The System Components

If you have just taken delivery of your LI-6400XT check the packing list to verify that you have received everything that you ordered. Or, if you’ve just inherited an LI-6400 from someone else, check to see that you have everything. Here’s a brief description of what should be there:

Figure 1‑5. The LI-6400XT Portable Photosynthesis System.

The Standard Parts


The console has an environmentally sealed, 64-key, full ASCII keypad and 8 line × 40 character LCD. On the right side of the console are the sensor head connectors, 6400-03 battery compartments, and RS-232C connector. CO2 scrubber and desiccant tubes attach to the left side of the console, along with the optional 6400-01 CO2 source assembly or CO2 tank connector block. A field stand is normally attached to the underside of the console.

Sensor Head/IRGA

The sensor head/IRGA includes a leaf chamber, spring-loaded latching handle (squeeze and release to open, squeeze and release to close), two Peltier thermoelectric coolers, and the sample and reference gas analyzers. Up to two light measurements are provided for: most leaf chamber tops have a Gallium Arsenide Phosphide (GaAsP) PAR sensor, and a mounting fixture is provided for a 9901-013 external quantum sensor, if desired. (For a discussion of the logic of using two light sensors, see Why Two Sensors? on page 8-2 in the instruction manual.) Leaf temperature is measured with a thermocouple held in the bottom of the 2x3 and 2x6 cm leaf chambers; other chambers use energy balance to compute leaf temperature.

Cable Assembly

The cable assembly has two electrical cables and two air flow hoses, and connects the console to the sensor head / IRGA. These are held together with a flexible, outer wrapping.

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 safely stored away.

Chemical Tubes

These tubes are used during operation to remove CO2 and water vapor from the incoming air stream. One tube should contain soda lime, and the other tube should contain Drierite, a desiccant. Each tube has an adjustment valve at the top for partitioning the flow through the chemical contained in the tube.

6400-03 Rechargeable Batteries

The 6400-03 Rechargeable Batteries are shipped tested and fully charged. Because they slowly self-discharge with time, it is a good idea to test your batteries periodically. Leaving them discharged for an extended period can result in damage. (See 6400-03 Batteries for instructions concerning testing and charging batteries.) One 6400-03 battery provides approximately 1-2 hours of operational life. Recharge them with the LI-6020 Battery Charger.

LI-6020 Battery Charger

The LI-6020 can charge four 6400-03 Rechargeable Batteries simultaneously. It runs on 92-138/184-276 VAC, 47 to 63 Hz, but a selector switch on the back of the LI-6020 must be set to the appropriate mains voltage.

RS-232 Cable

Part number 9975-016 has a 9 pin to 9 pin cable, and a separate 9 to 25 pin adapter. Figure 11-21 on page 11-20 in the instruction manual illustrates how to use it.

6400-25 Compact Flash Memory Card

Can be installed in the expansion slot in the XT console.

6400-26 Ethernet adapter card

For use in the expansion slot in the XT console.

Field Stand

When shipped from the factory, the LI-6400’s field stand base plate is attached to the bottom of the console. It normally remains there, and you can attach or detach the legs as needed. Store the legs in the narrow front slot of the carrying case.

6400-60 CD

The CD contains a hyper-linked, electronic version (.pdf file) of this manual, plus a number of support programs for tasks such as (re-)installing instrument software, and remotely controlling the LI-6400 from a computer. See Support Software on page 11-2 in the instruction manual. Note: New versions of all of our software are released periodically. You can get the most recent version by contacting LI-COR, or by downloading it from our web site (

Calibration Sheet

This data sheet lists the calibration information entered into the LI-6400 at the factory. Keep it in a safe place for future reference.

Carrying Case

The hard-shell, foam padded carrying case can hold the console, sensor head, cables, some batteries, legs, and a few other accessories

The optional accessories

There are several optional accessories that you may have ordered with your LI-6400. Any of them can also be purchased later, and (with the exception of the 6400-01 CO2 Mixer), they do not require factory installation:

6400-01 CO2 Mixer

This consists of three components:

  • A control module that is inside the console
  • This part is factory installed in the console.
  • A cartridge holder and regulator
  • For use with the disposable 12 gram CO2 cartridges, this part is user-installable between the chemical tubes on the outside of the console (see Figure 2‑6).
  • An adapter block for CO2 tanks
  • This alternative to the cartridge holder and regulator allows tanks of compressed pure CO2 to be used instead of the 12 gram cartridges (see Figure 2‑8).

6400-02B LED Light Source

The 6400-02B replaces the top half of the standard 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 6400-02B replaces the 6400-02, which used only red LEDs. See Spectral Considerations on page 8-8 in the instruction manual for a comparison of the 6400-02 and 6400-02B.

6400-05 Conifer Chamber

A cylindrical chamber suitable for short-needled shoots. Leaf temperature is obtained by energy balance, for which an external PAR sensor reading is required. (External PAR sensor not included with this option.)

6400-07 Needle Chamber

A 2x6 cm chamber with Propafilm® top and bottom windows. Leaf temperature is not measured, but is computed using an energy balance. A GaAsP light sensor is included.

6400-08 Clear-Bottom Chamber

A 2x3 cm chamber bottom with a Propafilm® window. Leaf temperature is computed using an energy balance. This chamber can be used with any 2x3 cm chamber top (such as the fluorometer adapters) or 6400-02 or -02B LED source.

6400-09 Soil Chamber

For measuring soil CO2 efflux.

6400-10 MiniPAM Adaptor

This is a 2x3 cm chamber top that is designed to hold a 2 mm fiber probe, such as is used by the MiniPAM fluorescence system (Heinz Walz GmbH, Effeltrich, Germany). A GaAsP light sensor is included.

6400-11 Narrow Leaf Chamber

A 2x6 cm chamber with a Propafilm® top window, and an opaque bottom that holds the 6400-04 leaf temperature thermocouple. A GaAsP light sensor is included.

6400-13 Thermocouple Adapter

Allows a type E thermocouple to be connected to the 37-pin connector on the LI-6400 console. This adapter is included with the 6400-09 Soil Chamber.

6400-15 Extended Reach 1 cm Chamber

This is a chamber designed for Arabidopsis and other small leaves. The aperture is 1.0 cm in diameter, and has a Propafilm® top and bottom. No light sensor is included. Leaf temperature comes from an energy balance analysis, for which an external quantum sensor is necessary (but not included).

6400-17 Whole Plant Arabidopsis Chamber

Circular chamber for whole plant measurements of plants in small pots.

6400-18 RGB Light Source

Designed for the 6400-17 chamber, but can be used on other chambers.

6400-22 Opaque Conifer Chamber

Accommodates short needle shoots. Designed for use with the 6400-18 RGB Light Source. Top shell of chamber is clear, bottom is opaque.

6400-24 Bryophyte Chamber

This is the 7 cm diameter 6400-17 with a solid bottom, making it suitable for measuring unattached clumps of whatever material you’d care to drop into it.

6400-40 Leaf Chamber Fluorometer

Leaf Chamber Fluorometer covers installation and operation of this accessory.

6400-70 AC Adapter

This optional accessory fits in the battery compartment, and allows the LI-6400 to be powered from mains power. It can simultaneously (but slowly) recharge one battery.

9901-013 External Quantum Sensor

A LI-COR LI-190SA quantum sensor can be mounted on the sensor head. (The 9901-013 is an LI-190SA with a short cable.)

Display Backlight

If installed, the display backlight is toggled on and off by holding down shift + ctrl then pressing home.