LI-COR LI-600 User manual

Using the
Ll-600 Porometer/Fluorometer
Instruction Manual

i
Using the LI-600
Porometer/Fluorometer
Instruction Manual
LI-COR Biosciences
4647 Superior Street
Lincoln, Nebraska 68504
Phone: [phone]
Toll free: 800-447-3576 (U.S. and Canada)
envsale[email protected]om
LI-COR Distributor Network:
www.licor.com/env/distributors
Regional Offices
LI-COR Biosciences GmbH
Siemensstraße 25A
61352 Bad Homburg
Germany
Phone: [phone]
envsales-gmb[email protected]om
LI-COR Biosciences UK Ltd.
St. John’s Innovation Centre
Cowley Road
Cambridge
CB4 0WS
United Kingdom
Phone: [phone]
envsale[email protected]om

Notice
The information 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 held liable for errors con-
tained herein or for incidental or consequential damages in
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Printing History
© Copyright 2020, LI-COR, Inc. All rights reserved.
Publication Number: 984-19037
Created on Wednesday, August 19, 2020
ii

iii
Notes on Safety
This LI-COR product has been designed to be safe when oper-
ated in the manner described in this manual. The safety of this
product cannot be assured if the product is used in any other
way than is specified in this manual. The product is intended
to be used by qualified personnel. Read this entire manual
before using the product.
Equipment markings:
The product is marked with this symbol
when it is necessary for you to refer to the
manual or accompanying documents in
order to protect against injury or damage
to the product.
WARNING Warnings must be followed carefully to
avoid bodily injury.
CAUTION Cautions must be observed to avoid dam-
age to your equipment.
Manual markings:
Warning Warnings must be followed carefully to
avoid bodily injury.
Caution Cautions must be observed to avoid dam-
age to your equipment.
Note Notes contain important information and
useful tips on the operation of your equip-
ment.

CE Marking:
This product is a CE-marked product. For conformity inform-
ation, contact LI-COR Support at [e-mail]. Out-
side of the U.S., contact your local sales office or distributor.
California Proposition 65 Warning
WARNING: This product contains chemicals known to the
State of California to cause cancer and birth defects or other
reproductive harm.
Federal Communications Commission
Radio Interference Statement
WARNING: This equipment generates, uses, and can radiate
radio frequency energy and if not installed in accordance with
the instruction manual, may cause interference to radio com-
munications. It has been tested and found to comply with the
limits for a Class A computing device pursuant to Subpart J of
Part 15 of FCC rules, which are designed to provide a reas-
onable protection against such interference when operated in a
commercial environment. Operation of this equipment in a res-
idential area is likely to cause interference in which case the
user, at his own expense, will be required to take whatever
measures may be required to correct the interference.
Waste Electronic and Electrical Equip-
ment (WEEE) Notice
This symbol indicates that the product is to be col-
lected separately from unsorted municipal waste. The
following applies to users in European countries: This
product is designated for separate collection at an
appropriate collection point. Do not dispose of as
household waste. For more information, contact your local dis-
tributor or the local authorities in charge of waste man-
agement.
iv

v
Contents
Section 1. Introduction
Online resources 1-1
LI-600 Computer software 1-1
Instruction manual 1-1
Components 1-2
Accessories kit 1-3
600-01F Fluorometer upgrade kit (optional) 1-3
Overview of the theory 1-4
Leaf porometer 1-4
Derivation of equations 1-5
Fluorometer 1-7
Dark-adapted vs light-adapted measurements 1-8
Section 2. Initial setup
Charging considerations 2-1
Powering on and off the LI-600 2-2
Using the universal charging adapter 2-2
Battery warnings and disposal 2-2
Section 3. Using the LI-600 menus
Navigation keys & enter button 3-1
Menu screens 3-1
Select Configuration screen 3-1
Highlighted Configuration Details screen 3-2
Clamp to Leaf screen and Press Enter to Log screen 3-2
Logged screen and Flash Complete screen 3-3
Press enter to edit highlighted values screen 3-3
Scan Barcode screen 3-4
Next Step screen 3-4
Advanced Settings screen 3-5

