LI-COR LI-6400 User manual

PRIMER
LI-6400
Portable
Photosynthesis
System
®

NOTICE
The information contained in this document is subject to change without notice.
LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING,
BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE. LI-COR shall not be liable for errors contained herein or for incidental or
consequential damages in connection with the furnishing, performance, or use of this material.
This document contains proprietary information which is protected by copyright. All rights are reserved. No part
of this document may be photocopied, reproduced, or translated to another language without prior written consent
of LI-COR, Inc.
© Copyright 1995, LI-COR, Inc.
Publication Number 9501-110
Printing History:
1st Printing January, 1995 - OPEN Software version 1.10
2nd Printing August, 1995 - OPEN Software version 2.0
Macintosh®is a registered trademark of Apple Computer, Inc.
Printing History
New editions of this manual will incorporate all material since the previous editions. Update packages may be
used between editions which contain replacement and additional pages to be merged into the manual by the user.
The manual printing date indicates its current edition. The printing date changes when a new edition is printed.
(Minor corrections and updates which are incorporated at reprint do not cause the date to change).
U.S. Patent Numbers: 5,332,901 & 5,340,987. Other patents pending in the U.S. and other countries.
LI-COR, Inc. • 4421 Superior Street • Lincoln, Nebraska 68504
Phone: [phone] • FAX: [phone]
Toll-free: 1-800-447-3576 (U.S. & Canada)

iii
Table of Contents
Section 1. Unpacking and Initial Inspection
What’s What ...................................................................................................................................... 1-1
Optional Accessories......................................................................................................................... 1-3
Section 2. Overview and System Assembly
System Overview............................................................................................................................... 2-1
Hardware Overview.................................................................................................................... 2-1
Equation Summary ............................................................................................................................ 2-6
Assembling the LI-6400 .................................................................................................................... 2-8
6400-02 LED Light Source Installation ............................................................................................ 2-11
Connecting the LI-6400 to Mains Power .......................................................................................... 2-14
Note on Battery Life .......................................................................................................................... 2-14
Mounting the Sensor Head on a Tripod ............................................................................................ 2-15
Installing the 6400-01 External CO2Source Assembly .................................................................... 2-17
General Description.................................................................................................................... 2-17
Installation .................................................................................................................................. 2-17
Using the CO2Tank Connector Block .............................................................................................. 2-20
General Description.................................................................................................................... 2-20
Installation .................................................................................................................................. 2-20
Installation Using 4mm Copper Tubing..................................................................................... 2-22

iv
Section 3. Software Tour
Overview............................................................................................................................................ 3-2
Power On........................................................................................................................................... 3-2
Power Off .......................................................................................................................................... 3-4
Using the Keypad .............................................................................................................................. 3-4
Welcome Menu.................................................................................................................................. 3-6
About This Unit... ...................................................................................................................... 3-6
Help Menu.................................................................................................................................. 3-7
Tests and Diagnostics Menu ...................................................................................................... 3-7
Quit OPEN - IRGAs Left ON .................................................................................................... 3-7
Quit OPEN - IRGAs OFF .......................................................................................................... 3-7
Configuration Menu .......................................................................................................................... 3-9
About the Compute List ............................................................................................................. 3-11
The Configuration Editor ........................................................................................................... 3-12
Calibration Menu............................................................................................................................... 3-16
New Measurements ........................................................................................................................... 3-17
About the New Measurements Screen ....................................................................................... 3-17
New Measurements Screen Function Keys................................................................................ 3-18
Changing the New Measurements Display ................................................................................ 3-19
Changing Display Definitions .................................................................................................... 3-21
Saving Display Definitions ........................................................................................................ 3-22
New Measurements Variables.................................................................................................... 3-23
About Status Variables............................................................................................................... 3-26
New Measurements Function Keys............................................................................................ 3-27
Using Strip Chart Mode..................................................................................................................... 3-32
Using the StdFileDialog Box............................................................................................................. 3-35
Utility Menu ...................................................................................................................................... 3-36
Access the FILER....................................................................................................................... 3-37
Configure the COMM Port ........................................................................................................ 3-37
File Exchange Mode................................................................................................................... 3-38
Graph Stored Data ...................................................................................................................... 3-38
Choosing and Editing the Axes........................................................................................... 3-40
New File (Editor)........................................................................................................................ 3-42
Recompute Stored Data.............................................................................................................. 3-42
Set the Time and Date ................................................................................................................ 3-45
Sleep mode ................................................................................................................................. 3-45

