1

Introduction to the LI-6800

What it is, what it does, and how it does it

What's what

Chambers and light sources

2

Assembling the LI-6800

Putting it all together

Preparing the console

Powering the LI-6800

Connecting an external air supply

The tripod, monopod, and harness

3

Preparations and verification

Learning how to make it work

Controlling the LI-6800 from a computer

The Start Up tab

The Constants tab

The Environment tab

The Measurements tab

4

Operation

Data files, results, and configuration information

The Log Setup tab

The Programs tab

The Tools tab

Managing logged data on the console

Transferring files to a computer

Folders

More details on files

Summary of symbols

5

System tests and messages

Trying to get your attention

Warmup tests

Controller tests

Fluorometer tests

Messages

6

Troubleshooting

When things go wrong

Can't copy files using USB

The log button on the head does not work

CO2 cartridge exhausts quickly

Issues with environmental controls and setpoints

Cannot control the fluorometer output

Fluorometer does not flash on log

Chamber and light source warning messages

Chamber leak warning message

Instrument fails the leak test

Pump/flow meter issues

Unreasonable results

Touchscreen not responding

Power on problems

7

Maintenance and calibration

The difference between data and good data

Updating the software

User calibration - zero and span

Intake air filter

Column air filters

Head and IRGA maintenance

Storing the LI-6800

Preparation for shipping

8

Measuring chlorophyll a fluorescence

Fluorometer theory and equation summary

What's what

Installing the fluorometer chamber

Fluorometer software controls

8.1

Fluorescence measurement examples

Determine PSII efficiency

Determine Fv/Fm and quenching coefficients

An induction kinetics measurement

Additional fluorescence measurements

8.2

Optimizing flash settings

The measuring beam

The rectangular flash

The square flash correction

The multiphase flash

The induction flash

The dark pulse

8.3

The FlashAnalysis application

Importing data files

Using the FlashAnalysis application

8.4

Custom events

A quick tour

Custom event definition files

The table editor

Basic controls

Automatic rule enforcement

Custom event parameter reference

Meta commands

Fluorometer events file structure

User-defined meta extras

8.5

Maintaining the fluorometer

9

Measuring leaf-level gas exchange

Theory and equation summary

What's what

Installing the small leaf chamber

Leaf chamber software controls

9.1

Preparing for measurements

Start up checklist

Clamping onto your first leaf

9.2

Matching the IRGAs

The match screen

Acquiring range match data

Range match stability

Match information in data files

Range match information storage

Suggested range match protocol

Match failure message

9.3

The Dynamic Assimilation™ Technique

A quick introduction

Using DAT

The dynamic tests

Dynamic details

9.4

Leaf measurement examples

Survey measurement considerations

CO₂ response curves

Light response curves

Fluorescence and leaf-level gas exchange measurement

9.5

More options

Installing the large leaf chamber

Using two light sources simultaneously

Conifer sprig kit

Bryophyte chamber

Small plant chamber

Insect respiration chamber

Custom chamber adapter

Using auxiliary channels

9.6

Maintaining chambers and light sources

10

Measuring assimilation from aquatic samples

Theory and equation summary

What's what

Installing the chamber

Aquatic chamber software controls

10.1

Preparing for measurements

Measuring the response time of blank media

Light transfer and reported light intensities

Tips for success

10.2

Measurement examples

Preparing the sample

Measuring PI response using a program

Measuring PI response with a Background Program

10.3

More options

Using a pH probe

Controlling temperature with a water bath

Using auxiliary channels with the aquatic chamber

Measuring the subsample loop flow rate

10.4

Troubleshooting the aquatic chamber

10.5

Maintaining the aquatic chamber

11

Measuring soil CO2 flux

Theory and equation summary

What's what

Installing the soil chamber

Connecting external soil sensors

Soil chamber software controls

11.1

Preparing for measurements

Installing soil collars

A basic measurement protocol

Viewing results

Soil variables and constants

11.2

Troubleshooting the soil chamber

11.3

Maintaining the soil chamber

12

Using Background Programs

Nomenclature and symbols

Python

Consider using VNC

12.1

Overview of Background Programs

Work flows

A tour

Creating custom interface dialogs

12.2

Example Background Programs

Early morning FoFm

Variations on AutoLog

Monitoring match mode

Record and replay a time series

12.3

Response curve Background Programs

Basic

Multiple controls

Higher dimensions

Variable stability wait times

12.4

Background Program screen reference

The Open/New screen

The Build screen

The Set screen

The Start screen

The Monitor screen

Set screen interface tools

Debug mode

Directory information

Saving BPs

12.5

Step reference

Control dictionary map

Status dictionary map

12.6

The list_utility module

12.7

Controlling custom events from a BP

SETCONTROL command

custom_flash_lib.py