LI-COR LI-600 Instruction Manual
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LI-COR LI-600 Instruction Manual

Using the porometer/fluorometer
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Ll-600 Porometer/Fluorometer
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  • Page 1 Using the Ll-600 Porometer/Fluorometer Instruction Manual...
  • Page 2 Using the LI-600 Porometer/Fluorometer Software v3.0 LI-COR Environmental 4647 Superior Street Lincoln, Nebraska 68504 Phone: +1-402-467-3576 Toll free: 800-447-3576 (U.S. & Canada) envsales@licor.com envsupport@licor.com licor.com/env LI-COR GmbH, Germany Siemensstraße 25A 61352 Bad Homburg Germany Phone: +49 (0) 6172 17 17 771 envsales-gmbh@licor.com...
  • Page 3 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 con- nection with the furnishing, performance, or use of this material.
  • Page 4 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.
  • Page 5 CE Marking: This product is a CE-marked product. For conformity inform- ation, contact LI-COR Support at envsupport@licor.com. 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.

  • Page 6: Table Of Contents

    Taking a measurement Match mode Taking a measurement in Auto Mode Taking a measurement in Manual Mode Using the barcode scanner Viewing measurement data on-screen Section 4. Using the computer software Download the software and connect the LI-600 Connection Overview...
  • Page 7 Display Layout Preview 5-10 Save Configuration 5-11 Upload configuration to instrument 5-11 Section 6. Data files Downloading data from the LI-600 Exporting data files from the computer software Data dumps Data file structure Groups, variables and units Groups, labels and descriptions...
  • Page 8 Instrument will not seal on a leaf Instrument will not automatically log a measurement The display layout is blank Software warning when connecting the LI-600 Software warning when updating the firmware The new RH sensor serial number has not updated...
  • Page 9 Fluorescence detector 8-19 Changing the RH sensors serial number 8-19 Section 9. Theory of operation Leaf porometer Derivation of equations Boundary layer conductance Water vapor sensors Flow sensors Leaf temperature sensor PAR sensor Vapor pressure deficit Leak rate Stability criteria User calibration procedures 9-10 Fluorometer...
  • Page 10 Appendix A. FlashAnalysis App Standard Terms and Conditions Index...

  • Page 12: Section 1. The

    These measurements, along with information from the GPS receiver, enable the LI-600 software to calculate the angle of incidence of a leaf for each measurement. The LI-600 computer software is available for both Win- ®...

  • Page 13: Components

    LI-600 Porometer/Fluorometer Instruction Manual Components The LI-600 components are as shown below. Figure 1-1. LI-600 Components. Aperture. (0.75 cm diameter) Surrounds the leaf gasket, is the active measurement. Aperture clamp. Closes onto the leaf. Fluorometer (optional). Takes PAM chlorophyll a fluor- escence measurements.

  • Page 14: Parts And Accessories Kit

    Tripod mount. (1/4-20 UNC) Attaches to a tripod. Porometer. Takes stomatal conductance measurements. Parts and accessories kit The LI-600 comes with a kit that includes the following accessories and replacement parts. Additional parts and accessories can be purchased separately (see Support on the next page).

  • Page 15: Support

    1 Amp at 5 VDC. The LI-600 can be charged when powered on or off. Before using the LI-600 for the first time, charge the bat- tery to 100%. Charging with the instrument powered off and using the universal charging adapter takes approximately 3.5 hours.
  • Page 16 Powering the LI-600 on and off To power on the LI-600, press and hold the round enter button on top of the instrument. To power off the LI-600, navigate to Settings by press- ing the left arrow at the Select Configuration screen, then select Shut Down and press the Enter button.
  • Page 17 LI-600 Porometer/Fluorometer Instruction Manual interior indicate the location of the lithium ion battery compartment. Caution: Lithium ion batteries may cause environmental damage or damage to human health if they are disposed of improperly. Do not dispose of the batteries in unsorted muni- cipal waste or an incinerator.