Section 4. Measurements
Preparing for measurements 4-1
Measurement precautions 4-1
Measurement techniques 4-2
Taking measurements 4-3
Taking a measurement 4-3
Using the barcode scanner 4-6
Viewing measurement data on the LI-600 4-7
Section 5. Configuring computer software
Connecting the LI-600 with the computer software 5-1
Connection Overview screen 5-2
Explore LI-600 5-4
Toolbar 5-4
Home Screen 5-7
Offline Mode 5-16
Toolbar 5-16
Home Screen 5-18
Section 6. Creating a new configuration
General 6-1
Data Labels 6-2
Automode Setup 6-3
Remarks 6-5
Measurement Settings 6-6
Display Layout 6-7
Preview 6-8
Section 7. Data files
Data file components 7-1
Downloading data from the LI-600 7-3
Downloading data from the computer software 7-5
vi

vii
Section 8. Troubleshooting
Potential issues 8-1
Instrument will not power on 8-1
Instrument will not seal on a leaf 8-1
Instrument will not automatically log a measurement 8-2
The display layout is blank 8-2
The computer software displays a warning message when
connecting the LI-600 8-2
The computer software displays a warning message when
updating the firmware 8-4
The new RH sensor serial number has not updated 8-4
The RH values and sample RH are high 8-5
Instrument warnings 8-5
Matching. Do not clamp on leaf. 8-5
Low memory 8-6
Low battery 8-6
Blower off 8-6
Pump 8-6
Section 9. Maintenance
Storing the LI-600 9-1
Cleaning the LI-600 9-1
Removing the instrument head shells 9-3
Removing and inserting a battery 9-4
Replacing the air intake filter 9-6
Calibrating the sensors 9-7
RH sensors 9-8
Flow sensors 9-16
Fluorescence detector 9-17
Changing the RH sensor serial number 9-17
Section 10. Theory of operation
Leaf porometer 10-1
Derivation of equations 10-2

Boundary layer conductance 10-5
Implementation of equations in the LI-600 10-5
Matching RH sensors 10-7
Flow sensors 10-7
Infrared temperature sensor 10-8
PAR sensor 10-8
Additional calculations for porometry 10-8
User calibration procedures 10-9
Fluorometer 10-11
Implementation on the LI-600 10-12
Calculating light intensity from LED calibration coef-
ficients 10-13
Dark-adapted vs light-adapted measurements 10-14
Steady-state fluorescence 10-14
Logged Variables 10-16
Porometry group 10-16
Fluorometry group 10-18
References 10-18
Section 11. Specifications
General 11-1
Porometer 11-2
Fluorometer 11-3
Appendix A. Warranty
Appendix B. Index
viii

1-1
Section 1.
Introduction
The LI-600 Porometer/Fluorometer is a lightweight and
handheld porometer and fluorometer instrument that takes
combined stomatal conductance and Pulse Amplitude Mod-
ulation (PAM) chlorophyll afluorescence measurements on
opposite sides of a leaf in seconds. It delivers precise, high-
throughput stress evaluations over the same leaf area and
quickly surveys plants under ambient conditions.
This section describes what the LI-600 is, including its com-
ponents, accessories kit, and optional fluorometer upgrade
kit.
Online resources
LI-600 Computer software
The LI-600 computer software is available for both Win-
dows® and macOS® operating systems. It is used to create
and upload configurations to the instrument, download
data from the instrument, and record live data. Computer
software is available at licor.com/600software.
Instruction manual
This instruction manual can be downloaded to your com-
puter. A PDF version is available at licor.com/600support.

LI-600 Porometer/Fluorometer Instruction Manual
1-2
Components
The LI-600 is comprised of the following major com-
ponents.
1Aperture. (0.75 cm diameter) The active measurement site
that surrounds the leaf gasket.
2Aperture clamp. Closes onto the leaf for secure meas-
urements.
3Barcode scanner. Scans barcodes to help organize
measurement data.
4Display. Shows measurement data and menus on the
screen.
5Enter button. Powers on the instrument and selects
options on the display.
6Fluorometer (optional). Takes PAM chlorophyll afluor-
escence measurements.
7Lithium ion battery. Powers the instrument,
rechargeable.
8Navigation keys. Move up, down, right, and left through
the menus.
9Porometer. Takes stomatal conductance measurements.
10 Quantum sensor. Measures ambient light level.
11 Tripod mount. (1/4-20 UNC) Attaches to a tripod for data
streaming and easy measurements.