v
Low Battery Warning ........................................................................................................................ 3-46
Humidity Warning............................................................................................................................. 3-46
Disk Full Warning ............................................................................................................................. 3-47
Adjusting the Display Contrast.......................................................................................................... 3-47
Section 4. Making Measurements
Overview............................................................................................................................................ 4-2
User Calibration................................................................................................................................. 4-2
Before Beginning Calibration Procedures.................................................................................. 4-3
Zero the CO2/H2O IRGAs.......................................................................................................... 4-3
Span the CO2/H2O IRGAs ......................................................................................................... 4-5
Independent Calibration of the Analyzers.................................................................................. 4-7
Flowmeter Zero .......................................................................................................................... 4-7
Storing the Zero and Span Values.............................................................................................. 4-7
Logging Data..................................................................................................................................... 4-8
Using the LogList....................................................................................................................... 4-9
Automatically Logging Data ...................................................................................................... 4-11
Using the Log Button ................................................................................................................. 4-12
Viewing Data..................................................................................................................................... 4-12
Recovering Lost Data ........................................................................................................................ 4-14
Changing the Flow Rate .................................................................................................................... 4-14
Null Balancing on Water Vapor................................................................................................. 4-14
Using Fixed Flow Rates ............................................................................................................. 4-16
Controlling Chamber Air and Leaf Temperatures............................................................................. 4-17
Matching the Analyzers..................................................................................................................... 4-18
Why Match? ............................................................................................................................... 4-19
When Do I Match? ..................................................................................................................... 4-20
Making a Light Response Curve ....................................................................................................... 4-22
Changing Light Intensity............................................................................................................ 4-22
Using the Auto Light Curve Program ........................................................................................ 4-23
Making a CO2Response Curve......................................................................................................... 4-25
Preliminary Considerations ........................................................................................................ 4-25
Manual Control ACiProtocol..................................................................................................... 4-25
Auto ACiProtocol ...................................................................................................................... 4-28
Light Sensors Used in the LI-6400.................................................................................................... 4-29
Gallium Arsenide Phosphide (GaAsP) Sensor........................................................................... 4-30

vi
Generating an Approximate GaAsP Sensor Calibration Using a Quantum Sensor and the
Quantum Sensor Chamber Mount.............................................................................................. 4-31
Section 5. File Management
Data Storage and File Management .................................................................................................. 5-2
Using the FILER................................................................................................................................ 5-3
Opening and Closing the FILER ................................................................................................ 5-3
File Naming Conventions........................................................................................................... 5-3
Directories .................................................................................................................................. 5-3
Directory Operations ......................................................................................................................... 5-4
Viewing and Changing Directories ............................................................................................ 5-4
Creating and Deleting Directories.............................................................................................. 5-4
File Operations .................................................................................................................................. 5-6
Viewing File Details................................................................................................................... 5-6
Viewing and Editing Files.......................................................................................................... 5-6
Tagging Files.............................................................................................................................. 5-7
Purging Files .............................................................................................................................. 5-9
Copying Files.............................................................................................................................. 5-9
Moving Files .............................................................................................................................. 5-9
Duplicating Files ........................................................................................................................ 5-10
Renaming Files........................................................................................................................... 5-10
Printing Files .............................................................................................................................. 5-10
Executing Programs.................................................................................................................... 5-11
Disk Operations................................................................................................................................. 5-11
About Flash Memory... .............................................................................................................. 5-11
Space Available.......................................................................................................................... 5-12
Defragmenting Disks.................................................................................................................. 5-12
Formatting Disks ........................................................................................................................ 5-13
Using the Hidden Disk ............................................................................................................... 5-14
Data Communications ....................................................................................................................... 5-15
Setting the Communications Parameters.................................................................................... 5-15
Cables......................................................................................................................................... 5-16
Sending Files to a Personal Computer........................................................................................ 5-18
Sending Files to a Macintosh®................................................................................................... 5-19

