Thermal Air Velocity Transducers
ICI Films
P.O. Box 15391
Wilmington, DE 19850
Phone: 302-887-3000
FAX: 302-887-5365
Sierra Instruments, Inc.
5 Harris Court, Building L
Monterrey, CA 93940
Phone: 408-373-0200
FAX: 408-373-4402
Temperature Sensors - Thermocouples
Omega Engineering, Inc.
P.O. Box 4047
Stamford, CT 06907-0047
Phone: 203-359-1660
FAX: 203-359-7700
Distributed by:
Transilwrap Company, Inc.
13592 N. Stemmons
Dallas, TX 75234
Phone: 214-484-3211
FAX: 214-484-3171
(Note: Minimum order $500.00)
Temperature Sensors - Thermistors
Yellow Springs Instruments
1725 Brannum Lane
P.O. Box 465
Yellow Springs, OH 45387
Phone: 513-767-7241
FAX: 513-767-9353
Humidity and Temperature Sensors
Rotronic Instrument Corp.
7 High Street
Huntington, NY 11743
Phone: 516-427-3994
FAX: 516-427-3902
Vaisala Inc.
100 Commerce Way
Woburn, MA 01801-1068
Phone: 617-933-4500
FAX: 617-933-8029
Measuring Canopy Gas
Exchange with the LI-6400
Portable Photosynthesis System
2
LI-6400 Portable Photosynthesis System
Transparent Films
APPLICATION NOTE
Suppliers (continued)
Introduction
Canopy gas exchange systems are useful for
quantifying the effects of environmental changes
on the instantaneous productivity of a plant
community. Measuring the gas exchange of the
entire canopy with a chamber system obviates
difficulties encountered when extrapolating leaf
measurements to the canopy scale such as
accurately modeling the distribution of absorbed
radiation. Canopy gas exchange systems, if
properly designed and operated, can provide a
measure of CO2 flux that closely approximates
natural conditions. However, it is important to
consider how the chamber may alter, among other
factors, the canopy temperature, wind speed (and
therefore boundary layer conductance), and
radiation balance of the plant community. When
possible, canopy chamber results should be
compared to micrometeorological flux measurements, since they do not disturb the environment
around the canopy (Baldocchi et. al., 1988).
This application note will be concerned with the
design and implementation of a simple continuous
flow “open” canopy chamber system based around
the LI-6400 Portable Photosynthesis System. This
system allows steady-state canopy fluxes to be
measured over a period of several hours or days,
and is less susceptible to errors introduced by
leaks and water sorption than a closed system.
(Water sorption can have a significant effect on
transpiration estimates until equilibrium conditions
are reached.) Nonetheless, depending on plant
material and experimental design, a closed system
may be more suitable. In that case, the LI-6200
Portable Photosynthesis System may be readily
adapted for closed system canopy measurements
(Vourlitis et. al., 1993). For soil respiration
measurements, the LI-6200 with the 6000-09 Soil
Respiration Chamber has been thoroughly tested
(Norman et. al., 1992) and is recommended.
Oftentimes the focus of a
study is an individual
species of a plant community, or field plots are too
small to make use of
micrometeorological
techniques. In these cases
enclosure methods are the
only methods available to
determine instantaneous
canopy CO2 flux.
Many types of chambers
and systems have been
designed and will not be
reviewed here. Garcia et.
al. (1990) summarize
some of the advantages
and disadvantages of open
and closed canopy
chamber systems.
Canopy gas exchange system installed in August, 1995, in Lincoln, Nebraska.
®
LI-COR, inc.
●
Environmental Division ● 4421 Superior Street ● P.O. Box 4425
Phone: 402-467-3576 ● FAX: 402-467-2819
Toll-free 1-800-447-3576 (U.S. & Canada)
●
Lincoln, Nebraska 68504 USA
®
1
Materials and Methods
The LI-6400 system hardware and software flexibility make it
a simple procedure to configure it for continuous flow canopy
gas exchange measurements. The purpose of this application
note is to provide a generic protocol for a wide variety of userbuilt chambers. Because of the diverse measurement requirements LI-COR does not market a canopy chamber; however
some general guidelines for chamber materials and construction, flow measurement, blowers, pumps, external sensors, and
a flow schematic are given here to assist you in getting started.
A continuous flow canopy chamber was built and tested to
prove the concept and to provide an example of how to design
and configure the system.
Flow Schematic, System Hardware, and
External Sensors
Figure 1 shows the path of air flow through the system and the
system components. The system was designed to be portable
enough to be moved with reasonable ease from one site to
another while operating entirely from 12VDC battery power.
The chamber consists of an extruded cylindrical section of
acrylic approximately 45 cm inside diameter (ID), 0.6 cm wall
thickness, and 61 cm tall. The top of the chamber is covered
with PVdC coated polypropylene (Propafilm®-C, ICI Americas Inc., Wilmington, DE, USA), a transparent film with a
high thermal transmittance which helps to moderate temperature increases inside the chamber. The bottom of the chamber
is open so that it can be placed over the individual plant or
plant canopy. Sufficient air moves through the system so that,
due to the flow resistance from the wind incursion baffle at the
effluent side of the chamber, a positive pressure is created
inside the chamber and leaks are outward.
Air enters a large buffer volume (which also serves as a
carrying case for the chamber) through a 5 cm (2 inch) ID
rigid PVC plastic pipe that is positioned to pull air from
several meters above the canopy. This serves to dampen
fluctuations in the incoming CO2 concentration. A miniature
centrifugal blower (TBK-2, Brailsford & Company, Rye, NY,
USA) provides about 0.54 m3 min-1 of flow through the
system. It is mounted on the buffer volume. The buffer
volume and the chamber are connected by about one meter of
flexible tubing and approximately 2 meters of 6.2 cm (2.5
inch) ID schedule 40 PVC plastic pipe. The pipe is painted
white to minimize deterioration due to UV radiation. This
pipe was selected for its rigidity and size to accomodate the
flow measurement.
