Another selection box
allows the user to define maximal signal range for
display at different sensitivities. The F-bar shows
60
the current fluorescence yield (Ft) in the Measure- mode. In the

View-mode the F-value sampled in conjunction with the
corresponding saturation pulse is displayed.
The Ft-values, as well as the corresponding indicator-bars, reflect
the on-line measured deconvoluted contributions of the three types of
phytoplankton to the overall fluorescence signal (i.e. the sum of the
4-channels signals). The sum of the three Ft-values displayed under
Algae and the sum of the four Ft-values displayed under Channels
are almost identical, with the difference increasing with the "Fit
error". The F-values correspond to the fluorescence yields measured
briefly before the saturation pulse and the dF-values represent the
increases induced by the pulse (F + dF = Fm). On the basis of
dF/Fm, the quantum yield of photochemical energy conversion in
PSII, Yield, is calculated (see 3.6.1 and 4.2.2).
In the given example, the water contains similar amounts of
cyanobacteria and green algae (grown at the same light intensity),
and almost no diatoms/dinoflagellates. The Yield-values determined
for the two types of phytoplankton are similar under the given
experimental conditions (Measuring Light Frequency 32, MF32). It
may be noted, however, that at lower MF-values the Yield of the
cyanobacteria decreased whereas at the same time the Yield
increased in the case of the green algae (see Light Curves, section
4.5).
4.3.1 Chlorophyll concentration

The Chl concentrations of the three different types of
phytoplankton are determined on the basis of the current
fluorescence yields at a given Measuring Light Frequency (MF). The
determined values depend on the currently valid Chlorophyll
Calibration file that is shown on the Reference-window (see 4.7 and
61
4.9). Chl determination should be carried out under the same

conditions as the Chl calibration. In particular, the same measuring
light frequency (MF) should be used and the actinic light should be
off (see section 3.6.3 on "How to determine chlorophyll
concentration" and section 4.9 on "Chlorophyll calibration and
determination").
Upon pressing the Chl(MF) button, first the deconvoluted F-
values for the three types of phytoplankton are determined.
Depending on the noise level, between 1 and 2000 data points are
averaged, with corresponding differences in the time required for the
determination. The noise, N(F), may be displayed alternatively to
Chl, by clicking N(F) in the corresponding selection box. Normally,
however, it is sufficient to observe the "status LED" below the PAR-
field. When this lights up green, the noise level is sufficiently low for
Chl determination (as well as for any other type of measurement, like
Zoff- and Yield-determination). After exposure to an increased light
level, e.g. due to the filling of cuvette in daylight or to an actinic
illumination within the instrument, some time should be given for
adaptation to the given Measuring Light intensity and for
fluorescence yield to approach a steady state value.
4.3.2 Apparent electron transport rate ETR
The apparent electron transport rates, ETR, of the three

phytoplankton species can be selected for display alternatively to the
Chl concentrations. ETR is calculated on the basis of the effective
quantum yield of PS II (Yield=dF/Fm) and the PAR (µmol quanta
m-2s-1). Under Options/ETR Parameters the user may chose
between two different ways of calculation of ETR:
62
Relative ETR: When Relative ETR is selected, no attempt is

made to estimate the absolute rate of photosynthetic electron
transport, as no assumption is made on the absorption of the incident
PAR. In the case of dilute phytoplankton suspensions, it is clear that
only a minute fraction of the incident light is actually reaching the
PS II reaction centers where primary charge separation takes place.
Nevertheless it is informative to compare values of relative ETR of
various photosynthetic organisms at the same intensity of incident
light. Many researchers are familiar with ETR measurements in
higher plant leaves for which normally an absorptivity of 0.84 is
assumed. For the sake of comparison the same fictive absorptivity
may be assumed for a phytoplankton suspension:
Relative ETR = Yield x PAR x 0.5 x 0.84 (µmol electrons m-2s-1)
It is assumed that half of the quanta of the incident PAR are
distributed to PS II, the quantum yield of charge separation of which
is measured via fluorescence. Maximum relative ETR-values
calculated in this way, range from ca. 30 µmol electrons m-2s-1 with
shade grown samples to ca. 150 µmol electrons m-2s-1 in the case of
high light grown samples, irrespectively of whether phytoplankton
suspensions or leaves (or any other photosynthetically active
organisms, like corals, sea grasses or lichens) are studied.
63
Estimate of absolute ETR: In order to estimate absolute ETR-

values, quantitative information on the absorption of the incident
PAR is required. Such information can be obtained from
measurements of the absorbance spectrum and the Actinic Light
spectrum (see e.g. Gilbert et al 2000. J Plant Physiol 157: 307-314).
Alternatively, the so-called PSII absorption cross-section can be
determined from the light saturation curve of the fluorescence
increase induced by a single turnover flash (Ley and Mauzerall 1982.
Biochim Biophys Acta 680: 95-106; Dubinsky et al 1986. Plant Cell
Physiol 27: 1335-1349). Under Options/ETR Parameters a value
for Absorption Cross Section (in m2/gChl) can be entered on which
the estimate of absolute ETR is based. The default value of 4.5
m2/gChl was proposed by Nicklisch A and Köhler J (2001)
Estimation of primary production with Phyto-PAM-fluorometry. Ann
Report Inst Freshw Ecol Inland Fish Berlin 13: 47-60.
4.4 Report-window
In the Report-file all measured data are stored. It can be edited by
the user and exported into other programs. The data stored in the
Report-file are the basis for display and analysis of data in the
VIEW-mode of the PhytoWin-program (see 4.11).
64
Fig. 11 Typical Report recording
The Report is organized in terms of separate "Records", each of

which contains a number of "measurements", normally defined by
application of a saturation pulse. Other types of measurements,
which are documented in the Report as well, are Chl determination
(see 4.9) and determination of a new Reference Spectrum (see 4.7).
In Fig. 11 a typical Report documenting a Light Curve recording is
shown (see also 4.5). Text lines start with a semicolon. The user may
add new text lines by marking the site with the cursor/left mouse
click, followed by Return. Before writing a text, a semicolon must be
written. If a semicolon is put by the user at the beginning of a data
line, the corresponding data are ignored upon data analysis in the
VIEW-mode (see 4.11). In this way, data can be temporarily erased
(e.g. a noisy point in a Light Curve) without deleting it.
It is recommended to enter a short comment at the start of each
new Record. A new record can be manually defined with the help of
the New Record button. A comment written at the start of a Record
65
will show in the heading of the given record when displayed in

VIEW-mode (see 4.11). At the start of a New Record the date and
time as well as the current Gain- and Zoff- settings are documented.
The number (No) at the beginning of a Report-line refers to the
current number of a Yield-measurement (by saturation pulse) in the
course of a particular Record. A Light Curve automatically features
as a New Record (a separate "Record" in VIEW-mode, see 4.11).
Also upon program start and when returning to the MEASURE-
mode from the VIEW-mode, automatically a New Record is started.
The headline preceding a New Record shows time and date as well
as the given Gain-setting and Zoff-values. For each Yield-
measurement the Time, Gain, current PAR-value, the F-values of the
four channels and the calculated Yield-values for the four channels
are displayed. Additional information may be called on display in the
VIEW-mode (see 4.11). For each Chl determination, a line starting
with cF is entered in which the Time, Gain, current PAR, the
averaged F-values and calculated Chl concentrations c(Bl), c(Gr) and
c(Br) (of cyanobacteria, green algae and diatoms, respectively) and
their sum are displayed. In addition, also Total c is documented that
is calculated without deconvolution from the original 4-channel
signals on the basis of the calibration for green algae (see 4.6 and
4.9). When Chl is determined on the basis of variable fluorescence
(see Chapter 4.8 on Delta F-mode), the corresponding line starts with
cd and contains additional information (see 4.8 and 4.9.2).
66
A horizontal indicator-bar above the Report-file display

provides information on the extent to which the storage capacity (ca
320 data records) of the Report-file presently is occupied. Before 100
% is reached, the Report-file should be saved and then cleared, to
start at 0 % again. When use of 95 % of the Report-file capacity is
reached, there is a warning: "Capacity of current Report-file
exhausted! First save and then clear current file, in order to start new
file."
Saved Report-files can be analysed at any later
time in the VIEW-mode (see 4.11), which allows
the user to try out different Reference Spectra
for minimizing the fitting error etc.The Save
Report and Clear Report commands are carried
out with the help of the File-submenu (at the top
of the screen). The Open Report and Export
Report commands apply to the VIEW-mode only. In the VIEW-
mode the Report-file (or parts of it) can be exported into other
programs, like Excel or Sigma Plot for further analysis and different
forms of data presentation. The Report-file can be printed out,
provided a suitable serial printer is connected that has been defined
by the Printer Setup routine.
Parts of the Report-file may be marked with the
help of the cursor/mouse, by pulling with the
left key pressed. After clicking the right mouse
key, a pop-up-menu appears, which allows the
usual Windows-specific operations Copy, Cut,
Paste and Print. The Cut can be used for
deleting part of the Report. Goto Record applies in the VIEW-Mode
only (see 4.11). The Copy Zoff function allows the user to install
previously measured Zoff-values that are listed in the Report-file on
the Channels-window. By this way, it is not necessary to prepare a
67
new filtrate of a particular sample and to redetermine Zoff, after this

for some reason was cancelled or overwritten. It should be noted,
however, that the Zoff-values depend on the Gain-setting. Hence,
identical values of Zoff will be installed by the Copy Zoff command
only if the Gain-setting is the same. The Create reference function
allows the user to mark a particular measurement and to define the 4-
Channels F-values as a new Reference Spectrum (see 4.7). Please
note that for Goto Record, Copy Zoff and Create reference it is
sufficient to place the cursor into the corresponding line and click the
left mouse key.
4.5 Light Curve-window

Light curves give information on the light adaptation state and
photosynthetic capacity of a sample (see 3.6.4). With increasing
quantum flux density the effective quantum yield of PSII decreases,
as PSII reaction centers progressively close and an increasing
amount of energy is dissipated into heat.
68
Fig. 12 Light Curve-window showing the effective quantum yield of PS II