vii
Section 6. Maintenance and Service
Recalibration...................................................................................................................................... 6-2
Filling the Desiccant Tube................................................................................................................. 6-2
About Drierite ............................................................................................................................ 6-2
Regenerating Drierite ................................................................................................................. 6-3
Ordering Information.................................................................................................................. 6-3
Filling the Scrubber Tube .................................................................................................................. 6-4
A Quick Soda Lime Test ............................................................................................................ 6-4
Replacing the Air Mufflers................................................................................................................ 6-5
Replacing the Leaf Temperature Thermocouple............................................................................... 6-6
Setting the Leaf Temperature Thermocouple Zero ........................................................................... 6-8
Recharging the 6400-03 Batteries ..................................................................................................... 6-9
Storing the 6400-03 Batteries..................................................................................................... 6-9
Replacing the Battery Fuse ........................................................................................................ 6-10
System Console ................................................................................................................................. 6-10
Cleaning and Removing the Card Cage ..................................................................................... 6-10
Replacing the Fuses.................................................................................................................... 6-11
Leaf Chamber Care............................................................................................................................ 6-14
Replacing the Leaf Chamber Foam Gaskets ..................................................................................... 6-14
Replacing the Upper Leaf Chamber Film.......................................................................................... 6-15
Internal Air Filter............................................................................................................................... 6-18
Soda Lime/Desiccant Bottles in the Sensor Head ............................................................................. 6-19
Cleaning the Optical Bench............................................................................................................... 6-22
Servicing the External CO2Source Assembly .................................................................................. 6-27
Oil Filter Replacement ............................................................................................................... 6-27
Making Your Own Filters .......................................................................................................... 6-28
If the Regulator Becomes Clogged ............................................................................................ 6-28
Shipping Your LI-6400...................................................................................................................... 6-32

viii
Section 7. Troubleshooting
Appendix A. Configuration List
Appendix B. Specifications
Appendix C. Connector Descriptions
Warranty

Unpacking and Initial Inspection 1-1
1
1
1
Unpacking &
Initial Inspection
Contents
What’s What ..................................................................... 1-1
Optional Accessories ........................................................ 1-3
What's What
If you have just taken delivery of your LI-6400 check the
packing list to verify that you received everything ordered,
including the following items:
Calibration Sheet
This data sheet is a copy of the calibration information entered
into the LI-6400 by LI-COR. Keep it in a safe place for future
reference.
Spare Parts Kit
This box contains replacement parts for your LI-6400. As you
become familiar with the system you will learn which items to
keep close at hand and which items can be stored away.

Section 1
1-2 Unpacking and Initial Inspection
External Scrubber and Desiccant Tubes
These tubes are used during operation. Several spare air
mufflers (located inside the tubes) have been included for
future use.
6400-03 Rechargeable Batteries
(10.5-16 VDC). The 6400-03 Rechargeable Batteries are
tested and fully charged before they leave the factory, but may
discharge during shipping. It is a good idea to test your
batteries to make sure they are charged. See "Recharging the
6400-03 Batteries" in Section 6 for instructions about testing
and charging batteries. The 6400-03 requires the LI-6020
Battery Charger for recharging. One 6400-03 battery provides
approximately 1-2 hours of battery life.
LI-6020 Battery Charger
(92-138/184-276 VAC, 47 to 63 Hz). The LI-6020 can charge
four 6400-03 Rechargeable Batteries simultaneously.
1000-90 Data Communications and Utility Software
This software can be used to communicate with PC-
compatible computers. The software is provided on a 3 1/2
inch diskette.
RS-232C Cables
(Part #’s 1800-04 and 1000-09). Use the 1000-09 to connect
the LI-6400 to a 25-pin DTE device; use both cables to
connect to a 9-pin computer serial port.
Field Stand
The LI-6400 field stand is mounted to the console. The four
legs can be attached to the underside of the LI-6400 to provide
a sturdy base for field measurements. When not in use, the
legs can be stored in the carrying case.
6400-50 System Software
The System Software disk is a complete backup of the system
software in your LI-6400. Keep this disk in a safe place in
case you need to re-install the system software.