Section 1. Introduction
1-3
12 USB port. Connects the instrument to the computer or uni-
versal charging adapter via micro-USB cable.
Accessories kit
The LI-600 includes a standard accessories kit, which has
the following accessories and replacement parts for your
instrument.
Description Quantity Part Num-
ber
Aperture clamp 2 6360-350
Face seal O-rings 2 192-17935
Filters 2 301-16918
Foam swabs 6 610-16093
Leaf gasket 2 6360-318
Microfiber cloth 1 229-16069
Radial seal O-rings 4 192-18368
Scrub tube zero kit 1 9968-258
Spare screws 20 150-14386
Universal charging adapter 1 591-19074
USBcable 1 392-19077
USB power supply prong
kit
1 591-19075
Wrist strap 1 610-19076
Zero adapter assembly 1 9960-327
Table 1-1. Accessories kit for the LI-600. Additional
accessories can be purchased separately.
600-01F Fluorometer upgrade kit (optional)
The 600-01F Fluorometer Upgrade Kit for the LI-600 adds
the fluorometer module to the porometer-only model (LI-
600P) to convert it to the porometer/fluorometer model
(LI-600PF).

LI-600 Porometer/Fluorometer Instruction Manual
1-4
The LI-600P includes a fluorometer blank. If the instru-
ment is upgraded and the fluorometer needs to be
removed, reinsert the fluorometer blank. The gray ribbon
cable does not attach to the fluorometer blank. Store the
fluorometer in the carrying case with the instrument.
Overview of the theory
Here we provide a brief summary of the operating pri-
ciples of the LI-600 porometer and fluorometer. The full
equation summary is provided in Theory of operation on
page10-1.
The LI-600 is equipped to measure two different aspects
of leaf photosynthesis. The porometer uses a mass balance
for water vapor flux from the leaf to compute stomatal con-
ductance. The fluorometer uses optical techniques to
probe the quantum yield of photosystem II. This section
describes the theory and equations behind these meas-
urements and provides an overview of other sensors in the
LI-600.
Leaf porometer
The LI-600 porometer is an open system. Stomatal con-
ductance (gsw) is computed from transpiration (E) in a leaf
cuvette and leaf temperature (Tleaf) is measured by a non-
contact infrared thermometer. Transpiration is computed
from the difference in H2O in an air-stream flowing
through a leaf cuvette (Figure 1-1 on the facing page).

Section 1. Introduction
1-5
Figure 1-1. The cuvette has relative humidity (RH) sensors
that measure the air stream before and after it interacts with
the leaf. Flow rates are measured before and after the
cuvette, and leaf temperature is measured in the cuvette.
Derivation of equations
The mass balance of water vapor in an open system at
steady-state is given by
1-1
where sis leaf area (m2), Eis transpiration (mol m-2 s-1), ui,
uo(µmol s-1) are flow rates into and out of the leaf cuvette,
respectively, Wref,Wsam are water vapor mole fractions into
and out of the leaf cuvette (mol H2O mol air-1). Since

LI-600 Porometer/Fluorometer Instruction Manual
1-6
1-2
we can substitute equation 1-2 into equation 1-1 to write
1-3
Solving equation 1-3 for Egives
1-4
Total conductance to water vapor is given by
1-5
where gtw is total conductance to water vapor (mol H2O
m-2 s-1), and Wleaf is the calculated molar concentration of
water vapor within the leaf inter-cellular air-space (mol
H2O mol air-1). Wleaf is calculated from measured leaf tem-
perature and pressure (equations 10-7 and 10-9).
Calculation of stomatal conductance (gsw) requires
removal of the contribution from the boundary layer (gbw)
1-6
where (gsw) is the one-sided stomatal conductance to water
vapor, and (gbw) is the one-sided boundary layer con-
ductance, both in (mol H2O m-2 s-1).
Boundary layer conductance in the LI-600 cuvette is a
function of the flow rate (equation 10-10).