The chamber volume is approximately 0.094 m3, so the air in
the chamber is exchanged more than 5 times per minute. Flow
rate may be adjusted by varying the voltage to the blower or
by changing the resistance to flow by inserting foam or paper
screens inside the wind incursion baffle. As a general rule of
2
thumb the air should be exchanged at least 3 to 4 times per
minute through the chamber. A flow transducer (8450-50MV-03-NC, TSI Inc., St. Paul, MN, USA) measures the air
velocity just upstream from the chamber. Volumetric flow is
computed from the air velocity and the diameter of the pipe
and then converted to mole flow rate.
Mixing the air to prevent stratification or “dead” air pockets
within the chamber is crucial because the sample that is
withdrawn from the enclosure must represent the entire
volume. Chamber mixing is accomplished by two small axial
fans (LI-COR part #6000-17) positioned tangential to the
chamber wall and opposite of one another about halfway up
the chamber. A cone-shaped perforated mixing baffle is
mounted just beyond the point at which the air enters the
chamber and supplements the mixing of the mixing fans by
distributing the incoming flow to the upper, center, and lower
portions of the chamber.
It is possible to quantitatively test the efficiency of mixing and
flow measurement accuracy within a flow through system by
measuring the time response of the outlet minus the inlet CO2
differential resulting from continuous injection of pure CO2
into the chamber (Garcia et al., 1990). The mixing efficiency
will vary depending on the canopy height and density, fan type
and speed, fan position, and chamber geometry.
Air is sub-sampled just before it enters and just as it exits the
chamber by a miniature diaphragm pump with two pumping
sections that operate in parallel (TD-4X2NA-Type 4-Viton
Elastomers, Brailsford & Co., Rye, NY, USA). Air is pumped
to the reference analyzer from the incoming side and to the
sample analyzer from the effluent side. The flow rate is
approximately 1 liter min-1 from each side of the pump so that
the impact of water sorption and CO2 diffusion in the Bev-ALine tubing and filters between the chamber and the analyzers
is minimized. The air is filtered by two Gelman Acro-50 1 µm
filters (LI-COR part #9967-008) before entering the IRGAs.
The inlet air temperature and relative humidity are monitored
using a humidity and temperature sensor (Humitter 50Y,
Vaisala, Helsinki, Finland) mounted in the chamber inlet air
stream. Chamber air temperature is measured with a thermocouple (LI-6400 leaf temperature thermocouple, part #640004) positioned in the effluent airstream and connected to the
leaf thermocouple input on the LI-6400 sensor head.
This system did not have a means of measuring foliage
temperature. Depending on the canopy structure and view
angle of an infrared thermometer (IRT), it may be useful to
measure the canopy temperature inside the chamber by
infrared thermometry (Garcia et al., 1995).
Quantum flux density is measured inside the chamber approximately 2 cm below the top with a LI-COR LI-190SA quantum
sensor.
completed the plants which had been enclosed for the measurements were harvested for leaf area determinations. The
crop was flowering and had a leaf area index of about 3.7.
There were clear sky conditions on the first full day of
measurements (Figure 3), whereas, the second day of measurements could be characterized by scattered cloudy conditions. The canopy CO2 exchange rates generally followed the
diurnal courses of incident light. The maximum air saturation
deficits (D) were 3.5 kPa on 25 August and 3.4 kPa on 26
August.
The alfalfa photosynthesis data of 25 August are similar in
magnitude and in behavior to those of Baldocchi et. al. (1981).
They speculated that the "midday depression" in their data
may have been due to starch accumulation in the leaves.
Another possibility is that photoinhibition suppressed the
rates.
List of Suppliers
Variable Area Flow Meters
Dwyer Instruments, Inc.
102 Highway 212
P.O. Box 373
Michigan City, IN 46361
Phone: 219-879-8000
FAX: 219-872-9057
Blowers and Fans
Brailsford and Co., Inc.
670 Milton Road
Rye, NY 10580
Phone: 914-967-1820
FAX: 914-967-1836
We did not do a time course assay of starch in the leaves;
however, a comparison of the photosynthesis data of 25 and 26
August plotted against light (Figure 4) would lend support to
either of these hypotheses. In contrast to 25 August, CO2
exchange rates on 26 August, a scattered cloudy day, did not
light saturate.
W.W. Grainger, Inc.
333 Knightsbridge Parkway
Lincolnshire, IL 60069
Phone: 708-913-7218
FAX: 708-913-7392
References
Pumps
Baldocchi, Dennis D., Bruce B. Hicks and Tilden P. Meyers,
1988. Measuring Biosphere-Atmosphere Exchanges of
Biologically Related Gases with Micrometeorological
Methods. Ecology 69(5), 1331-1340.
Brailsford and Co., Inc.
670 Milton Road
Rye, NY 10580
Phone: 914-967-1820
FAX: 914-967-1836
Baldocchi, Dennis D., Shashi B. Verma and Norman J.
Rosenberg, 1981. Seasonal and Diurnal Variation in the CO2
Flux and CO2-Water Flux Ratio of Alfalfa. Ag. Met. 23, 231244.
Garcia, R.L., John M. Norman and Dayle K. McDermitt,
1990. Measurements of Canopy Gas Exchange Using an
Open Chamber System. Remote Sensing Reviews, Vol 5(1),
141-162.
Norman, J.M., R. Garcia and S.B. Verma, 1992. Soil Surface
CO2 Fluxes and the Carbon Budget of a Grassland. J. of Geo.
Res. 97, 18845-18853.