  • Page 18: Section 2. Using The Li-600 Interface

    Section 2. Using the LI-600 interface The LI-600 user interface includes four arrow buttons, a round enter button, and the display. The up and down arrows navigate through options in the display, and the left and right arrows navigate through the screens. The Enter button powers the LI-600 on, selects highlighted options, and initiates or logs a measurement.

  • Page 19: Measurement

    Select Configuration is Home in the navigation, and from it you access Settings and Info with the arrow buttons. After a configuration is selected, the LI-600 will go into Matching. Matching may include user prompts asking whether a leaf is in the chamber. For a full description of RH sensor matching and user prompts, see Match mode on page 3-4.
  • Page 20 Manual mode. When taking a measurement with the LI-600 Porometer/Fluorometer, the heading cycles through Logging, Flashing, Complete, and Logged. When taking a measurement with the LI-600 Poro- meter, the heading cycles through Logging, Complete, and Logged. At the bottom of the screen, the prompt for the Enter button in Auto mode is New;...

  • Page 21: Data Labels And Remarks

    Figure 2-3. Inverted variables on the Measurement screen. Since the LI-600 has an open cuvette, the leak_pct vari- able will be inverted when the chamber is empty. Data labels and remarks Data labels and remarks are configured in the LI-600 computer software (see Data Labels on page 5-5 and...
  • Page 22 Section 2. Using the LI-600 interface Figure 2-4. Data labels and remarks are selected in the "Press enter to edit highlighted values" and "Mark Reason" screens. The data label options appear (Press enter to edit highlighted values) after each measurement if Prompt on log is enabled in the configuration.

  • Page 23: Matching

    Settings options include Shut Down, Match, Instru- ment Settings, and Warning(s). Navigate to Settings with the left arrow from Select Configuration. Shut Down powers off the LI-600. Match manually matches the RH sensors; it will beep when complete. Instrument Settings sets the time or clears all data.

  • Page 24: Info

    Section 2. Using the LI-600 interface syncing the time with GPS. See Clocks on page 9-20. Clear All Data: erase all of the data on the instru- ment. Back: go back to Select Configuration. Warning(s) shows instrument warnings (see Instru- ment warnings on page 7-5).

  • Page 26: Section 3. Taking Measurements

    Observe these precautions and practice these techniques before and while taking measurements with the LI-600. Precautions To protect the LI-600 when not in use, turn it off and place it in the carrying case. Before using the LI-600, take the following precautions.

  • Page 27: Techniques

    Measuring a wet leaf may result in over- estimation of stomatal conductance, and water ingress into the instrument may cause damage. This is referred to as a "Madsen Error" within LI-COR.

  • Page 28: Taking A Measurement

    Taking a measurement The workflow for taking a measurement on the LI-600 will vary depending on two settings in the active con- figuration: whether the measurements are taken in...

  • Page 29: Match Mode

    If the leak percent is lower than the leak maximum, the LI-600 will prompt the user to ask if a leaf is in the chamber. If the user answers yes, the instrument prompts the user to remove the leaf. If the user answers no, the instrument will wait 10 seconds and compute the match adjustment without the valve.

  • Page 30: Taking A Measurement In Auto Mode

    Section 3. Taking Measurements "no" and the LI-600 will perform a serial, valveless match. Do not enter match mode with a leaf in the chamber. Matching with a leaf in the chamber will ruin sub- sequent measurements. Taking a measurement in Auto Mode...

  • Page 31: Taking A Measurement In Manual Mode

    LI-600 Porometer/Fluorometer Instruction Manual arrow key (Mark). Remarks are set in the computer software when editing or creating a configuration. Press Enter to initiate a new measurement. Shutdown the instrument when you are done taking meas- urements. Press the left arrow key (Home) to go back to the Select Configuration screen, then press it again to go to Set- tings, and press Enter while Shutdown is highlighted.