(Yield) and the relative electron transport rate (ETR) as a function
of incident PAR. Display of original Channels-data.
69
Fig. 13 Light Curve-window showing the effective quantum yield of PS II

(Yield) and the relative electron transport rate (ETR) as a function
of incident PAR. Display of deconvoluted data (Algae) and the
derived fit curves calculated on the basis of a modified version of
the model of Eilers and Peeters (1988).
The Light Curve-window shows plots of effective quantum yield

(Yield) and relative electron transport rate (ETR) versus the incident
photosynthetic active radiation (PAR). The PAR-scale is
automatically adjusted to the selected range of light intensities,
which are defined by the Edit-subroutine (see below). By double
mouse-click on the Light Curves of Yield or ETR, either of these can
be displayed full scale. With another double mouse click
simultaneous display of both curves can be reinstalled.
70
It is possible to display either the

Light Curves of the Channels-data
(Yield and ETR measured with 4
different excitation wavelengths in
Ch1-Ch4) or the Algae-data (Yield
and ETR of 3 different types of
phytoplankton, deconvoluted using
Reference Spectra for Blue, Green
and Brown). For selection of Channels- or Algae-display the
corresponding radio buttons are used. Check boxes are provided to
select the displayed channels or types of phytoplankton.
If it is known that a sample does not contain a particular type of
phytoplankton, the corresponding Reference should be inactivated at
the Reference-window level (e.g. Reference for diatoms in the
experiment of Fig. 12). In this way, the fitting error can be reduced.
Please note that the deconvolution does not depend on the display of
the Light Curve of a particular type of phytoplankton (i.e.
deconvolution is independent of the status of the check-boxes).
A Light Curve recording is started by clicking
the Start-button. The recording follows the
protocol defined by Edit (see 4.5.1), unless stopped via Stop. The
first measurement is made in the absence of actinic illumination at
the given Measuring Light Frequency.
While in green algae, just like in green leaves, maximal PS II
quantum yield (Fv/Fm) is observed after dark adaptation (or
adaptation to low Measuring Light Frequency), this is not the case
with other types of phytoplankton. Particularly in cyanobacteria dark
adaptation leads to a state of low PS II excitation and low PS II
quantum yield (so-called state 2). In this case, maximal PS II
quantum yield is induced at moderate light intensities (ca. 20 to 40
µmol quanta m-2 s-1, corresponding to measuring light frequencies 32
71
to 64), presumably by a state 2-state 1 pigment transition. This aspect

is illustrated in the Light Curve recordings of Fig. 12 and Fig. 13. A
mixture of Anacystis (cyanobacteria) and Ankistrodesmus (green
algae) was preadapted to MF16 before the Light Curve recording.
While the two ETR curves look very similar, suggesting similar light
saturation characteristics, considerable differences occur in the Yield
curves at low intensities. When light intensity is increased from
MF16 to MF32 and MF64, in the green algae the Yield declines,
whereas it increases in the cyanobacteria. On one hand, this shows
the high quality of the deconvolution. On the other hand, it illustrates
the fact that maximal quantum yield and a maximal positive slope in
the light response curve in phytoplankton do not necessarily occur
after dark adaptation. This point is important for the fitting of the
Light Curve parameters α, ETRmax and Ik (see below).
As already pointed out in section 3.6.4, despite similarity of
Light Curves with common P-I light response curves, there are also
some basic differences, which should be kept in mind when
evaluating Light Curves. In particular, the illumination time at each
PAR-value generally is much shorter for Light Curves than for P-I-
curves. At the default setting of 20 s not sufficient time is given for
the sample to reach a light equilibrated state. Hence, such Rapid
Light Curves (RLC) are expression of the momentary light
adaptation state of a sample. For one and the same sample, there are
as many different RLCs as there are different states of light
adaptation. The user may convince himself about this fact by
recording several consecutive RLCs starting with a dark-adapted
sample. With increasing number of RLC-recordings, the ETRmax will
increase (unless there is photoinhibition). On the other hand, there
should be only one P-I-curve for a given sample when illumination
times are sufficiently long to allow full light adaptation at each
intensity setting. In practice, however, it is not always possible to
72
keep a collected sample physiologically healthy over longer periods

of time.
During a Light Curve recording the number of the
current illumination step is indicated in the Step-
field. The remaining illumination time during a current step is shown
in the AL Time-box (above Gain-box).
Light Curves can be autoscaled by clicking the Autoscale-
icon.
A Print-icon is provided for print-out of Light Curves via a

serial printer.
Under Options (Main Menu) some details in the way of Light

Curve presentation can be defined. Grid: For display of grid. Join:
To connect data points by line segments. For display of the Light
Curve Fit Parameters a separate window is opened, which is
outlined in sub-section 4.5.2.
4.5.1 Edit Light Curves

The Edit-function allows the user to define the Intensity-settings
and the time intervals of up to 20 steps in a Light Curve. This
function provides a high flexibility in Light Curve programming.
73
Fig. 14 Edit-window for definition of Light Curve parameters
For changing the Intensity-setting or Time (in units of 10 s) of a

particular step, the corresponding fields first have to be marked by
cursor/mouse click and then the desired setting can be typed in. It is
recommended to select progressively increasing PAR-values, with
the highest value being at least two times higher than the PAR at
which a sample was grown. One can choose between 20 intensity
settings of actinic light (see 3.1.6 and 3.6.1) and 8 frequency settings
of the measuring light (MF1, MF2, MF4, MF8, MF16, MF32, MF64
and MF128), which at higher frequencies has a distinct actinic effect.
The latter is relevant for assessment of the early part of the Light
Curve, where only a small decrease of Yield occurs (or even a rise in
some types of phytoplankton) and ETR increases almost linearly
with PAR. MF128 is equivalent to Actinic Intensity-setting 0 (see
4.6).
Please note that there is a significant difference between the
spectral composition of the 4-wavelength Measuring Light and the
red (655 nm) Actinic Light. The latter generally is better absorbed by
74
all types of phytoplankton than the average of the former. For

example, for cyanobacteria the actinic effect of 470 nm is very low.
Therefore, as Yield or ETR are plotted against incident PAR (and not
absorbed PAR, which is different for the various types of
phytoplankton) there may be a relatively large decline in Yield, when
actinic illumination is increased from the level of high frequency
Measuring Light (e.g. MF128) to a mixture of MF128 plus red
Actinic Light. This effect is particularly pronounced with low light
adapted or stressed samples, which already are limited by dark
enzymatic reaction at MF128 (i.e. ca. 20 µmol quanta m-2 s-1).
The illumination period at each step is defined by
Time/10s. When "Uniform time" is activated, the
same time can be entered for all steps by typing a new value for one
step and confirmation by mouse-click.
A Light Curve recording does not necessarily have to involve 20
illumination steps. When at a particular step under Time/10s a 0
(zero) is entered, the Light Curve is terminated with the preceding
step.
Alternatively, it is also possible to record up-down Light
Curves with light intensity first increasing to saturation and then
decreasing again. The observed hysteresis pattern provides
information on light activation parameters.
Light Curve recordings may be started repetitively with the help
of the Clock-function (see 4.1). In this way, changes in the light
adaptation state and the physiological health of a sample can be
followed over longer periods of time.
The Light Curve Parameters can be saved in lcp-files
and reinstalled at any time by opening the
corresponding file. This provides great flexibility in Light Curve
recordings. An lcp-file applies to a particular type of Measuring
75
Head and is stored in the corresponding PhytoPam sub-directory

(Data_US, Data_ED or Data_EDF).
Upon pressing the Default-button, a standard list of
intensity settings (with 9 steps ranging from F64 to
AL7) and a uniform illumination time of 20 s are
installed (see Fig. 14). Using this Default-list, a preadaptation to
MF32 is appropriate. Together with the first measurement at the start
of the Light Curve after MF32 adaptation, the 9 intensity steps result
in a Light Curve with 10 data points.
After a previously defined list was changed, the changes

can be confirmed by OK or cancelled by Cancel. In the
latter case, the previously defined list of Light Curve
parameters is maintained.
Two different lists of PAR vs. Actinic Light Intensity Setting
apply depending on whether the Actinic LED-Array-Cone PHYTO-
AL is connected or not, which is automatically recognized upon start
of the PhytoWin-program. With most samples, the use of the Actinic
LED-Array Cone PHYTO-AL is required for reliable Light Curve
recordings, as light adapted samples require higher saturation pulse
intensities for closing PSII reaction centers than dark-adapted
samples. If the intensity of the saturation pulses is too low, dF and,
hence, also Fm, YIELD and ETR will be underestimated.
4.5.2 Light Curve Fit-parameters

