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LI-6400 Preparation Checklists.

Instructions given here are based on OPEN version 5 software which is installed in the CRC unit. The Ecofiz unit has the
more recent OPEN version 6 software installed (also known as XT), as such there are subtle differences in the way you set
some parameters and navigate through the software. I have tried to differentiate between the commands for the 2 operating
systems in these instructions, if unsure, consult the appropriate manual.

The information listed here can also be viewed in part in the LiCor operator’s manual, chapter 4 ‘Preparation Check Lists’.
I have expanded many of the sections to offer greater understanding and provide tips based on my experience.

Part A. System Check & Assembly.


1. Air Supply: Prepare CO2 mixer or buffer volume container
2. Drierite and Soda Lime: Check scrubber tubes
3. Connect cuvette Cables and air lines in good condition?
4. Battery: What source of power will you use?

Check chemical scrubbers, cuvette gasket condition and individual batteries are fully charged voltage before leaving for the
field or glasshouse.

1. Air Supply
In most situations, you will use the CO2 mixer; check small o-ring is in good condition, replace if required then install
the CO2 cartridge so the system can begin pressurizing. A fresh CO2 cartridge is needed each day, and will usually
last 6-8 hours.

2. Chemical Scrubbers
Good condition Drierite is blue, used or wet Drierite is pink. Replace if reasonable pink color seen (i.e. > 1/3 of tube).
Good condition soda lime is white and deep purple when saturated with CO2. (N.B. Drierite needs more frequent
replacement than soda lime). When changing chemicals, ensure o-ring and thread on bottom part of the chemical
tubes are clean and in good condition to provide a good seal, wipe clean if necessary.

3. Connect cuvette
When connecting data cable and air lines from console to cuvette, check their integrity. Check the cuvette leaf
chamber foam pads are not torn or too compressed, replace if necessary. When using the LED light source, top
gasket MUST be white for correct light transmittance; bottom gasket is black.

4. Battery
Take enough batteries including spares, LiCor batteries last approx. 3-4 hours and can be changed without switching
unit off. You may also connect a car battery for longer use.
If using a car battery ensure you connect with correct polarity, red or +ve lead to +ve terminal on battery and black or
–ve lead to –ve terminal, otherwise you will blow a fuse and unit won’t work
If available, run the unit with mains power by connecting both a single battery and the charger to the LiCor console.
Battery power can be saved by putting the unit into sleep mode, under ‘Utilities’ menu (function 5) from the main
OPEN screen. Do this when taking a break or moving sites in the field. Upon waking up from sleep mode, no need to
do full checks again, simply let run for a couple of minutes and continue with your measurement.

5. Turn unit on

6. Select the appropriate cuvette configuration from the list TAKING SPECIAL NOTE OF SELECTING DIRECT LEAF TEMPERATURE
MEASUREMENT VERSUS ENERGY BALANCE. (Use the latter if you can’t ensure leaf comes into contact with leaf
thermocouple for EVERY measurement)

7. When you are prompted if the cuvette is connected, choose Y/N accordingly, the screen will then proceed to the main
OPEN view, from here you can view the software version and battery charge level.

8. Finally, in the main OPEN view, ensure the date and time are correct, if not, you should change this. Also check battery
voltage

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Part B. During Warm Up.
1. Temperatures: Are the values OK? Tleaf responding?
2. Light Source and Sensors: Responding? Values OK?
3. Pressure Sensor: Value OK? Stable?
4. Leaf Fan: Running?
5. Flow Control: Maximum flow OK? Chemical tube restrictions?
6. AGC values: Record these for maintenance purposes

The following steps require you to navigate to ‘New Msmnts’ mode from the main OPEN screen, access by function 4 button
(f3)

1. Temperatures
The 3 measured temperatures (block, chamber and leaf) are together in display group h. Check values are
‘reasonable’ and are within a few degrees of each other.
Position the thermocouple as desired by gently moving the stem of the thermocouple under the cuvette. Just above
the cuvette gasket for direct leaf measurement (guarantee leaf touches every time) or pulled down for air temperature
differential based measurement (energy balance).