Vourlitis, G.L., W.C. Oechel, S.J. Hastings and M.A. Jenkins,
1993. A System for Measuring in situ CO2 and CH4 Flux in
Unmanaged Ecosystems: An Arctic Example. Functional
Ecology 7, 369-379.
KNF Neuberger, Inc.
Two Black Forest Road
Trenton, NJ 08691-9428
Phone: 609-890-8889
FAX: 609-890-2838
Thomas Compressors and Vacuum Pumps
1419 Illinois Avenue
Sheboygan, WI 53082-0029
Phone: 414-457-4891
FAX: 414-451-4276
Thermal Air Velocity Transducers
TSI Inc.
P.O. Box 64394
St. Paul, MN 55164
Phone: 612-490-2888
FAX: 612-490-2874
7
●
●
●
1200
40
900
20
600
0
300
-2 -1
60
0
It may be necessary to match the IRGAs periodically.
This can be accomplished in the AutoLog program.
Do not use the evapotranspiration measured in the
chamber to estimate that which is occurring in natural
field conditions.
In well-developed canopies, make sure the chamber is
large enough so that edge effects have a minimal impact
on the canopy radiation climate.
The pump in the LI-6400 console is not used for the
hardware configuration as described here. However, if
you intend to program your system to autolog data and
you are using the Match option, then it is currently
necessary to leave the pump ON. This is because the
automatch routine uses the flow rate through the IRGAs,
as measured by the mass flow meter in the console, to
determine how long to delay matching after the match
valve has been activated. If the console pump is shut off
and the console flow meter reads zero, the system will
not match.
PPFD (µmol m-2 s-1)
1500
Air Stream
(4 m above canopy)
1500
Medicago sativa L.
26 August, 1995
A
PPFD
D
80
1200
60
900
40
600
20
Polypropylene Film top
PPFD (µmol m-2 s-1)
●
Check the external sensors by blowing on the Humitter
sensor; turn the blower on and off to check the flow
transducer.
-2 -1
●
Zero and span the LI-6400 IRGAs before measuring. It
may be necessary to zero the IRGAs during the measurement sequence: refer to the calibration section of the
Primer.
Medicago sativa L.
25 August, 1995
A
PPFD
D
80
A (µmol m s ) & D ( kPa × 10)
●
A (µmol m s ) & D ( kPa × 10)
Precautions
Quantum Sensor
Inlet Air Temperature
& Relative Humidity
300
0
Flow
Transducer
0
4
8
12
16
20
Wind Incursion
Baffle
Mixing
Baffle
Figure 3. Diurnal courses of photosynthetic photon flux
density (PPFD), water vapor saturation deficit of air (D) and
the corresponding canopy CO2 exchange rates (A) for two
days in a field of alfalfa (Medicago sativa L.) in Lincoln,
Nebraska, USA. The leaf area index of the crop was 3.7.
Blower
To Auxiliary Input
Filter
Filter
Pump
LI-6400 Console
100
Medicago sativa L.
25 and 26 August, 1995
O 25 August
● 26 August
200 stdflowcal 1 Pick =
80
●
A (µmol m-2 s-1)
●●
●
●●
60
●
●
●
●
●
● O
To Sample In
●
●
O
O
O
O
O
OO
O
O O O
O
O
O
●
●O
LI-6400 Sensor Head
O
O
40
To Reference In
●
●
right before the line that reads quitAfter NLOOP,
and by adding a line that reads
right after the line that reads LPCleanup at the end of
the program.
Chamber
Air Temperature
Buffer Volume
(Carrying Case)
Time (h)
Alternatively, you can edit the AutoLog program (found
in the /User/Configs/AutoProgs directory) by adding a
line that reads
0 stdflowcal 1 Pick =
Mixing Fans
●
O
O
●O
20
●
●
O
O
See LI-6400 Technical Note #6 for more discussion on
AutoLog routines.
O
●
0
O●
O●
●
●
●
O
O●
●
O
O
●
O
E
CO
NS
T
+
400
600
800
1000
1200
1400
1600
+
CHROMEL
200
ECONST
0
OMEGA
-20
+
CONST
E +CH
Results
-2 -1
PPFD (µmol m s )
The system as described was installed in a field of alfalfa
(Medicago sativa L.) in late August (photo on page 1). The
system was programmed to record observations every 2
minutes and to automatically match the analyzers every 5
observations. After the gas exchange measurements were
6
Figure 4. CO2 exchange rate (A) plotted against photosynthetic photon flux density (PPFD) for 25 and 26 August,
1995, in a field of alfalfa (Medicago sativa L.) in Lincoln,
Nebraska, USA. The leaf area index of the crop was 3.7.
Figure 1. A flow-through canopy chamber system configured to operate with the LI-6400 Portable Photosynthesis System.
3
Follow these 6 steps to set up the software and auxiliary port:
1. Connect the external sensors to the auxiliary port.
2. Add the spare analog channels being used to the Con3.
4.
5.
6.
1.
figuration File.
Change the Compute List File to accomodate the new
calculations and store it.
Edit and store the Displays File to include external
sensors.
Edit and store the LogList File to record the additional
sensor information.
Store the Configuration File with the new Compute List,
Displays, and LogList Files.
Connect the external sensors to the auxiliary port.
Pin assignments for the 37-pin auxiliary port are given in
Appendix C of the LI-6400 Primer. The pin numbers are
stamped on the connector provided in the spares kit. We have
configured the connector to use differential input channels 20,
21, and 22 (Figure 2). The differential ground of the Vaisala
sensors is tied to the digital ground because the Vaisala 50Y
has no separate ground for signal and power.
2.
Add the spare channels to the Configuration File.
Select User Compute List Editor from the Config Menu. Add
the following channels, plus decimal time to the compute list.