When the Fit-button is clicked, a routine is started for
fitting the displayed Light Curves with a theoretical
light response function according to a modified version of the
photosynthesis model of Eilers and Peeters (1988):
76
PAR
ETR =
a ∗ PAR + b ∗ PAR + c
2
with the coefficients a, b and c being fitted for least square deviation.
The fitted curves are displayed as continuous lines superimposed on
the data points of the Yield- and ETR-Light Curves (see Fig. 13).
The original version of the model had to be modified in order to take
account of the fact that some types of phytoplankton (particularly
cyanobacteria) do not show maximal PS II quantum yield at PAR=0,
as assumed by the model, but at significant levels of PAR (ca. 20-40
µmol quanta m-2s-1), corresponding to measuring light frequencies
MF32-MF64) (see also 4.5.1). Hence, there is an initial rise and peak
of Yield, before the usual decline sets in at higher PAR values (see
typical example in the Light Curve of the cyanobacteria in Fig. 13).
This phenomenon is likely to reflect a state 2 - state 1 pigment
change. The fitting routine applied by the PhytoWin program ignores
the data points in the rising part of the Yield Light Curve, including
the peak value.
A speed-button is provided for opening a window listing the L
Curve Fit Parameters for Ch1-Ch4 and for the deconvoluted
types of phytoplankton (Blue, Green and Brown). The same window
can be opened via the Main menu. The parameter α (alpha) reflects
the maximal slope of the ETR Light Curve that, as outlined above, in
phytoplankton samples is not necessarily observed close to PAR=0.
The numerical value of α is equivalent to the maximal Yield
multiplied by a PS II absorptivity term. If, as usually the case,
relative ETR is determined, a value of 0.42 is assumed for this term
(see 4.3.2). For measurement of absolute ETR the optical cross-
section of PS II must be known, the value of which can be entered
under Options/ETR Parameters (see 4.3.2). ETRmax represents
maximal electron transport rate (relative units). Ik corresponds to the
particular PAR-value at the crossing point of the lines defined by the
77
initial slope (going through origin) and ETRmax (parallel to PAR-

axis). It is calculated from the expression α/ETRmax. Ik is
characteristic for onset of light saturation.
Fig. 15 Light Curve Fit Parameters calculated for the Light Curve
recordings displayed in Figs. 12 and 13
The quality of Light Curves for Blue, Green and Brown, just like
the deconvoluted values for fluorescence yield of Blue, Green and
Brown (see section 4.3), strongly depends on proper choice of
Reference Spectra (see 4.7). Actually, in many cases the noise
introduced by the fitting may prevent a satisfactory assessment of
Light Curves for all three types of phytoplankton. This will be
particularly true for a component at low content, when another type
is dominating. The less Reference Spectra are used for fitting, the
lower will be the fitting noise. Hence, if e.g. it is known from
microscopic inspection that no or only few cyanobacteria are present,
the Blue reference spectrum (see 4.7) should be eliminated, to
improve the results for green algae and diatoms.
78
4.6 Settings-window
Fig. 16 Settings-window showing default settings
Under "Settings" a number of instrument settings are accessible

for manual adjustment and display:
Meas. Freq.: Pulse frequency of the Measuring Light in relative
units. The lowest value of 1 corresponds to 13 Hz. At the
standard setting 2 the quantum flux of photosynthetically
active radiation corresponds to ca. 1 µmol quanta m-2s-1, which
in most cases is sufficiently low to allow assessment of the
dark-adapted fluorescence yield, which in phytoplankton is not
necessarily identical to minimum fluorescence yield. The
effective intensities of Measuring Light at different
frequencies are shown in the PAR-box. During actinic
illumination and saturation pulses, Meas. Freq. automatically
is increased to setting 128.
Act. Light: Dial-boxes for Intensity and Width. A total of 20
intensity settings are provided. When Width is set to 0
79
(default-setting), the actinic illumination period is indefinite

and must be manually terminated using the AL-switch. At
Actinic Light setting 0 (zero) no separate Actinic Light is
given, but measuring light frequency is switched to maximal
setting.
Damping: Signal damping by digital low pass filter. Standard
damping at setting 3. Damping is not effective when
Measuring Light Frequency is automatically increased to
setting 128 during actinic illumination and saturation pulses.
Sat. Pulse: Dial boxes for Intensity and Width of saturation pulses.
A total of 10 intensity settings is provided. The pulse length
(Width) can be varied between 40 ms and 500 ms. Default
settings are 10 for the Intensity and 200 ms for the Width.
Whether or not Sat. Pulse Intensity and Width are appropriate,
may be judged for a particular sample with the help of the
View Pulse function (see 4.2.2 and Fig. 9).
Averaging: Dial boxes for No. of averages and the Interval between
consecutive saturation pulses. Up to 100 Yield-measurement
by repetitive saturation pulses may be averaged. It is important
to note that Yield-calculation for all repetitive saturation pulses
is bases on the same F-value measured briefly before the first
saturation pulse. Hence, the relaxation kinetics of Ft following
a saturation pulse are of no concern. However, particularly at
low settings of actinic intensity, each saturation pulse may
cause an increase of nonphotochemical quenching, with
corresponding lowering of Fm and Yield. Hence, for
determination of Fv/Fm or ∆F/Fm at low actinic intensities,
the Averaging-function should be used in conjunction with
relatively long time intervals between consecutive saturation
pulses (at least 20 s). When a No. > 1 of averages is set, the
SAT-pulse-button for triggering a saturation pulse is replaced
80
by a Avg. n-button, which in its resting state shows the total

number, n, of repetitive saturation pulses and after Start the
number of the remaining saturation pulses.
Chlorophyll: Choice between two different modes of calculation of
Chl content. When "Total" is active, Chl concentration is
calculated on the basis of the sum of the original 4-channel
signals, i.e. without differentiation into the three main types of
phytoplankton. The calibration factor for green algae is
applied. Hence, on the Algae-window (see 4.3) only one value
is displayed in the Chl-box for total Chl concentration. On the
other hand, when "Fit" is active, Chl concentrations of the
three main types of phytoplankton are displayed, which are
calculated on the basis of the deconvoluted signals (Blue,
Green and Brown). The sum of the fitted contributions
generally are close (but not identical) to the "Total"
chlorophyll due to the unavoidable fitting error. Calculation of
Chl concentration relies on previous calibration. As calibration
normally is carried out with pure cultures, the calibration
routine involves determination of Total Chlorophyll in order to
avoid fitting errors irrespective of whether Total Chlorophyll
or Fit is active (see 4.9).
Battery: Display of present voltage of internal battery of Power-and-
Control-Unit. When voltage drops below 11 V and the blue
indicator-bar disappears, the battery is almost empty and the
battery charger should be connected. There is a warning:
"Attention low battery! Please connect battery charger."
Recharging of an empty battery takes ca. 12 hours. During use
in the laboratory the battery charger can be permanently
connected.
81
Default: Clicking the Default-box will restore the standard settings.

Settings changed by the user remain valid after the program is
left (via Exit) and started again at a later time.
Save: Upon clicking the Save-button a line with the current
instrument settings is entered into the Report-file. For the
default-settings this line shows:
; G=20, MF=2, D=3, AI=3, AW=0, SI=10, SW=20, AN=1,
AV=3, CW=20
The abbreviations denote the following functions:
G=Gain, MF=Measuring Frequency, D=Damping, AI=Actinic
Intensity, AW=Actinic Width, SI=Sat. Pulse Intensity,
SW=Saturation Pulse Width, AN=Average Number,
AV=Average Interval, CW=Clock Width.
4.7 Reference-window and deconvolution of main groups of

phytoplankton
The primary signals measured by the PHYTO-PAM are 4
different fluorescence signals obtained by excitation of the sample
with 4 Measuring Light beams at 4 different wavelengths (470, 520,
645 and 665 nm). For the sake of deconvolution, the 4 wavelengths
were chosen to give optimal differences in the excitation of the
various antenna pigments that transfer excitation energy to the Chl a
in PS II (see 3.6.2). Each of the three main groups of phytoplankton
(cyanobacteria, green algae and diatoms/dinoflagellates) is
characterized by a typical set of F-values at the 4 excitation
wavelengths, which are called the "Reference Spectra" or more
shortly "References". While they carry the information of 4-point
fluorescence excitation spectra, these "spectra" also are shaped by
the intensities of the 4 differently colored excitation beams that on
82
purpose are not equal. For the sake of higher and more uniform
fluorescence yields, the intensities of the 470 nm and 520 nm beams
generally are increased relative to the 645 nm and 665 nm beams.
Furthermore, due to differences in individual LED intensities, each
instrument features somewhat different relative intensities of the four
excitation beams. Therefore, the References of the same sample
measured with different instruments are similar, but not identical.
They differ substantially between the different types of heads
(standard Optical Unit, PHYTO-ED and PHYTO-EDF). The
difference between a Reference Spectrum and the corresponding
Excitation Spectrum can be described by "transfer-factors" that are
specific for each individual Measuring Head and contained in the so-
called Trans-file of a particular Measuring Head (see below).
4.7.1 Reference Spectra for F and dF

In older versions of the PhytoWin software (issued before July
2003) it had been assumed that the fluorescence excitation spectrum
of a particular sample in first approximation does not change
between dark-adaptation and illumination. It has, however, turned
out that depending on conditions the fluorescence excitation spectra
for the fluorescence yield, F, and the saturation pulse induced
increase, dF, can show significant differences. Therefore, with the
new version of PhytoWin Reference Spectra for F and dF are
measured and applied for deconvolution. The new dual-type
References are stored in Ref2-files, while previously recorded one-
type References are stored in Ref-files. The latter still can be applied
with the new software.
83
Fig. 17 Reference-window with display of Reference Spectra for

fluorescence yield F
The "Reference Spectra" are defined as the normalized 4-

channels fluorescence signals of a particular sample, measured with a
given instrument. The Reference-window shows 2x4 Reference
Lines with the data-boxes containing the numerical values of the
normalized 4-channels fluorescence signals F and dF in different
colors (blue, green, brown and white). The corresponding data points
and connecting lines in the displayed Reference Spectra are blue,
green, brown and black. Blue, Green and Brown Reference Spectra
are delivered together with each instrument on the disc with the
Configuration-data (see 3.5). The fourth Reference Line contains the
normalized 4-channels background signal (Zoff, see 4.2.1), which is
automatically updated with a new Zoff-determination. At the
beginning of each Reference Line there is a check-box to activate or
deactivate a particular Reference. Only when activated, the spectrum
84
of a particular Reference is displayed and participating in

deconvolution. Proper choice of References requires some
background knowledge on the investigated sample. For first
orienting assessment, it is recommended to apply the standard
References Blue, Green and Brown and not to make use of the fourth
Reference (Zoff, see below).
If it is known, that a given sample does not contain substantial
amounts of a particular type of phytoplankton (e.g. green algae in
certain ocean waters), deconvolution of the other types of
phytoplankton will be improved by deactivating the corresponding
Reference.
Fig. 18 Simultaneous display of F and dF Reference Specta
As already mentioned above, the fluorescence yield, F, and the

saturation pulse induced increase, dF, display somewhat different
Reference Spectra. Check boxes are provided for display of F or dF
or of both parameters together. Please note, that in any case the
deconvolution is based on both Reference Spectra.
The 4-channel values of F and dF also depend to some extent on
the light intensity, to which a sample is adapted. Therefore, for
optimal results of deconvolution, the Measuring Light Frequency,
MF, should correspond to the MF at which Reference Spectra were
85
measured. Strong actinic illumination complicates deconvolution