2. Light Source and Sensors


Connect external PAR sensor (if required) and check LI6400 is configured for light source you are using. Light
sensors (ParIn_m and ParOut_m) are in display group g. See they respond as expected when sensors are
illuminated and darkened. If using LED light source, turn it on to check its inbuilt sensor, go to menu 2 in ‘New
Msmnts’ then function 5 (2 f5)
A negative light reading probably means you have selected the wrong light source in the first instance. A trip to Light
Source Control will soon rectify this.

3. Pressure Sensor
Display group g. Check value is reasonable and stable. (Typical value at sea level is 101 kPa)

4. Leaf Fan
Turn off both Lamp (2 f5) and flow (2 f2) to make it easier to hear leaf fan switching on and off. In menu 3 of ‘New
Msmnts’ function 3 (3 f3) turn leaf fan off (O) and then on again (F), 3 f3 for CRC unit and 2 f1 for Ecofiz unit and
listen for sound changes in the leaf cuvette as the fan motor stops and starts. Leave the fan on fast when you have
checked this. No sound may mean a blown fuse or debris jamming the actual fan.

5. Flow Control
Use flow control (2 f2) increase flow to 1000 mol/s; watch Flow_ms display group b to determine the actual
maximum flow. Value is typically high 700’s to low 800’s when a mixer installed and higher without mixer.

Reset flow to 500 µmol/s when finished this test

Now test the chemical tubes for flow restrictions by changing each from full bypass to full scrub watching the effect on
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flow rate. Normally, scrubbing will drop the maximum flow by 5 or 10 μmol s per tube. Larger drops may indicate that
the air mufflers in the chemical tubes are getting clogged, or that a flow diversion tube is pinched shut. See
Pump/Flow Problems for more details.

6. AGC Values
Before making measurements, record AGC values in display group l. AGC values indicate how much radiation is
‘absorbed’ in the non-absorbing IR bands for both CO2 and H2O and range is -5000 to + 5000 mV. With a good IR
source and clean optics, these values are typically 0 or less. As the optics become dirty, these values will increase.
Invert the cuvette and observe if the values, especially the sample AGC values change significantly.
If fluctuating significantly (> 20 mV), it may mean dirt or plant material is trapped within the IRGA’s optical bench.
This needs to be cleaned before undertaking (accurate) measurements.
If the AGC values are large (> 2000 mV), quite variable &/or changing irregularly, unit may need to be cleaned before
use, see Greg Cawthray.

Created by Greg Cawthray Page 2 of 8 5/30/2014


Part C. After Warm Up.
1. Check the flow zero
2. Adjust latch, close chamber
3. Check CO2 zero
4. Check H2O zero
5. Mixer calibration (optional)
6. Lamp calibration (optional)
7. Check Tleaf zero
8. Check ambient water
9. Set reference CO2
10. Set reference H2O
11. Test for leaks
12. Recheck Soda Lime
13. Match the IRGAs. Valve working?

If IRGA’s have not reached optimum operating temperature, a message will flash across the ‘New Msmnts’ screen.

1. Check Flow Zero


In New Measurement mode, monitor Flow_ms (display group b), turn pump (2 f2 N) and leaf fan off (3 f3 O for off
for CRC unit and 2 f1 O for off for Ecofiz unit). Flow should drop to within 1-2 mol s of zero. If this doesn’t occur,
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re-zero flow meter (page 18-17 in book#3). Turn chamber fan back on when finished this check.

2. Adjust Latch and Close Chamber


Adjust latch such that the gaskets are slightly apart when the chamber is closed. With the chamber closed, turn the
adjustment screw until both gaskets just touch. Open the chamber and turn the screw ½ to a full turn to ensure a full
seal is obtained when a leaf is clamped onto, as well as when the cuvette is empty. Close the chamber for the next
2 steps. You will loosen the chamber latch at the end of all measurements to reduce compressing the foam pads
unnecessarily.