Assign decimal time to user variable ID 01; humidity and
temperature to user variable ID's 91 and 92, respectively; and
flow into user variable ID 93. Below is a sample of how the
first 5 items in the compute list could be programmed to
accomplish this (include all spaces):
##01F5 “Hrs” “Decimal hrs. of OBS Time”
“$ GETTDS TIME ROT 3600. / SWAP 60. / + +”
##91F1 “xRH” “external humidity”
“chan20_mv * 0.1”
##93F0 “xFlow” “external flow”
“chan22_mv * 0.1 * 30.1907 * 44.64”
##10 “(U/S)” “flow:area ratio”
“#93 / area_cm2 / 100.0”
“Hrs” will allow us to record the observation time in decimal
hours, which is needed to plot data against time. “xRH” and
“xTair” are values of external humidity and air temperature,
respectively. “xFlow” is the value for air flow through the
canopy chamber system.
●
Press OK to implement the new LogList.
5.
●
Use the arrow keys to highlight xRH.
●
Press Select (f5).
●
Select xTair and xFlow, then Escape to quit after adding
the three variables.
Access the "Canopy Config" file again by selecting Config
Editor in the Config Menu. Press labels and then press
StoreAs (f5). Name the file "Canopy Config" if it is not
already named. It should look similar to the following list
(depending, of course, on the optional accessories you may
have installed):
●
Press OK (f5). When prompted to store the changes,
press Y. Name the new Display file “Canopy Displays”,
and press Select. When you return to the New Measurements screen, you can put this line on the screen by
pressing the letter associated with this new line. The
new line will be displayed at the end of the Display
Editor list.
Store the new Config File.
UserChan= 20 5 0
UserChan= 21 5 0
UserChan= 22 7 0
LightSource= “Sun+Sky” 1.0 0.19
AREA= 1543 (ground area in cm2 covered by the chamber)
STOMRAT= 1
ComputeList= “Canopy”
Displays= “Canopy Displays”
StripDefs= “Photo & CV” (or whatever you want this to be)
LogFormat= “Canopy Output”
Edit and store a new LogList file.
In order to record data from the external sensors, we must edit
the LogList file. While still in New Msmnts, select the Loglist
Editor function key (level 5, f5).
Now OK this configuration to store your changes and the
system software is ready.
Add and store the new channels to the LogList file as described below.
TSI 8450 Air Velocity Transducer
SIG
+
12V GND
FLOW
+
SIG
GND
+ 12V
19 18 17 16 15 14 13 12 11 10 9
8
7
6
5
4
3
2
1
37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20
Yellow
Green
Green
Vaisala Humitter 50Y
HUMITTER
P1620016
4
Press Store and enter "Canopy Output" for the file name.
6.
Brown
User channels 20 and 21 now are configured for the humidity
and temperature sensors, respectively; they use differential
●
Press Add (f2) to add an additional display line.
Store this new compute list file by pressing Escape and S to
store it with a new file name. Let’s call this new Compute List
file “Canopy”. When you Quit the Editor and are asked if you
want to implement this new file, type Y for yes.
If you would like to add other computations to the “Canopy”
file, such as Transpiration Efficiency, the procedure is discussed in LI-6400 Technical Note #2 - Defining Equations for
Open.
Select xTair and xFlow as described above.
●
Violet
UserChan= 21 5 0 (Press 1, 5, L)
UserChan= 22 7 0 (Press 2, 7, L)
●
Press Display Editor (f4).
Note that external flow measured from the flow transducer
(user variable ID 93) is now used in the flow:area ratio (user
variable ID 10), which in turn is used in the transpiration and
photosynthesis computations in user variable IDs 20 and 30,
respectively.
Edit the remaining two channels to look like this:
Use the arrow keys to scroll down until the Insert label
appears. Press Insert (f2) to add a variable from the list
before the currently highlighted variable. Scroll the list
until xRH is highlighted and press Select (f5) or Enter.
●
- SIG
UserChan= 20 5 0
Follow these steps to add and store the three new sensors to a
display definition:
Change the Compute List to accomodate the new
calculations.
##92F2 “xTair” “external temperature”
“chan21_mv * 0.1 - 40”
●
Since we want to view the status of our sensors in the New
Measurements Display, enter New Msmnts from the OPEN
screen, and press the Display Editor function key (level 6, f4).
+ SIG
From the initial startup screen go to the Config Menu and
enter the Config Editor. Press Add (f2) and the Master List of
configuration options will appear. Scroll to the UserChan=
command and press Select (f5). Repeat this process of adding
a user channel to the config list 2 more times. You will have
three entries that appear as UserChan= 0 0 0. Highlight the
first entry and press Edit. Press 0, 5, then L. Your entry will
now appear as
3.
Add the external sensors to the Display file.
AIR VELOCITY
TRANSDUCER
NOTE: The procedure for configuring the system software
requires OPEN version 2.0 or greater, and may vary between
different software versions. The description given here is for
OPEN software version 2.0.
Store this as “Canopy Config” by pressing the labels key and
then choosing the StoreAs (f5) function key. Press the labels
key and then OK (f5) to implement this Config file. For
further information about Config files see Technical Note #3.
4.
TSI®
In order to operate the flow transducer and external sensors it
is necessary to configure the software and auxiliary port to
accept and process these signals so that transpiration, assimilation, and other parameters may be computed and recorded in
real time.
ground number 5 (which is tied to the digital ground on pin
20); and the resolution is set to low (0). User channel 22 is
configured to measure the flow transducer, using differential
ground number 7 with low resolution.
MODEL:
SERIAL NO:
RANGE:
OUTPUT
4-20MA
0-5VDC
Configuring the Software and the Auxiliary
Port
Figure 2. Connection of external sensors to 37-pin auxiliary port of LI-6400.