and, if possible, should be avoided. Light Curve recordings (see 4.5)
constitute a special case, where strong actinic illumination is
unavoidable. In this case, normally an increase of the deconvolution
fitting error (see below) is observed at light intensities exceeding ca.
300 µmol quanta m-2s-1.
Deconvolution consists in the fitting of the measured 4-channel
signals (F and dF separately) by the sum of up to 4 components
(Blue, Green, Brown and Zoff). The relative contribution of each
component to the 4-channel signals is determined by the individual
Reference Spectra. The sum of the squares of the deviations of the
measured data points from the fitted values is minimized (least
squares method).
The quality of fitting with a particular set of
Reference Spectra can be judged by the Fit
Error, which is shown for the fluorescence
yield, Ft, and for the saturation pulse induced
fluorescence increase, dF. The Fit Error
depends on the selection of References (via check-boxes) and on the
choice of the particular Reference Spectra files. If it is known that a
sample does not contain a particular type of phytoplankton (e.g. by
microscopic inspection), it is better to inactivate the corresponding
Reference.
A New Reference can be either created from
any measurement documented in the Report (see 4.4) or
a new measurement can be started via the New-button
on the Reference-window. Reference Spectra are measured with
samples of pure cultures of phytoplankton. The sample should be
diluted to a point that no color is seen by the bare eye. If the Gain-
setting exceeds 14, a Zoff-determination with a filtrate should have
been carried out beforehand (see 4.2.1).
86
For optimal results it is important that the light intensity is well

defined, at which a Reference Spectrum was measured. As has been
outlined above (see 4.5), light intensity has an influence on the 4-
wavelengths excitation spectra. It is recommended to carry out all
calibrations (measurement of Reference Spectra as well as Chl
calibration) not after strict dark adaptation but rather after adaptation
of the sample to ca. 20-40 µmol quanta m-2s-1, which corresponds to
Measuring Frequency settings MF32-MF64. For most practical
applications MF32 can be recommended. Therefore, measurement of
a New Reference at MF32 is encouraged by the program. When the
measurement of a New Reference is started (New-button) or after the
Create Reference command at the Report-level (4.4), the following
message is displayed:
This message is not shown, if the Use MF32 checkbox is active

and MF32 already is effective. When Use MF32 is active and MF32
is not yet effective, it will be automatically installed upon Measure
Reference and the actual measurement will take place after 15 s
adaptation to MF32. When Use MF32 is inactive, upon Measure
Reference the measurement will be carried out immediately at the
given Measuring Light frequency.
After measurement of a New Reference, this can be saved in the
corresponding Data-directory of the PhytoPAM folder in form of a
87
Ref2-file. The 2 stands for the two References (F and dF) contained
in this file. With PhytoWin software versions issued before July
2003, only the F-Reference could be measured in form of a Ref2-
file.
Together with the Ref2-file a Comment file can be saved, in

which the type of sample and the conditions of Reference
measurement are documented. This Comment file can be readily
opened by clicking the speed-button in the corresponding Reference
line. If the user decides to save a new Reference under the same
name, the previously written comment is kept unchanged.
Previously saved References can be installed in the
corresponding Reference line by clicking the Load-
button and selecting the file name in the Data-directory of the
applied measuring head.
Either Ref2- or Ref-files
(recorded with older versions of
PhytoWin) can be loaded. While
88
it is also possible to load an Exc-file (Reference Spectra transformed

to Excitation Spectra, see below), for visual comparison with the
corresponding Ref-file, it should be noted that Exc-files are not
suited for deconvolution.
After loading of a particular file the pertaining information can
be viewed after calling up the corresponding Comment file
(see above).
It is recommended to measure a
Reference Spectrum with the same
sample of a pure phytoplankton culture
that is also used for Chl Calibration
(see 4.9.1). To emphasise this point, the currently valid Chl
Calibration file is displayed on the Reference-window. It is also
recommended to use the same Measuring Light Frequency for
Reference measurement and Chl Calibration (with pure cultures) as
well as for deconvolution of Chl content of the various types of
phytoplankton contained in mixed samples. Two speedbuttons are
provided to open a directory of the available Chl Calibration files,
from which a suitable file can be selected, as well as the Comment
file pertaining to the selected Chl Calibration file.
The Zoff-Reference plays a special role in optimizing
the fitting error, which is important at high Gain-setting
only, when the background signal is large and dominating the overall
signal. In most applications, the contribution of a background signal
is already taken sufficient account of by the Zero Offset function (see
3.6.1 and 4.2.1) and the Zoff-Reference does not need to be active.
Activating the Zoff-Reference can improve deconvolution, if the
amplitude of the background signal changes with time. This may be
e.g. related to the bleaching or binding of a dissolved fluorescent
substance or to a change in the extent of scattering of measuring
89
light, which can cause corresponding changes in filter fluorescence

and stray light signals.
The Zoff-Reference values are automatically written into the
corresponding Reference line when Zoff is determined at the
Channels level (see 4.2.1). Furthermore, a Zoff.Ref file is
automatically created and stored in the Data-directory of the applied
measuring head. This file is overwritten with every new Zoff
determination.
For saving of a Zoff-Reference, just like with the References for
the different types of phytoplankton, the current F-signals are
sampled via New-Reference. Please note that for this purpose at the
Channels level no Zoff determination should have been carried out.
4.7.2 Transformation of Reference Spectra into 4-point

Excitation Spectra and vice versa
As already pointed out above, the Reference Spectra differ from
Excitation Spectra, because the intensities of the 4 excitation beams
on purpose are not equal. A genuine Excitation Spectrum is
obtained with the help of a Spectrofluorometer, which measures
fluorescence intensity as a continuous function of excitation
wavelength, with numerous data points, each of which corresponds
to a narrow wavelength interval (in the order of a few nanometers)
and is normalized for an equal flux density of incident quanta. In
contrast, the Reference Spectra measured with the PHYTO-PAM are
measured with only 4 LED-excitation beams (half-band width of
approximately 25 nm), with large intervals between the peak
wavelengths and without any corrections for the differences in LED
intensities. Therefore, it is not possible to transform a Reference
Spectrum into a genuine Excitation Spectrum. The PhytoWin offers,
however, the possibility to create a 4-point Excitation Spectrum
90
from a Reference Spectrum on the basis of information on the

differences in LED intensities. This 4-point Excitation spectrum can
be displayed in the Reference-window and thus can be compared
with the corresponding Reference Spectrum. Please note, however,
that a 4-point Excitation Spectrum (Exc-file) cannot be used for
deconvolution (see 4.7).
Three different routines relating to the
transformation of Reference Spectra
into 4-point Excitation Spectra and
vice versa are offered under Options
in the Main Menu. Create Trans-file
refers to the information on the
differences in the intensities of the 4
LED excitation beams. With
Transform Ref-file into Exc-file the
currently valid Trans-file is applied to
transform a Reference into a 4-point Excitation Spectrum. And with
Transform Exc-file into Ref-file the currently valid Trans-file is
applied to transform a 4-point Excitation Spectrum (e.g. obtained
from another PHYTO-PAM user) into a Reference Spectrum.
When the Option Create Trans-file is selected, a window is

opened which shows the currently valid values of the Head-trans
91
file, which is stored in the Data-directory of the applied Measuring

Head. The displayed example shows values typical for the Phyto-US
Measuring Head. The various values are the factors by which the
corresponding values in the Reference Spectra have to be multiplied
in order to obtain the corresponding values of the 4-point Excitation
Spectra. It is evident that with the Phyto-US the 520 nm and 470 nm
excitation intensities are considerably higher than those at 645 and
665 nm. With every new instrument a specific Head-trans file for the
individual Measuring Head is delivered on the disc with the
Configuration-data.
When older instruments are used in conjunction with the new
software, the Head-trans file has to be created by the user. As long as
this file does not yet exist, upon opening the Create Head-trans file
window at all wavelengths values of 1.000 are shown. These can be
overwritten (after left mouse double click) by new values previously
determined (or estimated) by the user. The values can be obtained by
comparison of a genuine Excitation Spectrum (measured with a
Spectrofluorometer) with a Reference Spectrum measured with the
PHYTO-PAM using identical samples.
Once a Trans-file is available, it can be applied for
transformation of a Ref-file into an Exc-file or vice versa. The
comment file stored in conjunction with a particular Ref-file also
applies for the corresponding Exc-file. Exc-files can be exchanged
between users. They can be transformed back into the corresponding
Ref-files using the instrument specific Trans-files of different
instruments. It should be pointed out this transformation to some
extent depends on identical emission spectra of of the 4 types of
LEDs in different Measuring Heads. Small differences in peak
wavelengths may give rise to some error.
92
4.8 Delta F-window

The Delta F-mode employs a special saturation pulse technique
for assessment of Active Chl via "variable Chl fluorescence".
Outstanding advantages of this technique are its distinctly higher
sensitivity (approx. a factor of 10) and independence of background
signal. Only photosynthetically active phytoplankton contributes
to variable Chl fluorescence. Deconvolution is based on the dF-
Reference Spectra (see 4.7) and, hence, particularly reliable.
While the original fluorescence data give highly sensitive
information on relative changes of phytoplankton content, a
quantification of the absolute Chl contents of the various groups of
phytoplankton requires additional specific information on the
fluorescence properties of the particular types of phytoplankton
present in an investigated sample. In this case, not only suitable
Reference Spectra must be available, but also information on
variable fluorescence parameters and on the relationship between
fluorescence and Chl concentration is required.
93
Fig. 19 Delta F-window immediately following Start of repetitive

saturation pulses.
Upon clicking the Start check-box, the sample is illuminated by

repetitive saturation pulses with 3 s time intervals between pulses.
The first 6 pulses are applied without measuring variable
fluorescence, in order to allow adaptation of the sample to the new
light regime (display of "Please wait"). Then "Measuring" starts,
consisting in the following steps:
- determination of the dF-values of the 4-channels signals
- on-line averaging of consecutive signals
- on-line deconvolution of the dF-signals into the contributions of
the selected References (see 4.7) and
- on-line calculation of the concentration of active Chl (Act. Chl.)
of the three types of phytoplankton.
94
Fig. 20 Delta F-window following Stop of measuring routine after 36