Section 1. Introduction
1-7
Fluorometer
The LI-600 fluorometer is a Pulse-Amplitude Modulated
(PAM) fluorometer, with a measuring beam provided by
two LEDs focused on the portion of leaf in the porometer
cuvette. Fluorescence is detected via a single detector loc-
ated between the LED measuring beams, filtered by a 750
± 40 nm band-pass filter. Fluorescence is detected then
from ~700 to 780 nm, which gathers the majority of fluor-
escence from PSII, but is also contaminated with PSI flor-
escence in a similar fashion to the LI-6800 Portable
Photosynthesis System fluorometer (Genty et al., 1989,
Pfundel et al., 2013).
Actinic light is not provided by the LI-600 fluorometer
but rather by ambient light, which could be natural sun-
light or any number of artificial light sources. The two
LEDs are both modulated at a constant frequency and
provide both the measuring beam and saturating flash.
One unique aspect of the design (compared to other LI-
COR fluorometers), is that the saturating flash is not
delivered as a constant output but is modulated at high
frequencies to achieve the necessary high light intensity.
The use of both LEDs for providing the measuring beam
and saturating flash has a few advantages over using a
single LED for each purpose, including 1) improved light
uniformity from light reaching the leaf from multiple
angles and 2) increased peak intensity for the measuring
beam, leading to 3) improved signal-to-noise ratio.
The peak intensities of the measuring beam necessarily are
quite high in order to receive enough signal and are fact-
ory set to ~10,000 µmol m-2 s-1. Pulse width has been set
to 667 ns. Total integrated light intensity incident on the
leaf from the LEDs is calculated as

LI-600 Porometer/Fluorometer Instruction Manual
1-8
1-7
where Pfreq is the current pulse frequency (2 to 750,000
Hz), Pwidth is the pulse width (667 ns) and Qpeakx is the
peak intensity of the left and right LEDs, set by a factory
calibration.
The peak intensity is ~10,000 µmol m-2 s-1 and is cal-
culated from a calibration coefficient set at the factory. Fre-
quencies for steady-state measurements will be very low (4
to 8 Hz), while frequencies during the flash will be much
higher (250 to 750 kHz).
Dark-adapted vs light-adapted
measurements
Unlike previous LI-COR fluorometers, where the actinic
light is controlled by the fluorometer, here the actinic
light source is provided by external sources unknown to
the instrument. The instrument cannot know if a given
measurement being made is on a dark-adapted leaf or not.
The user must decide which type of measurement is being
made. The calculated yield uses the same equation in
either case, as shown here.
1-8
1-9

2-1
Section 2.
Initial setup
This section describes the initial setup methods for the LI-
600, including how to power it for use and safely handle its
battery.
Charging considerations
A power supply—either the universal charging adapter or an
external battery pack—can be connected to the LI-600. If
using an alternate USB wall charger, ensure that it has at least
1 Amp at 5 VDC.
The LI-600 can be charged when powered on or off. When
preparing to use the LI-600 for the first time, charge the bat-
tery to 100% capacity. Charging with the instrument
powered off and using the universal charging adapter takes
approximately 3.5 hours. Charging with the instrument
powered off and from a computer USB port takes 8 to 10
hours and is not recommended. To charge in less than two
hours, use a USB wall adapter that supports Qualcomm®
Quick Charge™ (QC) 2.0 or 3.0. When fully charged, the
instrument will operate for approximately 8 hours of active
use; however, battery life can vary due to its age and amount
of use. External battery packs are suggested for expected uses
that last longer than 8 consecutive hours.

LI-600 Porometer/Fluorometer Instruction Manual
2-2
The battery only charges when the pack temperature is
within 0 to 45° C. If the pack reaches a temperature out-
side this range, it will automatically stop charging.
Powering on and off the LI-600
To power on the LI-600, press and hold the enter button
on the instrument.
To power off the LI-600, navigate to the Advanced Set-
tings screen (see Advanced Settings screen on page3-5) and
select Power Down. If the LI-600 is not responding and
the Advanced Settings cannot be accessed, you can power
off the instrument by pressing and holding the enter but-
ton for seven seconds; this method is not recommended,
since the last data record can be lost. As preventative meas-
ures against any risks, always power off the instrument
when not in active use.
Using the universal charging adapter
The included universal charging adapter is compatible
with main power in most localities globally (input: 90 to
264 VAC, 50 to 60 Hz; output: 5 VDC, 1 Amp). You may
need to install different blades from the outlet adapter kit
to fit your wall outlets.
Battery warnings and disposal
The LI-600 includes a rechargeable lithium ion battery
(3.7 V, 5.2 AH) that must be disposed of safely. Contact
LI-COR for a replacement battery.

Section 2. Initial setup
2-3
Caution: Lithium ion batteries may cause envir-
onmental damage or damage to human health if
they are disposed of improperly. Do not dispose
of the batteries in unsorted municipal waste or
an incinerator. Many localities have battery recyc-
ling facilities that will accept lithium ion bat-
teries. For more information, contact your local
distributor or the local authorities in charge of
waste management to determine how to safely
dispose of the batteries.
The exclamation point label on the exterior and a warning
label on the interior indicate the location of the lithium
ion battery compartment.