5
Follow these 6 steps to set up the software and auxiliary port:
1. Connect the external sensors to the auxiliary port.
2. Add the spare analog channels being used to the Con3.
4.
5.
6.
1.
figuration File.
Change the Compute List File to accomodate the new
calculations and store it.
Edit and store the Displays File to include external
sensors.
Edit and store the LogList File to record the additional
sensor information.
Store the Configuration File with the new Compute List,
Displays, and LogList Files.
Connect the external sensors to the auxiliary port.
Pin assignments for the 37-pin auxiliary port are given in
Appendix C of the LI-6400 Primer. The pin numbers are
stamped on the connector provided in the spares kit. We have
configured the connector to use differential input channels 20,
21, and 22 (Figure 2). The differential ground of the Vaisala
sensors is tied to the digital ground because the Vaisala 50Y
has no separate ground for signal and power.
2.
Add the spare channels to the Configuration File.
Select User Compute List Editor from the Config Menu. Add
the following channels, plus decimal time to the compute list.
Assign decimal time to user variable ID 01; humidity and
temperature to user variable ID's 91 and 92, respectively; and
flow into user variable ID 93. Below is a sample of how the
first 5 items in the compute list could be programmed to
accomplish this (include all spaces):
##01F5 “Hrs” “Decimal hrs. of OBS Time”
“$ GETTDS TIME ROT 3600. / SWAP 60. / + +”
##91F1 “xRH” “external humidity”
“chan20_mv * 0.1”
##93F0 “xFlow” “external flow”
“chan22_mv * 0.1 * 30.1907 * 44.64”
##10 “(U/S)” “flow:area ratio”
“#93 / area_cm2 / 100.0”
“Hrs” will allow us to record the observation time in decimal
hours, which is needed to plot data against time. “xRH” and
“xTair” are values of external humidity and air temperature,
respectively. “xFlow” is the value for air flow through the
canopy chamber system.
●
Press OK to implement the new LogList.
5.
●
Use the arrow keys to highlight xRH.
●
Press Select (f5).
●
Select xTair and xFlow, then Escape to quit after adding
the three variables.
Access the "Canopy Config" file again by selecting Config
Editor in the Config Menu. Press labels and then press
StoreAs (f5). Name the file "Canopy Config" if it is not
already named. It should look similar to the following list
(depending, of course, on the optional accessories you may
have installed):
●
Press OK (f5). When prompted to store the changes,
press Y. Name the new Display file “Canopy Displays”,
and press Select. When you return to the New Measurements screen, you can put this line on the screen by
pressing the letter associated with this new line. The
new line will be displayed at the end of the Display
Editor list.
Store the new Config File.
UserChan= 20 5 0
UserChan= 21 5 0
UserChan= 22 7 0
LightSource= “Sun+Sky” 1.0 0.19
AREA= 1543 (ground area in cm2 covered by the chamber)
STOMRAT= 1
ComputeList= “Canopy”
Displays= “Canopy Displays”
StripDefs= “Photo & CV” (or whatever you want this to be)
LogFormat= “Canopy Output”
Edit and store a new LogList file.
In order to record data from the external sensors, we must edit
the LogList file. While still in New Msmnts, select the Loglist
Editor function key (level 5, f5).
Now OK this configuration to store your changes and the
system software is ready.
Add and store the new channels to the LogList file as described below.
TSI 8450 Air Velocity Transducer
SIG
+
12V GND
FLOW
+
SIG
GND
+ 12V
19 18 17 16 15 14 13 12 11 10 9
8
7
6
5
4
3
2
1
37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20
Yellow
Green
Green
Vaisala Humitter 50Y
HUMITTER
P1620016
4
Press Store and enter "Canopy Output" for the file name.
6.
Brown
User channels 20 and 21 now are configured for the humidity
and temperature sensors, respectively; they use differential
●
Press Add (f2) to add an additional display line.
Store this new compute list file by pressing Escape and S to
store it with a new file name. Let’s call this new Compute List
file “Canopy”. When you Quit the Editor and are asked if you
want to implement this new file, type Y for yes.
If you would like to add other computations to the “Canopy”
file, such as Transpiration Efficiency, the procedure is discussed in LI-6400 Technical Note #2 - Defining Equations for
Open.
Select xTair and xFlow as described above.
●
Violet
UserChan= 21 5 0 (Press 1, 5, L)
UserChan= 22 7 0 (Press 2, 7, L)
●
Press Display Editor (f4).
Note that external flow measured from the flow transducer
(user variable ID 93) is now used in the flow:area ratio (user
variable ID 10), which in turn is used in the transpiration and
photosynthesis computations in user variable IDs 20 and 30,
respectively.
Edit the remaining two channels to look like this:
Use the arrow keys to scroll down until the Insert label
appears. Press Insert (f2) to add a variable from the list
before the currently highlighted variable. Scroll the list
until xRH is highlighted and press Select (f5) or Enter.
●
- SIG
UserChan= 20 5 0
Follow these steps to add and store the three new sensors to a
display definition:
Change the Compute List to accomodate the new
calculations.
##92F2 “xTair” “external temperature”
“chan21_mv * 0.1 - 40”
●
Since we want to view the status of our sensors in the New
Measurements Display, enter New Msmnts from the OPEN
screen, and press the Display Editor function key (level 6, f4).
+ SIG
From the initial startup screen go to the Config Menu and
enter the Config Editor. Press Add (f2) and the Master List of
configuration options will appear. Scroll to the UserChan=
command and press Select (f5). Repeat this process of adding
a user channel to the config list 2 more times. You will have
three entries that appear as UserChan= 0 0 0. Highlight the
first entry and press Edit. Press 0, 5, then L. Your entry will
now appear as
3.
Add the external sensors to the Display file.