Measuring pulses.
The calculation of Act. Chl. for Blue, Green and Brown relies on
information on the relative extent of variable fluorescence, dF,
typically displayed by the given types of phytoplankton. For
example, it is known that many cyanobacteria are characterized by
quite small dF/F values, while green algae usually show rather large
values. However, considerable differences in dF/F are possible
within one group of phytoplankton and even within the same species,
depending on the physiological health and the light adaptation state.
Therefore, the calculated Act. Chl. may differ substantially from the
Chl concentration determined on the basis of the fluorescence yield
reached after dark-adaptation or to adaptation to the Measuring
Light, Chl (MF) (see 4.9.1). The Act. Chl. parameter not only reflects
Chl concentration, but also the effective quantum yield of a
particular type of phytoplankton. If, e.g. a water sample is poisoned
by a herbicide, dF and the calculated Act. Chl. will tend towards
zero, irrespective of the actual Chl concentration. The same
95
consideration also applies for photoinhibited or strongly "energy-

quenched" samples. Hence, determination of Act. Chl. in the Delta
F-mode cannot replace Chl determination via Chl (MF) or by other
methods (e.g. HPLC). However, it can provide complementary
information on the distribution and activity of various types of
phytoplankton. Its practical value is strongly enhanced by
background knowledge on a particular type of surface water.
Determination of Act. Chl. in the Delta F-mode is documented
in the Report-file (see 4.4). The corresponding data line starts with
cd. It shows the original 4-channels F- and dF-values, the
deconvoluted concentrations of active Chl ac (Bl), ac (Gr) and ac
(Br) and the sum of Act. Chl., the dF/F-values on which calculation
of Act. Chl. is based, and the number of dF-measurements which
were averaged.
Just like with the normal mode of operation, also in the Delta
F-mode proper choice of Reference Spectra is essential. It should be
noted, that choice of the Zoff-Reference does not make sense, as the
background signal does not display any variable component.
In practice, the Delta F-mode is most useful for assessment of
relative changes in phytoplankton composition and activity at very
low Chl contents. Ideally, the Reference Spectra for pure cultures of
the major types of phytoplankton (Blue, Green and Brown) should be
known (see 4.7). Also the Chl/F Factors (see 4.9) as well as the dF/F-
values should have been determined. However, in particular with
respect to Chl/F and dF/F, the absolute values may not be of primary
importance, as most of the time relative changes in content and
activity are investigated. If alternative methods for assessment of Chl
distribution and concentration (flow cytometry, HPLC) are available,
96
these methods should be applied for calibration of the PHYTO-PAM.

Once calibrated, the advantages of the PHYTO-PAM with respect to
sensitivity, reliability and speed of data acquisition will be hard to
beat by any other method.
4.9 Chlorophyll calibration and determination

The principles of Chl determination with the PHYTO-PAM were
already outlined in section 3.6.3. Two different ways of Chl
determination are offered, the Chl (MF)-mode (see 4.3.1) and the
Delta F-mode (see 4.8). In practice, the actual Chl determination in
both modes is very simple and fast. However, from a quantitative
point of view, the obtained values can be only as good as the quality
of Chl calibration, which for natural phytoplankton is not an easy
task. In many practical applications, information on absolute Chl
concentrations cannot be obtained, because the required information
on the quantitative relationship between Chl content and
fluorescence yield of the contained types of phytoplankton is not
available.
4.9.1 Chl (MF)-mode

For Chl calibration, a sample with known Chl concentration is
required. This should be a sample of a pure culture at a sufficiently
high content, such that the contribution of any non-chlorophyll
background signals can be ignored or accurately suppressed by the
Zoff-function (see 3.6.1 and 4.2.1). On the other hand, the
suspension density should not be too high, as this would lead to
reabsorption of Chl fluorescence. In practice, a Mean-signal in the
order of 500 at Gain-setting 14 is appropriate. As in vivo Chl
fluorescence yield depends on light intensity, illumination conditions
should be identical for Chl calibration and Chl determination. As the
97
pigment composition of phytoplankton and in particular the ratio of

Chl (PS I)/Chl (PS II) depends on the light intensity during growth, it
is also important that the calibration is carried out with a culture that
was grown under similar light conditions as the investigated sample.
Therefore, the PhytoWin offers the possibility to carry out a number
of Chl calibrations with various samples grown under different
illumination conditions. These calibrations can be saved in different
Chl calibration files, which can be applied for the analysis of
particular types of samples (see below).
In some types of phytoplankton (particularly cyanobacteria) a
relatively large decrease of Chl fluorescence yield is induced upon
strict dark-adaptation (transition to pigment state 2), which simulates
a low chlorophyll content. Therefore, it is recommended to use the
Measuring Light at a sufficiently high frequency, MF32-MF64,
where a stable pigment state 1 is reached, without significant
reduction of the intersystem electron transport chain.
Please note that data can be collected without a valid Chl
calibration. New Chl calibrations can be carried out at any later time
and previously collected data then can be analysed on the basis of a
selected Chl calibration file in the VIEW-mode (see 4.11). The same
is true for the selection of appropriate Reference-files (see 4.7.1). In
this way, the data stored in a Report-file (see 4.4) can be analysed in
many different ways and then exported in different forms into
spread-sheet programs.
For a New Chl Calibration (of one of the three major types of
phytoplankton) first the Chl concentration is measured on the basis
of the currently valid Chl calibration. Upon clicking the Chl (MF)-
box, the Chl-concentration (in µg Chl l-1) is displayed on the Algae-
window (see 4.3). As only one type of algae is involved, no fitting is
required and Total Chl can be measured. If the displayed
concentration differs from the true concentration, determined for this
98
particular sample with another method (e.g. HPLC), calibration can

be updated via the "Chlorophyll Calibration"-routine under
Options (Main menu). Please note that a new Chl calibration should
always be carried out only with pure cultures of the three major
phytoplankton groups.
The PhytoWin offers different ways of calibration, with different
prerequisites in terms of knowledge on the relationship between Chl
content and fluorescence yield of the involved phytoplankton groups.
The most simple way treats all phytoplankton as green algae, for
which a Chl/F factor of 1 is assumed. In the next step of
sophistication, different Chl/F factors for the three major groups of
phytoplankton can be entered and assumed to apply for all future
measurements (Fixed Chl/F factors). Finally, for optimal results the
variability of Chl/F factors (depending on sample composition and
physiological conditions) has to be taken into account (Variable
Chl/F factors).
Fig. 21 User surface for "Chlorophyll Calibration"
99
Fig. 21 shows the "Chlorophyll Calibration"-window opened via

Options/Chl Calibration after a Chl(MF)-determination with green
algae. Provided the proper References are installed, the program
recognizes the prevailing type of phytoplankton. Under "Algae" this
type of phytoplankton automatically is marked, in order to avoid
errors.
The Chl Concentration determined by the
last Chl(MF)-determination is displayed in
µg/l. It corresponds to the product of Chl.
Total and the Chl/F of the marked type of
phytoplankton. Chl Total is calculated on the basis of the current Chl
Calibration file, shown at the top of the Chlorophyll Calibration
window. This file also determines the currently valid Chl/F factors,
which are shown in the corresponding Chl/F Factors box. In the
given examples for all three groups of phytoplankton the same
default value of 1 is assumed. This corresponds to the least
sophisticated way of Chl calibration that treats all types of
phytoplankton as "green algae". Per definition, Total Chlorophyll
applies to green algae with a Chl/F factor of 1. The displayed value
may be manually modified, if the true Chl concentration is known, as
determined by an alternative, quantitative method (e.g. HPLC). The
value can be simply overwritten (after left mouse double click into
the box).
It will become effective only after clicking the
Calibrate-button. The New Calibration file is stored
under a name given by the user in the Data-directory of the used
Measuring Head. In conjunction with the storing of a New
Calibration file the user can enter a text with relevant information
into a Comment-file.
100
The information on the conditions of a particular Chl calibration

is important for judging the suitability of the corresponding file for
measurements at a later time. The name of the new current Chl
Calibration file is shown at the top of the Chl Calibration window as
well as on the Reference-window. The Comment file referring to a
particular Calibration file can be opened with the help of a
speedbutton on the Reference-window (see 4.7).
If the user has modified the Chl concentration value
displayed on the Chl Calibration window (or the Chl/F
values) and does not want to carry out a New Calibration based on
the modified values, he can just quit the Chl Calibration window via
Cancel. In this case the current calibration will remain valid.
By default the Chl/F factors are fixed at constant values,
unless the radio button position in the Chl/F box of the
Chl Calibration window is changed from Fixed to
Variable. In the Fixed-mode different Chl calibrations relate mainly
to differences in instrument sensitivity. In the Variable-mode
differences in the relationship between Chl content and fluorescence
101
yield are accounted for, assessment of which requires considerable

input from the side of the user.
In the Variable-mode, the Chl/F factors can be modified
manually by overwriting the current values (after double click with
left mouse into corresponding box). The modified values become
effective after pressing the Calibrate-button. The New Calibration
file is saved as described above for the Fixed-mode.
The most sophisticated way of creating a Chl Calibration file
involves three consecutive Calibrations in the Variable-mode
using pure suspensions of typical representatives of cyanobacteria
(Blue), green algae (Green) and diatoms/dinoflagellates (Brown). In
this case, the Chl content of the three types of "Algae" must be
determined by an independent other method (e.g. HPLC). After a Chl
determination on the basis of the current cal-file, the Chl
Concentration displayed on the Chl Calibration window is replaced
by the known value and after pressing the Calibrate-button a New
Calibration file is created with the corrected Chl/F factor for the
corresponding type of Algae. This procedure is repeated for all three
types of Algae and the result of the consecutive calibrations is saved
in the same Chl Calibration file. When e.g. first the calibration was
carried out with green algae and then with cyanobacteria, a definite
value of Chl/F of the cyanobacteria results. And if then e.g. also a
calibration for diatoms is carried out, a definite value of Chl/F of the
diatoms follows. For the three consecutive calibrations, which lead to
a joint Chl Calibration file, one and the same Comment file applies.
When a file is stored under the same name, the additional
information can be added to the previously entered comments.
Upon instrument delivery, only a coarse calibration value for
Green is given and the Chl/F Factors of Blue and Brown are assumed
to be 1.000. Hence, for the time being all phytoplankton is treated as
if it were green algae. It is recommended that each user calibrates his
102
instrument with pure cultures of the types of phytoplankton known to