  • Page 32: Using The Barcode Scanner

    At the Scan Barcode prompt, pass the red light from the bar- code scanner on the bottom of the instrument over the bar- code. When it reads the barcode the LI-600 will beep and return to the Data labels screen and display characters from the scanned barcode..

  • Page 33: Viewing Measurement Data On-Screen

    LI-600 Porometer/Fluorometer Instruction Manual Viewing measurement data on-screen Data from the most recent measurement appear on the Measurement screen after taking a measurement, and before pressing the Enter button for a new meas- urement. For information on configuring the variables shown on the Measurement screen, see Display Layout on page 5-9.

  • Page 34: Section 4. Using The Computer Software

    Install the computer software, which is downloaded at licor.- com/600software Press and hold the Enter button to power on the LI-600. Connect the LI-600 with your computer using the micro USB cable. The LI-600 will automatically connect with the com- puter software if the computer software and instrument firmware are up to date.
  • Page 35 LI-600 or safely eject a connected instrument. The software may display warning messages. See Soft- ware warning when connecting the LI-600 on page 7-3 and Software warning when updating the firmware on page 7-4. Figure 4-1. Connection overview.

  • Page 36: Home Screen

    Section 4. Using the computer software No LI-600 detected! Connect the instrument to the computer via USB, then wait for the LI-600 con- nected! prompt to appear, or select Offline Mode to proceed without a connected LI-600. Home screen When the LI-600 is connected, select Explore LI-600 to access the Home screen.

  • Page 37: Buttons

    LI-600 Porometer/Fluorometer Instruction Manual Code Generator, the drop-down menu offers access to the following: Instrument Calibration shows user calibration coef- ficients and user-adjustable parameters. Calibration para- meters can be adjusted for the relative humidity (RH) sensors, flow sensors, and a fluorescence detector if there is a fluorometer.

  • Page 38: Configuration Management

    Two configurations come preloaded onto each LI-600: Manual gsw and Auto gsw for the LI-600 Porometer, and Manual gsw+F and Auto gsw+F for the LI-600 Poro- meter/Fluorometer. They cannot be edited but can be saved as new configurations. If a downloaded con-...
  • Page 39 Local Configurations are the configurations created in the computer software. New indicates a configuration that has not been uploaded to an LI-600 since its cre- ation or most recent edit. Double-click on a column heading to sort. Configurations with the same name as another are assigned a randomly generated name to avoid a naming conflict.

  • Page 40: Data Management

    Excel files. LI-600 data Data on LI-600 lists the date of the last data download. This section indicates the instrument’s serial number and percent of data storage used.
  • Page 41 LI-600 Porometer/Fluorometer Instruction Manual Local Files Figure 4-5. Local data files. Local Files lists data and metadata stored in the com- puter software. You can sort the files by column and toggle the metadata view. Exporting files The two check boxes and icons in the upper right give you options for exporting Excel files with embedded equations and fluorometer flash files.

  • Page 42: Live View

    Delete Selected Files: Removes the selected data files from the Local Files. Live View Live View streams data from a connected LI-600 and is useful for educational settings. Live data for each selec- ted variable in graph format are displayed, allowing you to view and log data while taking measurements.

  • Page 43: Offline Mode

    LI-600 in the Data Management menu at any given time. If you navigate away from the Live View menu, sixty minutes of live data are automatically saved.
  • Page 44 Connection Overview. Figure 4-9. Offline Mode drop-down menu. When an LI-600 or LI-600N is not connected to the soft- ware, you can create and edit configurations locally, manage data that's been downloaded from the instru- ment, manage preferences, and create barcodes.

  • Page 45: Barcode Generator

    Barcode generator The LI-600 computer software can generate custom bar- codes for use with the LI-600 barcode scanner. From the home screen of the LI-600 computer software, select Bar Code Generator. Barcode generator screen The barcode generator screen includes options for bar- code format, importing and pasting text, and the bar- codes text area.
  • Page 46 Section 4. Using the computer software PASTE FROM CLIPBOARD: Paste delimited text that has been copied onto your computer's clipboard. IMPORT FROM FILE: Select a delimited text file from your computer and import it to the Barcodes Text field. CLEAR TEXT: Clear the contents of the Barcodes Text field.

