Professional Documents
Culture Documents
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.
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
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).
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.
Now test the chemical tubes for flow restrictions by changing each from full bypass to full scrub watching the effect on
-1
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.
If IRGA’s have not reached optimum operating temperature, a message will flash across the ‘New Msmnts’ screen.
re-zero flow meter (page 18-17 in book#3). Turn chamber fan back on when finished this check.
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.
-1
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
-1
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
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.
11. Leaks?
With the chamber closed and empty set flow to 200 mol s . Gently blow around chamber gaskets and
-1
-1
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
done with the instrument left running, just don’t take any measurements!
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
-1
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
-1
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.
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.
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).
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.
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.
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.