be present in the investigated water samples. Furthermore, with the
same samples Reference Spectra should be measured (see 4.7). It is
essential that these Reference Spectra are selected for deconvolution
of Chl concentrations in mixed phytoplankton samples. Best results
are obtained when Chlorophyll Calibration and Reference Spectra
Recording are carried out with the same samples of pure
phytoplankton cultures.
For highest accuracy in Chl determination, calibration should be
carried out in the same range of Gain, as used for determination.
However, if calibration is carried out at high Gain, it is essential that
the unavoidable background signal is carefully suppressed using the
Zoff-function (see 3.6.1 and 4.2.1). A clean cuvette filled with pure
water displays a background signal corresponding to approximately
1,5 µg Chl l-1 of green algae using the standard Measuring Head
(ED-101US). Using the PHYTO-ED the background signal is ca. 0,5
µg Chl l-1. Actually, these values may be used for coarse Chl
calibration of the PHYTO-PAM, if the means for more precise
calibration presently are not at hand.
It is also possible to determine the apparent Total Chlorophyll
without deconvolution into the various types of phytoplankton
(Chlorophyll Total selected on Settings-window, see 4.6). In this
case, the 4-channels signals are treated as if originating from green
algae exclusively. Hence, also the calibration for green algae is valid.
The thus determined "Total c" is always documented along with the
fitted values of c(Bl), c(Gr) and c(Br) and their "Sum c" in the
Report-file (see 4.4).
In the VIEW-mode previously stored data can be analysed using
Chl Calibration files as well as Reference-files which were measured
after the analysed data were recorded (see 4.11).
103
4.9.2 Active Chlorophyll in Delta F-mode

Calibration of the Delta F-mode of Act. Chl.-determination is less
straight forward than calibration of the Chl (MF)-mode, as "Act.
Chl." is less clearly defined than Chl concentration (see 4.8).
Actually, Act. Chl. constitutes an empirical parameter, the relative
changes of which provide information on changes in content and
activity of the various types of phytoplankton present in a water
sample. At a given Chl concentration, changes in the measured Act.
Chl. reflect changes in photosynthetic activity. On the other hand, if
a standard activity is assumed, differences in Act. Chl. indicate
differences in Chl (or more generally pigment) content.
The basic Chl (MF)-calibration (see 4.9.1) is also effective in the
Delta F-mode. In addition, dF/F-values for the three types of
phytoplankton (Blue, Green, Brown) must be defined. Whereas
Chl(MF) is derived from the relative amplitude of fluorescence yield,
F, at a given Chl concentration and Measuring Light frequency (see
4.9.1), dF/F represents the typical extent of variable fluorescence
yield under the given conditions of illumination. The dF/F-
parameters are distinctly lower than Fv/Fo-values for the same types
of phytoplankton, as during the pulse illumination a fraction of PSII
reaction centers will close and also maximal fluorescence yield, Fm,
will be lowered by nonphotochemical quenching. Act. Chl. is
calculated from the product dF x dF/F, with the same calibration
applying for dF as for Chl(F).
The calculated values of Act. Chl. for the three types of
phytoplankton ac(Bl), ac(Gr) and ac(Br) (as well as their "Sum ac")
and the dF/F values d(Bl), d(Gr) and d(Br) on which they are based,
are documented in the Report-file (see 4.4).
104
4.10 Light Calibration of Internal PAR-list

Upon instrument delivery the PhytoWin program contains two
standard Light Calibration lists, which apply to the various
settings of Measuring Light Frequency and Actinic Light Intensity
with and without the Actinic-LED-Array-Cone Phyto-AL being
connected (see 4.6). The corresponding PAR-values are displayed in
the PAR-box and are effective during Light Curve recordings (see
4.5). In practice, the absolute PAR-values within the cuvette may
differ somewhat from the values of the standard lists. This is
particularly true for the circular cuvette used in conjunction with the
PHYTO-ED measuring head, where light intensity is distinctly
higher at the crossing point of the LED beams in the center of the
cuvette than at the periphery. In many applications, this is of no
concern, as responses to relative changes of a mean light intensity are
of primary interest.
A special Light Calibration routine is provided for recalibration
of the internal PAR-list with the help of the optional Spherical
Micro Quantum Sensor US-SQS (see 3.1.8) This routine is
accessible via Options in the Main Menu.
Options When Light Calibration is selected, a
L Curve Details 4
new window is opened for the
L Curve Fit Parameters
ETR Parameters
calibration routine. Before clicking
Light Calibration Start, it should be ascertained that the
Reset Light Calibration Spherical Micro Quantum Sensor US-
Chlorophyll Calibration
SQS is properly mounted in the cuvette
Create Trans-file
Transform Ref-file into Exc-file (see 3.1.8) and connected to the Aux.
Transform Exc-file into Ref-file Input of the PHYTO-PAM Power-and-
Control Unit. The Light Calibration routine may be quit with the
help of the Cancel-button. The standard Light Calibration list can be
restored via "Reset Light Calibration" in the Options-menu.
105
Fig. 22 Light Calibration window
The Light Calibration routine involves 21 consecutive 12 s

illumination periods at increasing light intensities. First only
measuring light at maximal frequency is turned on (Meas. Freq. 128,
equivalent to Act. Light Int. setting 0). Then actinic light at settings 1
to 20 is applied. The PAR-values are measured at the end of each
illumination period.
It should be noted that at a given intensity setting the actual PAR
depends on temperature. This is due to the fact that LED emission
decreases ca. 1 % per °C. There is a substantial rise of internal LED
temperature during illumination at high intensity settings which
causes a time dependent drop in PAR. For a 30 s illumination period
this drop amounts to less than 1 % at Act. Int. 5, but increases to 2 %
at Act. Int. 10 and reaches 6 % at Act. Int. 20.
Light calibration should be carried out under the same optical
conditions as the actual fluorescence measurements. This means that
the cuvette should be filled with water, the Measuring-LED-Array-
Cone PHYTO-ML as well as the Actinic-LED-Array-Cone PHYTO-
AL (if available) being properly mounted and the remaining two
ports of the Optical Unit being plugged by the reflecting metal rods.
As the Spherical Micro Quantum Sensor responds to light from all
directions, also the surrounding reflecting surfaces play a role in
determining the actual PAR. For physical optical reasons
(backscattering, immersion effect) the sensor is more sensitive in air
106
than when submersed in water (factor 1.5). This has to be taken into
account, if the sensor is recalibrated.
During Light Calibration and as well as during Actinic
Illumination the program recognizes whether the Actinic-LED-
Array-Cone PHYTO-AL is connected or not. Correspondingly, the
newly calibrated Internal PAR list applies either for the instrument
with and without PHYTO-AL. Please note that for recognition of the
PHYTO-AL it is important that the connector is completely pushed
into the AL Array socket and that the threaded ring has to be
fastened.
4.11 VIEW-mode
The PhytoWin software can be used in two different modes, the
MEASURE-mode and the VIEW-mode. While the MEASURE-
mode requires connection of the PC with the turned-on PHYTO-
PAM via the RS 232 interface cable, for the VIEW-mode only the PC
is required. In the MEASURE-mode, all data automatically are
written into the current Report (see 4.4) from where they can be
further saved in form of RPT-files (Save Report function in File-
submenu) and reloaded in the VIEW-mode.
In the VIEW-mode not only the data can be viewed in the form
as originally recorded and saved in the Report-file, but also in
modified form after selection of different Reference files (see 4.7) or
Chl calibration files (see 4.9.1). In this way, older data can be
analysed on the basis of new information on the composition and
properties of a particular sample.
A Report-file selected in the VIEW-mode can be exported in
form of a csv-file (comma separated values). In this form, the data
can be further analysed with a spread-sheet program like Excel.
Actually, when such a program is installed on the PC, a csv-file is
107
automatically opened in this program. As a Report-file can be viewed

after selection of different Reference-files or Chl calibration files
(see avove), different csv-files can be created on the basis of the
same Report-files. The selected Reference- and Chl calibration files
are documented at the end of the exported file.
If the instrument is properly connected, the user can switch

anytime from the MEASURE- to the VIEW-mode and vice versa.
Upon start of the VIEW-mode, a list of RPT-files stored in the Data-
directory of the PhytoPam-folder is shown, from which the file of
choice can be selected. For each Measuring Head the Report-files are
stored in separate Data-directories. The current Report-file, into
which new data were written before starting the VIEW-mode (and
will be written upon return to the MEASURE-mode), is called
REPORT.RPT.
The selected Report-file is displayed on the Report-window (see
4.4). For viewing details of the individual measurements on the other
windows (Channels, Algae, Light Curve, Reference and Delta F), the
Report is organized into Records, which are displayed in spread-
sheet format on a separate Record-window (see below). The
selection of a particular Record can be carried out at the Report-level
via the Goto Record command (right mouse click for opening pull-
down menu) or via the Select Record function (in the VIEW-mode
always accessible at the right hand side of the screen).
108
Fig. 23 Report-file display in the VIEW-mode with a particular Record

marked by the cursor (left mouse click) and Goto Record
command (after right mouse click) for display in the Record-
window
The arrows allow to jump to the first or the last