  • Page 47: Print Preview Screen

    10 per page. Print: Print or save as a PDF. Done: Go back to the barcode generator screen. When used with the LI-600 barcode scanner, the bar- code text for each measurement appears in the USERDEF group in LI-600 data files.

  • Page 48: Section 5. Configurations

    Configurations are uploaded to the instrument from the computer software (see Using the com- puter software on page 4-1). Figure 5-1. Default configurations on the LI-600. Configuration settings Configurations include settings for auto or manual mode, porometer and fluorometer options, measurement settings, data labels, remarks, and the instrument display layout.

  • Page 49: Data Labels

    Once two consecutive data points are below the set threshold, the meas- urement is considered stable, and the LI-600 logs the data point. This is based on monitoring changes over time (in seconds) to both the computed stomatal con- ductance (gsw) and/or the de-modulated fluorescence sig- nal (F).

  • Page 50: Measurement Settings

    See Taking a measurement on page 3-3. Measurement Settings Measurement Settings control the following aspects of measurements taken with the LI-600. If the fluoro- meter option is not available, the fluorometer meas- urement settings are not be included in the configuration.
  • Page 51 In General, add a Configuration Name and an Author. For the LI-600 with a fluorometer, check Use Fluorometer; fluorometer options are hidden if unchecked. For the LI-600 with leaf angle and GPS cap- ability, check Use GPS and Leaf Angle.
  • Page 52 Section 5. Configurations Data Labels Figure 5-3. The Data Labels screen. In Data Labels, you can create labels using a number, list, or barcode format. One label must be a barcode to enable the barcode scanner. Each configuration can have up to three labels. Check Prompt On Log if you want to set a data label after taking each measurement.
  • Page 53 LI-600 Porometer/Fluorometer Instruction Manual Number: Check the Auto-Increment box for automatic numbering. List: Add up to three selections with the plus button; drag and drop them to change their order. Barcode: Enable the barcode scanner. Automode Setup In Automode Setup, select Automode, gsw, and/or F (fluorometer).
  • Page 54 Section 5. Configurations Table 5-1. Automode Setup variable options. Stability Limit Slope Limit Period Preset Fast 0.005 Medium 0.001 Custom user specified user specified 1, 2, or 4 To set the instrument to Manual mode, uncheck Auto- mode. In manual mode, you set the display to view the F and g slopes and decide when to log the data by observing those variables on the instrument display (see...
  • Page 55 LI-600 Porometer/Fluorometer Instruction Manual Figure 5-6. Flow Rate and Match Frequency settings. High flow is recommended for most applications to provide the fastest measurement speed with no observed reduction in sensitivity. Match frequency determines how often the instru- ment will automatically match. Enter the interval in minutes.

  • Page 56: Display Layout

    Fluorescence Constants include Leaf Absorptance and Fraction Abs PSII. Modulation inputs the Actinic Modulation Rate. Integ- rated Modulation Intensity is automatically calculated. Display Layout In Display Layout, you can customize the layout and variables that are visible on the LI-600 Measurement screen.

  • Page 57: Preview

    LI-600 Porometer/Fluorometer Instruction Manual Figure 5-9. The Display Layout. Select a 2- or 8-panel lay- out for the Measurement screen. To change variables, click into the variable box then select a variable from the list. Select CLEAR to leave a variable box blank, Clear All to remove all variables, and Default to reset the layout.

  • Page 58: Save Configuration

    If your instrument is not connected, go to Connection Overview from the drop-down menu and connect it. Once conneted, select the Upload button under Local Configurations to add it to the LI-600. Up to four con- figurations can be loaded onto the instrument at a time. 5-11...
  • Page 59 5-12...