Unpacking & Initial Inspection
Unpacking and Initial Inspection 1-3
Optional Accessories
There are several optional accessories, including:
6400-01 CO2Injector
The 6400-01 mounts on the LI-6400 console to provide a
constant, regulated source of CO2to the leaf chamber. The
6400-01 uses disposable CO2cartridges to provide
concentrations up to 2000 µmol mol-1 CO2for up to 8 hours
per cartridge.
6400-02 LED Light Source
The 6400-02 replaces the top of the leaf chamber and provides
light from 0 to over 2000 µmol quanta m-2 s-1. The intensity
of the light is software adjustable to a resolution of 1 µmol
m-2 s-1 . The 670nm red Light Emitting Diodes (LED’s)
provide uniform chamber light distribution with low power
consumption and cool operation.
6400-20 FX (File eXchange) Software
The 6400-20 FX file exchange software is used for rapid file
transfer between the LI-6400 and a computer. In file exchange
mode, the LI-6400 becomes a “slave” to the computer. File
transfers and other file management operations are easily
accomplished.

Overview & Assembly 2-1
2
2
2
Overview &
Assemblyaaa
Chicago
Contents
System Overview.............................................................. 2-1
Hardware Overview................................................... 2-1
Equation Summary............................................................ 2-6
Assembling the LI-6400 ................................................... 2-8
6400-02 LED Light Source Installation............................ 2-11
Connecting the LI-6400 to Mains Power.......................... 2-14
Note on Battery Life ......................................................... 2-14
Mounting the Sensor Head on a Tripod............................ 2-15
Installing the 6400-01 External CO2Source Assembly ... 2-17
General Description................................................... 2-17
Installation ................................................................. 2-17
Using the CO2Tank Connector Block ............................. 2-20
General Description................................................... 2-20
Installation ................................................................. 2-20
Installation Using 4mm Copper Tubing .................... 2-22
System Overview
Hardware Overview
There are two major components of the LI-6400; the system
console and sensor head (Figure 2-1). The console has an
environmentally sealed, 64-key, full ASCII keypad for typing
and executing the menu-driven software. The 8 line ×40

Section 2 Chicago
2-2 Overview & Assembly
character LCD display shows measured and computed values,
software functions, and data plots. On the right side of the
console are the sensor head connectors, 6400-03 battery
compartments, and RS-232C connector. CO2scrubber and
desiccant tubes attach to the left side of the console, along
with the optional 6400-01 CO2source assembly or CO2tank
connector block. A field stand attaches to the underside of
the console.
The sensor head contains a leaf chamber, which is clamped
onto a leaf by compressing a spring-loaded handle. The upper
half of the leaf chamber can be replaced by the optional 6400-
02 LED light source. The bottom half holds the leaf
temperature thermocouple. Two Peltier thermoelectric
coolers provide automatic temperature control of the analyzer
block. The internal Gallium Arsenide Phosphide (GaAsP)
PAR sensor, located in the upper half of the leaf chamber, can
be supplemented with an optional 9901-013 external
quantum sensor, if desired. Two absolute analyzers make
sample and reference measurements of CO2and H2O. The
sample analyzer optical path is open to the leaf chamber,
eliminating time delays and back pressure from long hoses.
IRGA and CHAMBER connectors are mounted on the rear of
the analyzer housing. Note that one of the hoses leading from
the sensor head is marked with a black band; this tube is
connected to the sample inlet on the console. On the
underside of the sensor head is a matching valve that allows
exhaust flow from the leaf chamber to be diverted to the
reference analyzer in order to remove analyzer offsets without
disturbing the leaf conditions. The matching valve is
described in more detail later.