3. Check CO2 IRGA zero


In New Measurement mode, with mixer off (2 f3 N) and flow set 500 mol s (f2 F 500 enter), monitor CO2
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reference and sample (display group a). Turn soda lime on full scrub and the desiccant on full bypass. Reference
CO2 should approach zero quite quickly, while sample CO 2 will take a little longer to reach zero. If they are within 5
mol mol of zero, that will be adequate.
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This is a good time to familiarise yourself with the live data graph function. Shortcut to graph function from the ‘New
Measurements’ screen is the ‘]’ button. The ‘[‘ button shows the current calculated stability values for CO 2S, H2OS
and flow,
If the values are not within 5 mol mol of zero, it may be the soda lime needs replacing rather than the calibration
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being off. To check the soda lime, go to point 12 to do this. If the soda lime seems okay after testing, then re-
zeroing may need to be done, consult with Greg Cawthray first

4. Check H2O IRGA zero


Turn the desiccant to full scrub and watch the sample and reference H2O. Again reference will approach zero more
quickly than the sample. It will also zero more slowly than the CO 2 IRGA did due to water sorption. It may take 15-
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20 minutes to get a full zero, but usually after a minute or so, the values should be around the 0.2-0.3 mmol mol .
Clearly if it’s negative and falling after only 1 minute, then it will drop too far below zero, and a re-zero will be
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required. If it does not reach 0.2-0.3 mmol mol , it may mean that the Drierite requires replacing.
Revert to Full Bypass once you have checked the H2O zero to preserve the Drierite.

CAUTION: If your chemicals (soda lime and drierite) are not fresh then you will do more damage than good by re-
zeroing the instrument with them. Please only redo a zero if you are sure the chemicals are in excellent condition.

IRGA zeros are quite stable, especially in absence of big temperature changes. The exercise of checking zeros
each day is really a diagnostic check. When doing any re-zeros or re-calibrations certain values and settings need
to be recorded, hence why none of these instrument setting parameters should be changed without notifying Greg
Cawthray.

5. OPTIONAL Mixer calibration (usually not required)


You may wish to run the calibration program described on page 18-20, ensuring that the soda lime is on full scrub.
Please record in the logbook if you undertake CO2 mixer calibration.

6. OPTIONAL Lamp calibration (usually not required)


Usually not done during routine warm-up and operation of the LI6400 and see Greg Cawthray if you feel the light
needs to be re-calibrated, or is taking significant time to reach the set value.

Created by Greg Cawthray Page 3 of 8 5/30/2014


7. Check Tleaf zero
Unplug leaf temperature thermocouple connector (purple colour) and compare the leaf and block temperatures. If
they differ by more than 0.1C then adjust. (refer to page 18-19 for instruction on this AND see Greg Cawthray).
Re-connect the thermocouple and verify it is working by watching the leaf temperature increase when touching the
thermocouple.
Inspect thermocouple junction is at apex of smooth rounded wire support.

8. Check ambient water


With mixer off & soda lime full bypass, run Drierite full bypass to give ambient H2O in cuvette. Once H2O stable, run
soda lime full scrub and notice change in H2O. Some soda lime can significantly add water to the reference gas.
You may want to scrub out this extra water for your measurements.

9. Set reference CO2


With CO2 mixer, ensure soda lime is full scrub and set reference CO2 to level required menu 2 function 3 (2 f3). If
using buffer volume, most likely run the soda lime on full bypass.

10. Set reference H2O


To control H2O, use scrub/bypass knob on the Drierite tube to attain desired reference H 2O as determined from step
8. For optimum measurements you may need to change H2O reference frequently. Aim for a sample relative
humidity of 50-80%. Above 80% warning message sounds to protect the IRGAs, and below 50% stomata may begin
to close for water conservation.

11. Leaks?
With the chamber closed and empty set flow to 200 mol s . Gently blow around chamber gaskets and
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watch for any fluctuations in the sample CO2 concentration (CO2S_mol mol , display group a). If no leaks,
CO2S_mol mol value should not increase by more than 1-2 mol mol . Once done, increase flow to 500 mol s .
-1 -1 -1

12. Recheck Soda Lime


With the IRGAs now running, make a more definite check on the condition of the CO2 scrubber chemical tube.
With soda lime ion full scrub, gently blow near the air intake on the console, then immediately watch the CO2_R.
This should not rise by more than 3-5 mol mol . Greater than this, change soda lime. Changing soda lime can be
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done with the instrument left running, just don’t take any measurements!