AIR VELOCITY
TRANSDUCER
NOTE: The procedure for configuring the system software
requires OPEN version 2.0 or greater, and may vary between
different software versions. The description given here is for
OPEN software version 2.0.
Store this as “Canopy Config” by pressing the labels key and
then choosing the StoreAs (f5) function key. Press the labels
key and then OK (f5) to implement this Config file. For
further information about Config files see Technical Note #3.
4.
TSI®
In order to operate the flow transducer and external sensors it
is necessary to configure the software and auxiliary port to
accept and process these signals so that transpiration, assimilation, and other parameters may be computed and recorded in
real time.
ground number 5 (which is tied to the digital ground on pin
20); and the resolution is set to low (0). User channel 22 is
configured to measure the flow transducer, using differential
ground number 7 with low resolution.
MODEL:
SERIAL NO:
RANGE:
OUTPUT
4-20MA
0-5VDC
Configuring the Software and the Auxiliary
Port
Figure 2. Connection of external sensors to 37-pin auxiliary port of LI-6400.
5
●
●
●
1200
40
900
20
600
0
300
-2 -1
60
0
It may be necessary to match the IRGAs periodically.
This can be accomplished in the AutoLog program.
Do not use the evapotranspiration measured in the
chamber to estimate that which is occurring in natural
field conditions.
In well-developed canopies, make sure the chamber is
large enough so that edge effects have a minimal impact
on the canopy radiation climate.
The pump in the LI-6400 console is not used for the
hardware configuration as described here. However, if
you intend to program your system to autolog data and
you are using the Match option, then it is currently
necessary to leave the pump ON. This is because the
automatch routine uses the flow rate through the IRGAs,
as measured by the mass flow meter in the console, to
determine how long to delay matching after the match
valve has been activated. If the console pump is shut off
and the console flow meter reads zero, the system will
not match.
PPFD (µmol m-2 s-1)
1500
Air Stream
(4 m above canopy)
1500
Medicago sativa L.
26 August, 1995
A
PPFD
D
80
1200
60
900
40
600
20
Polypropylene Film top
PPFD (µmol m-2 s-1)
●
Check the external sensors by blowing on the Humitter
sensor; turn the blower on and off to check the flow
transducer.
-2 -1
●
Zero and span the LI-6400 IRGAs before measuring. It
may be necessary to zero the IRGAs during the measurement sequence: refer to the calibration section of the
Primer.
Medicago sativa L.
25 August, 1995
A
PPFD
D
80
A (µmol m s ) & D ( kPa × 10)
●
A (µmol m s ) & D ( kPa × 10)
Precautions
Quantum Sensor
Inlet Air Temperature
& Relative Humidity
300
0
Flow
Transducer
0
4
8
12
16
20
Wind Incursion
Baffle
Mixing
Baffle
Figure 3. Diurnal courses of photosynthetic photon flux
density (PPFD), water vapor saturation deficit of air (D) and
the corresponding canopy CO2 exchange rates (A) for two
days in a field of alfalfa (Medicago sativa L.) in Lincoln,
Nebraska, USA. The leaf area index of the crop was 3.7.
Blower
To Auxiliary Input
Filter
Filter
Pump
LI-6400 Console
100
Medicago sativa L.
25 and 26 August, 1995
O 25 August
● 26 August
200 stdflowcal 1 Pick =
80
●
A (µmol m-2 s-1)
●●
●
●●
60
●
●
●
●
●
● O
To Sample In
●
●
O
O
O
O
O
OO
O
O O O
O
O
O
●
●O
LI-6400 Sensor Head
O
O
40
To Reference In
●
●
right before the line that reads quitAfter NLOOP,
and by adding a line that reads
right after the line that reads LPCleanup at the end of
the program.
Chamber
Air Temperature
Buffer Volume
(Carrying Case)
Time (h)
Alternatively, you can edit the AutoLog program (found
in the /User/Configs/AutoProgs directory) by adding a
line that reads
0 stdflowcal 1 Pick =
Mixing Fans
●
O
O
●O
20
●
●
O
O
See LI-6400 Technical Note #6 for more discussion on
AutoLog routines.
O
●
0
O●
O●
●
●
●
O
O●
●
O
O
●
O
E
CO
NS
T
+
400
600
800
1000
1200
1400
1600
+
CHROMEL
200
ECONST
0
OMEGA
-20
+
CONST
E +CH
Results
-2 -1
PPFD (µmol m s )
The system as described was installed in a field of alfalfa
(Medicago sativa L.) in late August (photo on page 1). The
system was programmed to record observations every 2
minutes and to automatically match the analyzers every 5
observations. After the gas exchange measurements were
6
Figure 4. CO2 exchange rate (A) plotted against photosynthetic photon flux density (PPFD) for 25 and 26 August,
1995, in a field of alfalfa (Medicago sativa L.) in Lincoln,
Nebraska, USA. The leaf area index of the crop was 3.7.
Figure 1. A flow-through canopy chamber system configured to operate with the LI-6400 Portable Photosynthesis System.
3
Materials and Methods
The LI-6400 system hardware and software flexibility make it
a simple procedure to configure it for continuous flow canopy
gas exchange measurements. The purpose of this application
note is to provide a generic protocol for a wide variety of userbuilt chambers. Because of the diverse measurement requirements LI-COR does not market a canopy chamber; however
some general guidelines for chamber materials and construction, flow measurement, blowers, pumps, external sensors, and
a flow schematic are given here to assist you in getting started.
A continuous flow canopy chamber was built and tested to
prove the concept and to provide an example of how to design
and configure the system.
Flow Schematic, System Hardware, and
External Sensors
Figure 1 shows the path of air flow through the system and the
system components. The system was designed to be portable
enough to be moved with reasonable ease from one site to
another while operating entirely from 12VDC battery power.