Record and to move forward and backwards by
single steps in the Records. A speed button is provided for opening
the Data-directory of the current Measuring Head for selection of a
particular Report-file.
A selected Record is defined by Date and Time,
referring to the moment at which a particular Record
was started in the MEASURE-mode. The start of a
New Record occurs in the following situations:
- upon start of the program
- when returning from the VIEW-mode to MEASURE-mode
- upon start of a Light Curve and
- after clicking the New Record button.
109
The Records contained in a particular Report-file are

numbered. The number of the selected Record (characterized by Date
and Time) is shown, as well as the total number of Records.
A Record is organized into "Lines" which relate
either to a measurement involving the application of a saturation
pulse or to a Chl determination (see 4.9).
Fig. 24 Record-window in the VIEW-mode showing the Record selected

from the Report displayed in Fig. 23
The Record-window shows the selected Record in spread sheet

format, providing a list of all Lines (see Fig, 24). For the sake of
simplicity by default only the Yield values of the 4-Channel data are
displayed. If desired, other parameters (F, Fm, ETR and Zoff) can be
called on display as well.
The user may choose between display of the original 4-
Channel data and the deconvoluted Algae-data in
tabular form.
After selection of a particular Record, the first line in the Record-
display is marked. Any other line may be marked by left mouse click.
In this way, the data of the corresponding measurement are selected
to be viewed and analysed in detail on the various display windows
110
(Channels, Algae, Report, Light Curve, Reference, Delta F) in a

very similar way as in the on-line MEASURE-Mode. The user may
visualize this aspect by selecting a particular Record of interest and
calling up the Channels-window. With each jump on the Record-
display from one line to the next, there are corresponding changes in
the data displayed on the Channels-window.
In the examples of Figs. 25-27, details of a Light Curve
recording of River Main Water are shown (same Record as displayed
on the Report-window in Fig. 23 and in the display of Record 44 in
Fig. 24). For the sake of demonstration, the third step in the Light
Curve was chosen for closer inspection.
Fig. 25 Channels-window in VIEW-mode
The Channels-window shows the original 4-channel signals (Fig.

25). Please note that the four fluorescence values display similar
amplitude. Actually, the intensities of the 4 LED beams in the
PHYTO-PAM on purpose were adjusted to give close to equal signal
amplitudes with water samples of lakes and rivers, which often are
dominated by green algae and diatoms.
111
The deconvoluted F-signals of the three major phytoplankton

species are displayed on the Algae-window depicted in Fig. 27. If
desired, the user could select as well display of dF or Chl. And by
selecting different lines in the Record-display (Fig. 24), this could be
done for all light steps of the selected Light Curve.
Fig. 26 Display of Algae-data on Light Curve-window in VIEW-mode
In the given example, the water sample was preadapted to

minimal Measuring Light frequency in order to demonstrate the
peculiar behaviour of the cyanobacteria at low light intensities.
Please note the distinct differences in the light saturation
characteristics of the three different types of phytoplankton (Fig. 27).
112
Fig. 27 Display of Algae-window in VIEW-mode
The deconvolution of the 4-Channel data into the Algae-data is

based on the Reference Spectra shown on the Reference-window
(see Fig. 28). In the VIEW-mode the user can take the time to try out
various Reference-files in order to minimize the fitting error. As
outlined in section 4.7, the Reference-spectra should have been
measured under similar conditions under which the actual
measurements took place. Previously stored files can be called up for
each type of phytoplankton via Load. Please note that it is also
possible to analyse data on the basis of References that were
recorded after the actual measurements. New References can be
recorded/saved at any time in the MEASURE-mode and then used
for deconvolution of previously measured data.
113
Fig. 28 Display of Reference-window in VIEW-mode
Chlorophyll determinations are documented by separate Lines

in the Report-file (see 4.4). In the VIEW-mode these Lines can be
selected and the original data which led to particular values for Chl
concentrations may be inspected.
Fig. 29 Selection of Chlorophyll Determination Line
114
On the Algae-window Chl concentrations of the three types of

phytoplankton can be displayed. And on the Reference window
various combinations of Reference Spectra may be selected, the
fitting errors may be judged and the effect on the calculated Chl
concentrations may be assessed.
Fig. 30 Display of Chl concentrations on Algae-window
In the case of Chl determination in the Delta F-mode (Line in

Report-file starting with cd), following selection of the particular
Line (see above), the original data can be viewed on the Delta-F
window. It is possible to modify the dF/F values of the three types of
phytoplankton (overwrite after double click with left mouse key into
the corresponding field). The values of Act. Chl. are recalculated
after clicking on the corresponding Line in the Record-window. As in
the case of Chl determinations based on Chl (MF), different
combinations of Reference Spectra may be selected and the Fitting
Error may be minimized.
115
CHAPTER 5 TECHNICAL SPECIFICATIONS
5 Technical Specifications
5.1 General environmental conditions

The general environmental conditions are valid for all
instruments outlined in sections 5.2 to 5.4. The values referring to the
mains voltage apply only if the instrument features a mains
connector.
Permissible environmental temperature

During operation: -5 °C to +45 °C
In resting state: -30 °C to +60 °C
Environmental
humidity: up to 31 °C ≤ 80%,
linearly decreasing to 50 % at 40 °C
Maximal altitude
During operation: 4000 m
In resting state: 15000 m
Mains voltage
fluctuations: max. ±10 %
Overvoltage category: II
Contamination level: 1
116
5.2 Standard System I with Optical Unit ED-101US/MP
5.2.1 Basic System

Power-and-Control-Unit PHYTO-C
Microcontroller: RISC processor
User interface: Pentium-PC with Windows-Software
PhytoWin; connection via RS 232, 19200
baud; keyboard operation; monitor screen
display
Data output: Display and print-out via PC; analog output
of four channels (original fluorescence
data), 0 to 5 V
Power supply: Built-in rechargeable sealed lead-acid
battery 12 V/7.2 Ah; Battery Charger
MINI-PAM/L (100 to 240 V AC)
Power consumption: Basic operation 350 mA; with all LED
light sources turned on, max. 800 mA
Dimensions: 31 cm x 16 cm x 33.5 cm (W x H x D),
with carrying handle
Weight: 6.1 kg
Windows-Software PhytoWin
PC Requirement: Pentium 600 MHz processor (minimum);
128 MB RAM (minimum); Windows 98,
Me, 2000 or XP
Features: Seven main windows for data display and
analysis
• Channels: Original, unbiased fluorescence information at 4
different excitation wavelengths
• Algae: Deconvoluted fluorescence information for green algae,
diatoms and cyanobacteria based on previously recorded
reference excitation spectra
117
• Report: File in which all measured data and instrumental settings

are stored, which can be edited by the user and exported into
other programs
• Light Curve: Graphic display of light response curves; effective
quantum yield and relative electron transport rate (ETR) as a
function of PAR
• Settings: Controls for instrumental settings, like measuring pulse
frequency, actinic intensity, saturation pulse width and intensity,
clock interval, damping, number of averages, etc.
• Reference: Display of reference excitation spectra of green algae,
diatoms and cyanobacteria, previously recorded with the same
instrument
• Delta F: Special measuring mode restricted to assessment of
variable fluorescence induced by repetitive saturation pulses; for
ultrasensitive measurement of active chlorophyll
Optical Unit ED-101US/MP

Design: Black-anodized aluminum body with
central 10x10 mm standard glass cuvette;
for attachment of Measuring LED-Array-
Cone and Photomultiplier-Detector at right
angle; featuring perspex-light-guide
between cuvette and Detector Filter Box;
three additional optical ports to attach
Actinic LED-Array-Cone (optional) and
Miniature Magnetic Stirrer (optional);
light-tight hood with injection hole
Mounting: On special Stand with Base Plate ST-101
Weight: 850 g
Measuring LED-Array-Cone PHYTO-ML

Design: Array consisting of 25 measuring light
LEDs peaking at 470, 520, 645 and 665
nm, as well as 12 actinic light LEDs
118
peaking at 655 nm (max. intensity 600

µmol quanta m-2s-1 PAR), with light-
guiding perspex cone narrowing beam
down to 13 mm Ø; with short-pass filter
(λ < 695 nm) at cone-exit; mounted in
black-anodized aluminum housing
Dimensions: Ø 59 mm, length 190 mm
Weight: 630 g (incl. cable, 1.5 m long)
Photomultiplier-Detector PM-101P
Design: Mounted in aluminum housing containing
pulse-signal preamplifier; featuring on/off
push-buttons and special circuitry for
automatic overload switch-off; with light-
tight Filter Box and adapter for mounting
on Optical Unit
Signal detection: Miniature photomultiplier with high red
sensitivity (type H6779-01, Hamamatsu)
Detector filter: Combination of three filters passing wave-
lengths above 710 nm, optimized for low
background signal
Dimensions: 100 mm x 66 mm x 108 mm (L x W x H)
Stand with Base Plate ST-101

Design: Heavy base plate made from laminated
wood (39.5 cm x 30 cm x 2 cm); with stand
bar Ø 15 mm, height 76.5 cm (dividable in
two parts)
Weight: 2.8 kg
119
5.2.2 Accessories
Actinic LED-Array-Cone PHYTO-AL (strongly recommended)
Design: Array consisting of 37 actinic LEDs
peaking at 655 nm, (max. intensity 2000
µmol quanta m-2s-1 PAR), with light-
guiding perspex cone narrowing beam
down to 13 mm Ø; with short-pass filter
(λ < 695 nm) at cone-exit; mounted in
black-anodized aluminum housing
Dimensions: Ø 59 mm, length 190 mm
Miniature Magnetic Stirrer PHYTO-MS

Design: Based on rotating magnetic field;
connecting to Power-and-Control Unit;
with special adapter plug to be mounted in
bottom port of Optical Unit
Weight: 20 g (incl. cable, 1 m long)
Spherical Micro Quantum Sensor US-SQS