13. Match the IRGAs (Critical)


Matching the IRGAs must be done at the start of a measurement day, and routinely during the measurement day, as
frequent has every 30 min.
Also match the IRGA’s if;
 Photosynthesis rates are low (especially for small leaf area)
 After large CO2 changes
 After large flow rate changes
 Changing ambient temperature
In ‘New Msmnts’ select menu 1, function 5 (1 f5).
When entering the match IRGAs page, ensure the match valve is working by watching it change position. Refer to
page 4-34 for a full description of matching, however looking at the unit from underneath, the right hand side of the
paddle should be down when in MATCH mode. At times the paddle gets stuck, try and release it by exercising the
MATCH valve. In OPEN Welcome menu there is a menu titled “Tests and Diagnostics”, which leads to a menu
containing “Match Valve Tester”. This program allows you to “manually” (via the function keys) control or exercise
the match valve. If this fails see Greg Cawthray.

14. Check the IRGA’s baseline


With empty cuvette, check IRGA baseline by looking at ∆CO2 and ∆H2O (display group b) and ensure they are at
acceptable levels (should be ±0.5 and ±0.07 respectively).

IF YOU DO ANY RE-CALIBRATIONS OF FLOW, IRGAS OR LIGHT SOURCESAND ESPECIALLY CHANGES TO


CALIBRATION ZEROES PLEASE RECORD IN LOG BOOK AND LET GREG CAWTHRAY KNOW.

Created by Greg Cawthray Page 4 of 8 5/30/2014


Part D. Making the First Measurement.
Once you’ve got the system behaving with no leaf in the chamber, have matched the IRGA’s, you are ready to start. Basic
measurement procedure is quite simple: set conditions, insert leaf, revise chamber conditions, and then wait for stability
before logging the data. REPEAT (with frequent matching!)

1 File management,
Open a new or existing data file from menu 1, function 1. Once a data file is open, the number of measurements
made can be viewed at any time from the display in menu 1 function 1. Take a set of blank measurements at the
start and throughout your measurements over the day.

2 Light
If using the lamp, set to the desired value (you may even want to run a light response curve to find the appropriate
saturating light level you need to use for measurements). If you aren’t using the LED source, then orient the
chamber so that no shading of the leaf by the chamber walls will occur once you’ve installed the leaf.

3 Flow
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Set fixed flow at 500 μmol s and desiccant as determined in step 10 Part C. We’ll come back to this in Step 9.

4 CO2
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If using the CO2 mixer, set it to control reference CO2 with a target slightly above ambient (say, 400 μmol mol ). If
you aren’t using the CO2 mixer, but using a buffer volume instead, set the soda lime scrub knob to give you the
concentration you want. Usually, that means full bypass.

5 Temperature
(Optional) If you are going to be in direct sun, you will probably want to use the coolers to control the block
temperature of the cuvette. Check the temperatures to see their present values, and then set the control accordingly,
(2 f4).

6 Insert leaf
Check the latch adjustment for a good seal. Snug is fine; however be careful it’s not too tight. If you are using clear
chamber tops, be careful with the chamber’s orientation; avoid shading part of the leaf with the walls of the chamber.

7 OPTIONAL Set Stability (OPEN version 5 and above only)


Initially, monitor for stability manually using the graph function until you become familiar with the
instrument and the measurements process
Use Define_Stablty (f4 level 5) to setup the stability criteria you wish to use
(Defining Stability on page 6-24).
In most cases you will use the graph function of the Li6400 to monitor ΔCO2 and ΔH2O to assess when a stable
reading has been obtained and thus log the data. Graph function is found in menu 4. Shortcut to graph function from
the ‘New Measurements’ screen is the ‘]’ button. The ‘[‘ button shows the current calculated stability values for
CO2S, H2OS and flow,

8 OPTIONAL Log Options, Log Button (optional)


In most cases use the menu 1 function 1 button to record the data, there is also a log button on the actual
cuvette, left hand side of the handle
This is a good time to set your log options (Log Options, f3 level 5) and your log button behavior (f5 level 5), if you
wish. See User Definable Log Button on page 9-7 and Log Options on page 9-9.

9 Set Area and Stomatal Ratio


In ‘New Msmnts’ mode, menu 3, set the leaf area and stomatal ratio for this leaf via function 1 (3 f1). Leaf area is
simply the area exposed inside the chamber. If you are using a 2x3 chamber and filling it, the area is 6 cm2.
Stomatal ratio is an estimate of the ratio of stomata on one side of the leaf to the other. Use 1 for equal stomatal
density on top and bottom; 0 for stomata on only one side. If you aren’t sure, use 0.5. It doesn’t matter if you use the
ratio of top to bottom, or bottom to top. Thus, 0.5 is the same as 2; 0.333 is the same as 3, etc.
4
10 Revisit the flow control
Decide how you will operate: control flow to maintain constant humidity, or use a constant flow. (If you aren’t sure
what to do here, you probably skipped over Tour #3: Controlling Chamber Conditions on page 3-29. There may
still be hope for you, however; work through Humidity Control Experiments on page 4-9.)