Overview & Assembly
Overview & Assembly 2-3
System Console
Sensor Head
6400-02 LED
Light Source (optional)
Quantum Sensor
(optional)
Leaf Chamber
Keypad
Soda Lime/Desiccant
Tubes
Analyzers
Figure 2-1. LI-6400 system console and sensor head.
The LI-6400 Portable Photosynthesis System is an open gas
exchange system. An open system has a net flow of air
through the system.
This system was designed to provide steady state light, CO2,
H2O and temperature conditions for measurements. When
making measurements, the leaf chamber is clamped onto a leaf
section. In the light, the leaf removes CO2from the air (net
photosynthesis) and adds water vapor to the air (transpiration).
Net photosynthesis and transpiration are computed by
measuring the air flow rate, the incoming and chamber CO2
and H2O concentrations, and leaf area.

Section 2 Chicago
2-4 Overview & Assembly
Bypass
Valve
Air In
Desiccant
CO
2

Scrubber
Bypass Valve
Liquid CO
2
CO
2 Source Assembly


CO
2
-Free
Air In
Pure
CO
2
CO
2
Vent
Pump
Mixed
Air Out
Flow
Restrictors
Flow
Meter
Measurement Mode
Vent
75%
25%
Console With 6400-01 CO
2
Injector System Sensor Head
Exhaust
Leaf
Chamber
Sample
Reference
Analyzers
CO
2

Controller

CO
2

Flow
Control
Flow
Rate
Control
Figure 2-2. LI-6400 flow schematic (measurement mode).
Figures 2-2 and 2-3 show flow schematics of the LI-6400.
The pump draws air into the LI-6400 console.
A variable amount of incoming air flow may be routed
through chemical columns filled with a CO2scrubber (soda
lime) and a desiccant (Drierite). A valve on top of each
column controls the amount of air passing through the soda
lime and desiccant. This provides coarse control of the CO2
and water vapor in the incoming air.
The air flow is divided before it reaches the sensor head.
Approximately 75% of the flow goes through the leaf chamber
and sample analyzer, and 25% goes to the reference analyzer.
An electronic flow meter measures the flow rate of the air
going to the leaf chamber.
In measurement mode (Figure 2-2), parallel air flows pass
through the sample analyzer and the reference analyzer and
then combine and exit to the outside. In match mode (Figure
2-3), however, the exhaust flow from the sample analyzer is
diverted to the reference analyzer so that both analyzers "see"
the same gas. After leaving the reference analyzer the gas
mixes with the reference air flow and is exhausted. This

Overview & Assembly
Overview & Assembly 2-5
allows electronic matching of the analyzers, without disturbing
leaf chamber conditions.
Bypass
Valve
Air In
Desiccant
CO
2

Scrubber
Bypass Valve
Liquid CO
2
CO2Source Assembly 

CO
2
-Free
Air In
Pure
CO
2
CO
2
Vent
Pump
Mixed
Air Out
Flow
Restrictors
Flow
Meter
Match Mode
Vent
75%
25%
Console With 6400-01 CO2Injector System Sensor Head
Leaf
Chamber
Sample
Reference
Analyzers
CO2 
Controller

CO
2

Flow
Control
Flow
Rate
Control
Exhaust
Figure 2-3. LI-6400 flow schematic (match mode).
Pressure inside the leaf chamber is slightly positive to ensure
that leaks are outward, so outside air does not affect the
chamber CO2and H2O concentrations.
Net photosynthesis, A (µmol CO2m-2 s-1) and transpiration, E
(mol H2O m-2 s-1) are computed by measuring the air flow
rate, the incoming and leaf chamber CO2and H2O
concentrations, and leaf area. The governing equations follow.