The chamber consists of an extruded cylindrical section of
acrylic approximately 45 cm inside diameter (ID), 0.6 cm wall
thickness, and 61 cm tall. The top of the chamber is covered
with PVdC coated polypropylene (Propafilm®-C, ICI Americas Inc., Wilmington, DE, USA), a transparent film with a
high thermal transmittance which helps to moderate temperature increases inside the chamber. The bottom of the chamber
is open so that it can be placed over the individual plant or
plant canopy. Sufficient air moves through the system so that,
due to the flow resistance from the wind incursion baffle at the
effluent side of the chamber, a positive pressure is created
inside the chamber and leaks are outward.
Air enters a large buffer volume (which also serves as a
carrying case for the chamber) through a 5 cm (2 inch) ID
rigid PVC plastic pipe that is positioned to pull air from
several meters above the canopy. This serves to dampen
fluctuations in the incoming CO2 concentration. A miniature
centrifugal blower (TBK-2, Brailsford & Company, Rye, NY,
USA) provides about 0.54 m3 min-1 of flow through the
system. It is mounted on the buffer volume. The buffer
volume and the chamber are connected by about one meter of
flexible tubing and approximately 2 meters of 6.2 cm (2.5
inch) ID schedule 40 PVC plastic pipe. The pipe is painted
white to minimize deterioration due to UV radiation. This
pipe was selected for its rigidity and size to accomodate the
flow measurement.
The chamber volume is approximately 0.094 m3, so the air in
the chamber is exchanged more than 5 times per minute. Flow
rate may be adjusted by varying the voltage to the blower or
by changing the resistance to flow by inserting foam or paper
screens inside the wind incursion baffle. As a general rule of
2
thumb the air should be exchanged at least 3 to 4 times per
minute through the chamber. A flow transducer (8450-50MV-03-NC, TSI Inc., St. Paul, MN, USA) measures the air
velocity just upstream from the chamber. Volumetric flow is
computed from the air velocity and the diameter of the pipe
and then converted to mole flow rate.
Mixing the air to prevent stratification or “dead” air pockets
within the chamber is crucial because the sample that is
withdrawn from the enclosure must represent the entire
volume. Chamber mixing is accomplished by two small axial
fans (LI-COR part #6000-17) positioned tangential to the
chamber wall and opposite of one another about halfway up
the chamber. A cone-shaped perforated mixing baffle is
mounted just beyond the point at which the air enters the
chamber and supplements the mixing of the mixing fans by
distributing the incoming flow to the upper, center, and lower
portions of the chamber.
It is possible to quantitatively test the efficiency of mixing and
flow measurement accuracy within a flow through system by
measuring the time response of the outlet minus the inlet CO2
differential resulting from continuous injection of pure CO2
into the chamber (Garcia et al., 1990). The mixing efficiency
will vary depending on the canopy height and density, fan type
and speed, fan position, and chamber geometry.
Air is sub-sampled just before it enters and just as it exits the
chamber by a miniature diaphragm pump with two pumping
sections that operate in parallel (TD-4X2NA-Type 4-Viton
Elastomers, Brailsford & Co., Rye, NY, USA). Air is pumped
to the reference analyzer from the incoming side and to the
sample analyzer from the effluent side. The flow rate is
approximately 1 liter min-1 from each side of the pump so that
the impact of water sorption and CO2 diffusion in the Bev-ALine tubing and filters between the chamber and the analyzers
is minimized. The air is filtered by two Gelman Acro-50 1 µm
filters (LI-COR part #9967-008) before entering the IRGAs.
The inlet air temperature and relative humidity are monitored
using a humidity and temperature sensor (Humitter 50Y,
Vaisala, Helsinki, Finland) mounted in the chamber inlet air
stream. Chamber air temperature is measured with a thermocouple (LI-6400 leaf temperature thermocouple, part #640004) positioned in the effluent airstream and connected to the
leaf thermocouple input on the LI-6400 sensor head.
This system did not have a means of measuring foliage
temperature. Depending on the canopy structure and view
angle of an infrared thermometer (IRT), it may be useful to
measure the canopy temperature inside the chamber by
infrared thermometry (Garcia et al., 1995).
Quantum flux density is measured inside the chamber approximately 2 cm below the top with a LI-COR LI-190SA quantum
sensor.
completed the plants which had been enclosed for the measurements were harvested for leaf area determinations. The
crop was flowering and had a leaf area index of about 3.7.
There were clear sky conditions on the first full day of
measurements (Figure 3), whereas, the second day of measurements could be characterized by scattered cloudy conditions. The canopy CO2 exchange rates generally followed the
diurnal courses of incident light. The maximum air saturation
deficits (D) were 3.5 kPa on 25 August and 3.4 kPa on 26
August.
The alfalfa photosynthesis data of 25 August are similar in
magnitude and in behavior to those of Baldocchi et. al. (1981).
They speculated that the "midday depression" in their data
may have been due to starch accumulation in the leaves.
Another possibility is that photoinhibition suppressed the
rates.
List of Suppliers
Variable Area Flow Meters
Dwyer Instruments, Inc.
102 Highway 212
P.O. Box 373
Michigan City, IN 46361
Phone: 219-879-8000
FAX: 219-872-9057
Blowers and Fans
Brailsford and Co., Inc.
670 Milton Road
Rye, NY 10580
Phone: 914-967-1820
FAX: 914-967-1836
We did not do a time course assay of starch in the leaves;
however, a comparison of the photosynthesis data of 25 and 26
August plotted against light (Figure 4) would lend support to
either of these hypotheses. In contrast to 25 August, CO2
exchange rates on 26 August, a scattered cloudy day, did not
light saturate.
W.W. Grainger, Inc.