From this point on, what you do is going to depend on your experiment, or what it is you wish to accomplish. For
example, you might wish to measure a response curve (light, for example, is discussed on page 4-24), or make
survey measurements (page 4-21) by going from leaf to leaf and only taking a minute or so for each measurement.

11 Removing leaf at completion of measurement

Created by Greg Cawthray Page 5 of 8 5/30/2014


When you have determined that all measured parameters have reached equilibrium, and you have logged the data,
prior to removing the leaf from the cuvette, you may need to mark what area was actually within the cuvette to
determine actual leaf area measured. This will not be the case of course if your leaf takes up the whole area of the
cuvette used. Before opening the cuvette, hold the leaf in place with one hand to stop it moving.

Part E. Turning the LI-6400 off.


1. Record the final AGC values in the logbook and check if they changed significantly during your
measurements.
2. Close the data file you have used, menu 1 function 3 (1 f3)
3. Escape from the view you are in until you reach the main OPEN page.
4. At this stage, you may wish to transfer the data off the LiCor before shutting down the unit (refer to Part G below)
5. Select Welcome (Home in XT) from the OPEN menu (f1)
6. Scroll down and select “Quit OPEN and IRGAs off”
7. Wait until screen goes to a new display
8. Switch LI6400 off and disassemble
9. Disconnect the external PAR sensor on cuvette
10. Loosen cuvette latch to leave chamber slightly open
11. Replace all equipment in suitcase &/or field box
12. Record your usage details in the logbook in the suitcase.
13. Return and place any LiCor batteries you used on the charger, remove once recharged.
14. Have a nice day!

Part F. Measurement Tips.


1. Read the manuals and take the time to practice, think about what you really want to measure.

2. For optimum measurements


Parameter Description Range
RH-S_% Relative humidity - sample 50-80% (with & without leaf)
ΔCO2 Delta CO2, (reference – sample) ≥ 5 µmol/mol
Flow_µml Sample flow rate Highest to give ΔCO2 ≥ 5 µmol/mol
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3. Select flow rates that give ΔCO2 of ≥ |5| µmol mol ; this will mean changing the flow rate for different samples.
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Values ≤ |5| µmol mol approach detection limit of the unit and are subject to instrument drift influencing data
quality. If ΔCO2 okay, in most cases, the ΔH2O will be fine in terms of being well above the detection limit of the
LiCor unit.

4. Routinely match IRGA’s. As a guide every 30 minutes, more frequently if temperature &/or flow rate is
changing.

5. Check AGC values for any plant material or dirt that may be present in the optics of the IRGA’s, large fluctuations,
especially in the sample IRGA’s often indicates solid material in the optical bench. (This means a competent
person needs to dismantle the fragile optical bench and carefully clean). Inver the cuvette and observe if the AGC
values change significantly (~ > 20 mV)

6. Use graph display function to follow equilibration of the measurement so you know the correct time to log the
data, remember the lower the flow rate the longer time it takes for an equilibrated measurement. Shortcut to graph
function from the ‘New Measurements’ screen is the ‘]’ button. The ‘[‘ button shows the current calculated stability
values for CO2S, H2OS and flow,

7. When logging an equilibrated result, take 4-5 readings spaced approx 2 s apart (it takes this long for the data to
update for each reading).

8. Match Valve Problems.


A. “CO2 has Changed” Message
This message appears in match mode when the sample CO 2 concentration changes by more than 3 μmol
-1
mol since entry. This can be caused by:
 Match mode entered at the wrong time.
If the light just changed, or you just closed the chamber, or the CO 2 mixer target just changed, or you just
made an adjustment on a chemical tube flow knob, then the change in CO2 is not indicative of a problem with
the system, just with your timing. Wait for CO2S_μml to stabilize, and then match.
 Chamber leak
If CO2S never stabilises, then very likely a chamber leak. See Sensor Head Leaks on page 20-36.
Created by Greg Cawthray Page 6 of 8 5/30/2014
B. “Excessive Deltas” Message
Message appears when you try to match, but the differences between sample and reference are too large.
This could be due to poorly set IRGA span or zero, but may also indicate problem with match valve or its
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plumbing. The default limits are 10 µmol mol for CO2, and 1 mmol mol for H2O.
 Is the Match Valve functioning?
Figure 4-2 on page 4-34 shows how the match valve should be positioned in and out of match mode.
 Is the return flow tubing in place?
Check there is a piece of tubing connecting the chamber bottom with the match valve (Figure 20-5).