Section 2 Chicago
2-6 Overview & Assembly
Equation Summary
The governing equations for net photosynthesis, transpiration,
total conductance to water vapor, stomatal conductance to
water vapor, total conductance to CO2, and intercellular CO2
concentration are given below.
Transpiration (E)
Euw w
sw
ec e
c
=−
( )
•−





10 1 1000
5
Net Photosynthesis (A)
Auc c
scE
ee c c
=−
( )
−
100
Total Conductance to Water Vapor (gtw)
gEww
ww
tw
lc
lc
=−
+





−
1000 2
Stomatal Conductance to Water Vapor (gsw)
g
gk g
sw
tw
f
bw
=−
1
1
Total Conductance to CO2(gtc)
g
g
tc
sw
=+
1
16 137 .. k
gf
bw
Intercellular CO2Concentration (ci)
cgEcA
gE
i
tc c
tc
=−

 −
+
2
2
A= net photosynthesis, µmol CO2m-2 s-1
cc= mole fraction of CO2in the leaf chamber, µmol CO2
mol-1 air
ce= mole fraction of CO2entering the leaf chamber, µmol
CO2mol-1 air
ci= intercellular CO2concentration, µmol CO2mol air-1
E= transpiration, mol H2O m-2 s-1
gbw = boundary layer conductance to water vapor, mol H2O
m-2 s-1
gsw = stomatal conductance to water vapor, mol H2O m-2 s-1

Overview & Assembly
Overview & Assembly 2-7
gtc = total conductance to CO2, mol CO2m-2 s-1
gtw = total conductance to water vapor, mol H2O m-2 s-1
kf= (K2+ 1)/(K + 1)2, where K is an estimate of the ratio of
stomatal conductances of one side of the leaf to the other,
dimensionless
s= leaf area, cm2
ue= mole flow rate of air entering the leaf chamber, µmol s-1
wc= mole fraction of water vapor in the leaf chamber, mmol
H2O mol-1 air
we= mole fraction of water vapor entering the leaf chamber,
mmol H2O mol-1 air
wl= mole fraction of water vapor in the stomata, mmol H2O
mol-1 air

Section 2 Chicago
2-8 Overview & Assembly
Assembling the LI-6400
This section explains how to prepare the console and sensor
head for making measurements.
1. Fill the CO2scrub and desiccant tubes (see Section 6).
Caution: Never unscrew the top cap while the tubes
are full of chemicals. To change chemicals grasp the
tube (not the top cap) and unscrew the bottom cap. If
the top cap is unscrewed with chemicals inside,
damage to the air mufflers will occur.
Figure 2-5 shows the position of the CO2scrubber and
desiccant tubes.
Remove the bottom cap of the CO2scrub tube, and fill it
with soda lime (in the spares kit) to within 0.5 cm of the
end of the tube. Replace the bottom cap and attach the
tube to the console using the lower of the two knurled
knobs.
Follow the same procedure with the desiccant tube.
Indicating Drierite desiccant is provided in the spares kit.
When the LI-6400 is in use, the CO2scrub tube and
desiccant tube should remain attached to the console at all
times, except when changing chemicals.

Overview & Assembly
Overview & Assembly 2-9
Figure 2-5. Desiccant and CO
2
scrubber tubes.
2. Connect cables and hoses to the console.
Air inlet and outlet ports and electrical connectors are
located on the right side (end) of the console (Figure 2-6).
Two battery jacks are located beneath the ON/OFF
switch. Insert two 6400-03 batteries into the battery
compartment and connect both batteries. The 6200B
batteries used with other LI-COR instruments can also be
used, but they will not fit into the battery compartment of
the LI-6400.