  • Page 60: Section 6. Data Files

    Under Data on LI-600, select Download Instrument Data then Download on the prompt. All data on the LI-600 will be downloaded to the com- puter software. Clear on the confirmation prompt to clear all data from the instrument or Cancel. Clearing removes all data from the LI-600, not from the computer software.

  • Page 61: Exporting Data Files From The Computer Software

    LI-600 Porometer/Fluorometer Instruction Manual Exporting data files from the computer software To export data files from the computer software to your computer file system, select files to download under Local Files. Check the box next to Flash Files to save the fluorometer files with the data file.

  • Page 62: Data Dumps

    The fluorometer, leaf angle, and GPS groups will be absent from the data files of previous LI-600 models without those features. Groups, variables and units To view a variable's unit of measure or format, see the...

  • Page 63: Groups, Labels And Descriptions

    LI-600 Porometer/Fluorometer Instruction Manual sheet application. The example below shows inform- ation in the fluorometer configuration group. Figure 6-1. Variables and units in the fluorometer con- figuration group. Groups, labels and descriptions Following is a list of groups and labels in each data file, and the description for each label.
  • Page 64 O mole fraction H2O_s Chamber H O mole fraction H2O_leaf Leaf H O mole fraction leaf_area Leaf area in cm leaf_width Leaf width in mm Fluorometry The Fluorometry Group contains the data collected from the LI-600 Fluorometer. FLUORO flashID Flash file ID...
  • Page 65 LI-600 Porometer/Fluorometer Instruction Manual FLUORO Minimum fluorescence in dark Maximum fluorescence in dark Fv/Fm Quantum efficiency in dark Minimum fluorescence in light Maximum fluorescence in light PhiPS2 Quantum efficiency in light PS2/1 Ratio of PSII to PSII absorptance Leaf light absorptance...
  • Page 66 Section 6. Data files will not be included in data files from instruments without an accelerometer/magnetometer. LEAF_ANGLE pitch Slope from horizontal roll Rotation from horizontal heading Rotation from North angle_inc_ Angle of incidence between the leaf and the leaf direct_pct Proportion of direct irradiance incident on leaf slope_leaf Leaf inclination from horizontal...
  • Page 67 LI-600 Porometer/Fluorometer Instruction Manual Measurement Settings on page 5-7, and Taking a meas- urement on page 3-3 MATCH match_time Match time match_date Match date rh_adj Relative humidity sensor correction type Valved (0) or serial (1) match Stability The Stability group records the measurement stability of stomatal conductance(gsw), slope, and fluorescence (flr) at 1, 2, and 4 seconds.
  • Page 68 Section 6. Data files P_CONFIG Boundary layer coefficient e chamber Standard (0) or Needle (1) Fluorometer configuration See Measurement Settings on page 5-3. FL_CONFIG dark Dark adapted or not flash_type Flash type flash_intensity Flash intensity modrate Modulation rate flr_limit Flr slope limit flr_period Flr period P1_dur...
  • Page 69 The metadata for each measurement includes instru- ment and sensor serial numbers, embedded firmware version, and when the configuration was last updated. Metadata for each data file can be viewed in the LI-600 computer software. See Local Files on page 4-8. META...
  • Page 70 Section 6. Data files META lcrhSerNum RH sensor serial number version Embedded version configUpdatedAt Configuration update date Flash files Flash files are fluorometer data files. If a data file con- tains fluorometer measurements, a flash file for each measurement is downloaded and included in the .zip file exported from the computer software.
  • Page 71 6-12...

  • Page 72: Section 7. Troubleshooting

    Troubleshooting This section describes how to identify possible issues with the LI-600 and any warnings that may appear on the instru- ment display. If you cannot find a solution in this section, contact your local distributor or LI-COR support (see Sup- port on page 1-4).

  • Page 73: Instrument Will Not Automatically Log A Measurement

    LI-600 Porometer/Fluorometer Instruction Manual Caution: Do not apply pressure to the aperture clamp to achieve a seal on the leaf. This can warp the aperture clamp, interfere with the instrument’s optics, and produce measurement errors. Instrument will not automatically log a...