333 Knightsbridge Parkway
Lincolnshire, IL 60069
Phone: 708-913-7218
FAX: 708-913-7392
References
Pumps
Baldocchi, Dennis D., Bruce B. Hicks and Tilden P. Meyers,
1988. Measuring Biosphere-Atmosphere Exchanges of
Biologically Related Gases with Micrometeorological
Methods. Ecology 69(5), 1331-1340.
Brailsford and Co., Inc.
670 Milton Road
Rye, NY 10580
Phone: 914-967-1820
FAX: 914-967-1836
Baldocchi, Dennis D., Shashi B. Verma and Norman J.
Rosenberg, 1981. Seasonal and Diurnal Variation in the CO2
Flux and CO2-Water Flux Ratio of Alfalfa. Ag. Met. 23, 231244.
Garcia, R.L., John M. Norman and Dayle K. McDermitt,
1990. Measurements of Canopy Gas Exchange Using an
Open Chamber System. Remote Sensing Reviews, Vol 5(1),
141-162.
Norman, J.M., R. Garcia and S.B. Verma, 1992. Soil Surface
CO2 Fluxes and the Carbon Budget of a Grassland. J. of Geo.
Res. 97, 18845-18853.
Vourlitis, G.L., W.C. Oechel, S.J. Hastings and M.A. Jenkins,
1993. A System for Measuring in situ CO2 and CH4 Flux in
Unmanaged Ecosystems: An Arctic Example. Functional
Ecology 7, 369-379.
KNF Neuberger, Inc.
Two Black Forest Road
Trenton, NJ 08691-9428
Phone: 609-890-8889
FAX: 609-890-2838
Thomas Compressors and Vacuum Pumps
1419 Illinois Avenue
Sheboygan, WI 53082-0029
Phone: 414-457-4891
FAX: 414-451-4276
Thermal Air Velocity Transducers
TSI Inc.
P.O. Box 64394
St. Paul, MN 55164
Phone: 612-490-2888
FAX: 612-490-2874
7
Thermal Air Velocity Transducers
ICI Films
P.O. Box 15391
Wilmington, DE 19850
Phone: 302-887-3000
FAX: 302-887-5365
Sierra Instruments, Inc.
5 Harris Court, Building L
Monterrey, CA 93940
Phone: 408-373-0200
FAX: 408-373-4402
Temperature Sensors - Thermocouples
Omega Engineering, Inc.
P.O. Box 4047
Stamford, CT 06907-0047
Phone: 203-359-1660
FAX: 203-359-7700
Distributed by:
Transilwrap Company, Inc.
13592 N. Stemmons
Dallas, TX 75234
Phone: 214-484-3211
FAX: 214-484-3171
(Note: Minimum order $500.00)
Temperature Sensors - Thermistors
Yellow Springs Instruments
1725 Brannum Lane
P.O. Box 465
Yellow Springs, OH 45387
Phone: 513-767-7241
FAX: 513-767-9353
Humidity and Temperature Sensors
Rotronic Instrument Corp.
7 High Street
Huntington, NY 11743
Phone: 516-427-3994
FAX: 516-427-3902
Vaisala Inc.
100 Commerce Way
Woburn, MA 01801-1068
Phone: 617-933-4500
FAX: 617-933-8029
Measuring Canopy Gas
Exchange with the LI-6400
Portable Photosynthesis System
2
LI-6400 Portable Photosynthesis System
Transparent Films
APPLICATION NOTE
Suppliers (continued)
Introduction
Canopy gas exchange systems are useful for
quantifying the effects of environmental changes
on the instantaneous productivity of a plant
community. Measuring the gas exchange of the
entire canopy with a chamber system obviates
difficulties encountered when extrapolating leaf
measurements to the canopy scale such as
accurately modeling the distribution of absorbed
radiation. Canopy gas exchange systems, if
properly designed and operated, can provide a
measure of CO2 flux that closely approximates
natural conditions. However, it is important to
consider how the chamber may alter, among other
factors, the canopy temperature, wind speed (and
therefore boundary layer conductance), and
radiation balance of the plant community. When
possible, canopy chamber results should be
compared to micrometeorological flux measurements, since they do not disturb the environment
around the canopy (Baldocchi et. al., 1988).
This application note will be concerned with the
design and implementation of a simple continuous
flow “open” canopy chamber system based around
the LI-6400 Portable Photosynthesis System. This
system allows steady-state canopy fluxes to be
measured over a period of several hours or days,
and is less susceptible to errors introduced by
leaks and water sorption than a closed system.
(Water sorption can have a significant effect on
transpiration estimates until equilibrium conditions
are reached.) Nonetheless, depending on plant
material and experimental design, a closed system
may be more suitable. In that case, the LI-6200
Portable Photosynthesis System may be readily
adapted for closed system canopy measurements
(Vourlitis et. al., 1993). For soil respiration
measurements, the LI-6200 with the 6000-09 Soil
Respiration Chamber has been thoroughly tested
(Norman et. al., 1992) and is recommended.
Oftentimes the focus of a
study is an individual
species of a plant community, or field plots are too
small to make use of
micrometeorological
techniques. In these cases
enclosure methods are the
only methods available to
determine instantaneous
canopy CO2 flux.
Many types of chambers
and systems have been
designed and will not be
reviewed here. Garcia et.
al. (1990) summarize
some of the advantages
and disadvantages of open
and closed canopy
chamber systems.
Canopy gas exchange system installed in August, 1995, in Lincoln, Nebraska.
®
LI-COR, inc.
●
Environmental Division ● 4421 Superior Street ● P.O. Box 4425
Phone: 402-467-3576 ● FAX: 402-467-2819
Toll-free 1-800-447-3576 (U.S. & Canada)
●
Lincoln, Nebraska 68504 USA
®
1