Design: 3 mm Ø diffusing sphere coupled to 1 mm
Ø single plastic fiber connected via ST-
fiber coupler with amplifier box (battery-
driven); featuring special holder for
mounting on standard 10x10 mm glass
cuvette; to be connected to AUX-input of
Power-and-Control Unit; can be operated
alternatively in conjunction with the Light
Meter LI-189 or LI-250 (LI-COR)
120
5.3 System II with Emitter-Detector Unit PHYTO-ED
5.3.1 Basic System

see 5.2.1
see 5.2.1
Emitter-Detector Unit PHYTO-ED

Design: Metal housing with cables connecting to
the Power-and-Control-Unit PHYTO-C;
featuring measuring chamber with 15 mm
Ø quartz cuvette; housing Measuring and
Actinic/Saturation Pulse LED Arrays,
Photomultiplier Detector and Pulse Signal
Preamplifier
Measuring LED Array: Total of 18 LEDs for pulse modulated
Measuring Light peaking at 470, 520, 645
and 665 nm), focused on bottom part of
quartz cuvette via 18 individual short-pass
filters (λ<695 nm)
Actinic LED Array: Total of 16 LEDs for Actinic
Light/Saturation Pulses peaking at 655 nm,
focused on bottom part of quartz cuvette;
actinic intensity up to 2000 µmol quanta
m-2s-1 of photosynthetically active radiation
(PAR); Saturation Pulse intensity up to
4000 µmol quanta m-2s-1
Signal detection: Photomultiplier detector based on
Photosensor Module H-6779-01
(Hamamatsu) with high red sensitivity,
121
featuring pulse preamplifier and automatic

overload switch-off; fluorescence detection
at wavelengths > 710 nm; optimized for
low background signal by special filter
combination
Weight: approx. 600 g (incl. cables 0.6 m long)
5.3.2 Accessories
Spherical Micro Quantum Sensor US-SQS
see 5.2.2
Stirring Device WATER-S

Design: Miniature stirring motor in plastic housing
with adapter to mount on top of the
Emitter-Detector Unit PHYTO-ED;
equipped with disposible perspex stirring
paddle; self-contained unit featuring long-
life 3 V Lithium Battery; potentiometer for
adjustment of stirring rate
Weight: 95 g (incl. battery)
122

PHYTO-EDF
5.4.1 Basic System

see 5.2.1
see 5.2.1
Emitter-Detector-Fiberoptics Unit PHYTO-EDF

Design Emitter-Detector
box: Metal housing with cables connecting to
the Power-and-Control-Unit PHYTO-C;
containing Measuring and
Actinic/Saturation Pulse LEDs, miniature
fiber couplers with SMA-fiber connectors,
Photomultiplier and Pulse Preamplifier;
separate 9-armed fiberoptics
Weight: approx. 600 g (incl. cables 0.6 m long)
Measuring LEDs: Total of 4 LEDs for pulse modulated
Measuring Light peaking at 470, 520, 645
and 665 nm, focused by miniature
collimating lenses via 4 individual short-
pass filters (λ <695 nm) on entrance of 1
mm Ø single plastic fibers with SMA-
connectors
Actinic LEDs: Total of 4 LEDs for Actinic Light
/Saturation Pulses peaking at 655 nm
focused by miniature collimating lenses via
123
4 individual short-pass filters (λ<695 nm)

on entrance of 1 mm Ø single plastic fibers
with SMA-connectors; actinic intensity up
to 1800 µmol quanta m-2s-1 of
photosynthetically active radiation (PAR);
Saturation Pulse intensity up to 3500 µmol
quanta m-2s-1
Signal Detection: Photomultiplier detector based on
Photosensor Module H-6779-01
(Hamamatsu) with high red sensitivity;
featuring pulse preamplifier and automatic
overload switch-off; fluorescence detection
at λ>710 nm; optimized for low
background signal by special filter
combination
Fiberoptics: 8 arms with 1 mm Ø single plastic fibers
with SMA-adaptors to be connected to
Measuring Light and Actinic Light
connectors on top side of Emitter-Detector
box; central 1.5 mm Ø fiber with adaptor to
detector input; length 105 cm; joint end
with special endpiece featuring 4 mm Ø
perspex light mixing rod, length 50 mm
Special Stand: Heavy base plate made from laminated
wood (39.5 cm x 30 cm x 2 cm); with stand
bar Ø 15 mm, height 76.5 cm (dividable in
two parts; weight 2.8 kg; featuring special
holder for fiberoptics endpiece, dark-box
for shielding sample from ambient light
Technical specifications are subject to change without prior notice.
124
CHAPTER 6 RECHARGEABLE BATTERY
6 Rechargeable battery
The Phytoplankton Analyzer PHYTO-PAM is equipped with a
rechargeable sealed-lead acid battery.
The life time is 1-3 years and it depends on the specific

application. A 10 °C rise of the temperature will decrease battery life
by approx. 25%. Near the end-of-life the standby capacity of the
battery will be reduced. When this reduction becomes persistently,
please replace the battery.
The battery cannot be overcharged, when the battery charger

supplied with the instrument is used! Do not use any other battery
charger!
Never store the instrument with a discharged or partially

discharged battery! It is recommended to charge the battery every
three months during the storage period.
• For optimum performance always recharge the battery

immediately after discharging!
• Never leave the battery in a discharged stage!
• Never short-circuit the battery terminals!
125
CHAPTER 7 WARRANTY CONDITIONS
7 Warranty conditions
All products supplied by the Heinz Walz GmbH, Germany, are
warranted by Heinz Walz GmbH, Germany to be free from defects in
material and workmanship for one (1) year from the shipping date
(date on invoice).
The warranty is subject to the following conditions:
1. This warranty applies if the defects are called to the attention of
Heinz Walz GmbH, Germany, in writing within one year (1) of
the shipping date of the product.
2. This warranty shall not apply to any defects or damage directly
or indirectly caused by or resulting from the use of unauthorized
replacement parts and/or service performed by unauthorized
personnel.
3. This warranty shall not apply to any product supplied by the
Heinz Walz GmbH, Germany which has been subjected to
misuse, abuse, abnormal use, negligence, alteration or accident.
4. This warranty does not apply to damage caused from improper
packaging during shipment or any natural acts of God.
5. This warranty does not apply to underwater cables, batteries,
fiberoptic cables, lamps, gas filters, thermocouples, fuses or
calibrations.
To obtain warranty service, please follow the instructions below:
1. The Warranty Registration form must be completed and returned
to Heinz Walz GmbH, Germany.
2. The product must be returned to Heinz Walz GmbH, Germany,
within 30 days after Heinz Walz GmbH, Germany has received
written notice of the defect. Postage, insurance, custom duties,
126
CHAPTER 7 WARRANTY CONDITIONS
and/or shipping costs incurred in returning equipment for

warranty service are at customer expense.
3. All products being returned for warranty service must be
carefully packed and sent freight prepaid.
4. Heinz Walz GmbH, Germany is not responsible or liable, for
missing components or damage to the unit caused by handling
during shipping. All claims or damage should be directed to the
shipping carrier.
127

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Phytoplankton Analyzer

 Heinz Walz GmbH, 2003

Heinz Walz GmbH • Eichenring 6 • 91090 Effeltrich • Germany

Note regarding the US-SQS:

The diffusing sphere is slightly greater.

The comments in the manual in regard to bending the fiberoptics do not

Note regarding the wavelengths of the Measuring Light:

Note regarding the actinic and saturation pulse intensities of the

1 Safety instructions ........................................................................ 1

3.6.3 How to determine chlorophyll concentration....................... 43

5.2 Standard System I with Optical Unit ED-101US/MP ............. 117

1.1 General safety instructions

1.2 Special safety instructions

possibility to assess photosynthetic activity of the various types of

Handbook to point out potential problems and to help the user to

3 Components of the PHYTO-PAM Fluorometer

3.1 Standard System I with Optical Unit ED-101US/MP

Fig. 1 PHYTO-PAM Standard System I Components

The basic operational system of the PHYTO-PAM Fluorometer

1) the Power-and-Control-Unit PHYTO-C

8) the Miniature Magnetic Stirrer (PHYTO-MS) that can be

3.1.1 Power-and-Control-Unit PHYTO-C

• ML Array socket, to connect Measuring LED-Array-Cone

• AL Array socket, to connect Actinic LED-Array-Cone

• Aux. Input socket, to connect auxiliary devices, like the

• Magnetic Stirrer socket and potentiometer, to connect and

• Power switch and green indicator lamp, controlling connection

• RS 232 socket, to connect RS 232 interface cable for data transfer

• PM socket, to connect Photomultiplier-Detector PM-101P

• Charge socket, to connect Battery Charger MINI-PAM/L (100 to

• Fuse plug, containing M 1.6A (medium blow) main fuse of

• Excitation Channel Output sockets, to connect analog device of

3.1.2 Battery Charger MINI-PAM/L

voltage is displayed on the Settings-window in conjunction with the

3.1.3 Optical Unit ED-101US/MP

The top of the Optical Unit is covered by a special ring, which

3.1.4 Photomultiplier-Detector PM-101P

Fig. 2 Arrangement of the filters in front of the photomultiplier

The Photomultiplier-Detector can be manually switched on/off

3.1.5 Measuring LED-Array-Cone PHYTO-ML

3.1.6 Actinic LED-Array-Cone PHYTO-AL (recommended)

While not being required for basic operation of the PHYTO-

3.1.7 Miniature Magnetic Stirrer PHYTO-MS (optional)

The Miniature Magnetic Stirrer is connected to the

3.1.8 Spherical Micro Quantum Sensor US-SQS (optional)

optimal results it is recommended to apply the same light source for

reading decreases with decreasing bending radius. This effect may

3.1.9 Temperature Control Unit US-T (optional)

3.2 Steps for setting up the basic PHYTO-PAM System I

of 0.2 - 0.5 mm is alright. Then install covering ring, assure that

The following steps have to be taken for proper electrical

3.3 System II with Emitter-Detector Unit PHYTO-ED

Fig. 3 Emitter-Detector Unit PHYTO-ED (left) with Stirring Device

The PHYTO-ED is connected via three cables to the

• ML-Array, 4-wavelengths Measuring Light

• AL-Array, red Actinic Light

• PM, Photomultiplier Detector

It consists of the following components:

• Water-proof cast aluminium housing from which the external