C. “CO2R Didn’t Change” Message


After initial delay when entering match mode during which the H2O reference reading is supposed to stabilize,
if this message appears,
War ni ng
CO2R di dn' t c hange enough. Mat c h
v al v e OK? Ret ur n t ube i n pl ac e?
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it’s because the CO2 reference reading changed less than 1.5 µmol mol after match valve closed, and
-
expected change (the pre-match difference between sample and reference CO2) was larger than 10 µmol mol
1
. Reasons for this would be a sticking match valve, or air flow tube connecting the chamber to the match
valve not being in place, or some other flow related problem.

9. If you get a “High Humidity Alert”, this means relative humidity of sample is > 80%; the usual remedy is to;
A. Reduce incoming (i.e. reference) water content by scrubbing more out.
B. Increase chamber flow rate
C. Check what block temperature you have set, maybe it’s too low for the ambient conditions
D. Check water IRGA readings, do they make sense? If not might be a blown fuse.

New Measurements Display Line Groups

Created by Greg Cawthray Page 7 of 8 5/30/2014


Part G. Downloading data and recalculating for true leaf area.
If you have used a version of OPEN that does not generate data in excel file format, you will need to recompute your data set
using the LiCor Simulator software.

The PC in the lab where the Licors are kept, has the software installed, you need UWA login credentials to access this PC.

This link should run the program, version 5, I prefer over version 6
Windows LI-6400 software including Simulator, Term, and File Exchange Software for Version 5 v5.3.2 - LI-COR (8/2010)
This is the Installer for Windows programs for the LI-6400 running Version 5, including LI-6400 Simulator, LI-6400 Terminal
Program, and LI-6400 File Exchange.

If the above link fails, go to the LiCor page: http://envsupport.LiCor.com/index.jsp?menu=Photosynthesis_Systems&spec=LI-


6400,Software

Transferring data from LiCor to computer

1. Turn on the LiCor, no need to connect the cuvette


2. Connect the LiCor to the computer using the RS-232 connection on the console and appropriate connection for your
computer (i.e. USB converter; 9 pin port)
3. Open the File Exchange program on the computer
4. On the LiCor, navigate to the ‘Utility’ menu (f5) from the main OPEN screen
5. Scroll down and to ‘File Exchange mode’, press enter.
6. Click ‘connect’ on the computer File Exchange software
7. Locate the LiCor files you want to transfer in the right hand side window of the computer program
8. Copy the files to your required destination
9. Click ‘disconnect’ on the computer software
10. On the LiCor unit, press escape to return to main OPEN screen and shutdown LiCor as detailed in Part E.
11. Turn off the LiCor and close the file exchange program

Recalculating data (after you have determined leaf area)

1. Open the LiCor Simulator software version 5


2. Top right hand side, click on start to open the simulator
3. If error message comes up saying User disc not found, press enter.
4. Press ‘Y’ if message “OPEN’s Configs directory is not installed on /Sys/Configs”
5. Go through startup as you would on the actual LiCor
6. Once at the main OPEN view, select Utility Menu (f5)
7. Scroll down and select ‘Recompute Stored Data’ and ‘Y’ to open recompute window
8. Open the file (text file) you want to recompute via the ‘File’ menu
9. Choose the ‘data #1’ tab to see the data as recorded
10. Change values as required, namely leaf area
11. Click on the recompute button
12. Save the file as same name but with RCMP (recomputed) added, so as to leave the original data file unchanged
13. Close out of program
14. Open this recomputed data file in excel by importing the text file.

Take the opportunity to run different settings of the LiCor through your data, such as stomatal ratio, to observe if
there are any significant changes to your data with changes to these settings.

Created by Greg Cawthray Page 8 of 8 5/30/2014

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