  • Page 74: Software Warning When Connecting The

    Figure 7-2. A firmware update is available. LI-600 Firmware Is Incompatible With Software!: An LI-600 is powered on and has been discovered by the computer software via USB, but the instrument firm- ware is incompatible with the computer software. Select Install Bundled Firmware to update the firmware and proceed to the LI-600 connected! screen.

  • Page 75: Software Warning When Updating The Firmware

    Figure 7-3. Failed to identify this instrument! An LI-600 is powered on and has been discovered by the computer via USB, but it was disconnected while updat- ing the firmware. Power cycle the LI-600 by turning it off and on, then Reattempt Identification, or reinstall the firmware.

  • Page 76: The Rh Values And Sample Rh Are High

    RH (RH Ref). Instrument warnings This section describes the warnings that can appear on the LI-600 display and how to address them. Instrument warnings will appear with this symbol on the instrument display. To determine the warning type, open Instrument Set- tings by pressing the left arrow from the Select Con- figuration screen, then select Warnings.

  • Page 77: Low Battery

    Blower off The Blower Off warning appears when the blower is off. To turn the blower on, power on the LI-600 and select a configuration; the blower should automatically turn on. If the warning persists, power on the LI-600 then con- nect it to a computer via USB.

  • Page 78: Data Download Errors

    Section 7. Troubleshooting reception. GPS can be turned off to conserve battery power. Data download errors Data download error messages pop up with "Data Download Failed!" However, if a data download error occurs, the raw data file is still saved to your local com- puter.
  • Page 79 LI-600 Porometer/Fluorometer Instruction Manual configuration to the same spot on the instrument and takes more measurements. Unrecognized Row Type This error occurs when a barcode with a newline char- acter is scanned. Malformed Flash Data Reading If this error repeatedly pops up, each time referencing a different row, then the problem is likely a bad USB cable.

  • Page 80: Section 8. Maintenance

    Section 8. Maintenance This section describes typical maintenance procedures for the LI-600. For many of these procedures, support videos are available at: licor.com/env/support/LI-600/videos.html Storing the LI-600 Follow these guidelines when storing the LI-600. Power down and store it in the carrying case when not in use;...

  • Page 81: Clamp And Gasket

    LI-600 Porometer/Fluorometer Instruction Manual active use. Use a foam swab and deionized (DI) water to clean the quantum sensor and barcode window. Use the microfiber cloth to dry the surface if necessary. Clamp and gasket To clean the clamp and gasket, first remove them.

  • Page 82: Irt Sensor

    Section 8. Maintenance Figure 8-2. Removing the gasket. Use foam swabs and DI water to carefully clean the clamp window. Do not use soap on the window. If dirt remains on the leaf gasket, gently wash it in water and a mild detergent and completely dry it before rein- serting.

  • Page 83: Fluorometer

    LI-600 Porometer/Fluorometer Instruction Manual Figure 8-3. The IRT is under the center of the aperture. Use a foam swab and isopropyl alcohol (IPA) to carefully clean the sensor. Fluorometer Figure 8-4. The fluorometer LEDs and fluorescence detector. Regularly check that the fluorometer LEDs and fluor-...

  • Page 84: Internal Cleaning

    Section 8. Maintenance cloth, and isopropyl alcohol (IPA) to carefully clean the fluorometer optics. Internal Cleaning Internal maintenance procedures require removal of the instrument head shells. Removing the instrument head shells Work indoors in a clean environment when removing the instrument shells. Using a Phillips screwdriver, remove the seven screws on the left side of the instrument head.

  • Page 85: Cleaning The Rh Sensors

    LI-600 Porometer/Fluorometer Instruction Manual Figure 8-6. Remove the shell on the right side. Clean the vents on the shells. Check that the four vents on the instrument head shells are clean. With the shells removed, use compressed air to carefully clean the vents and other enclosure parts.

  • Page 86: Removing And Inserting A Battery

    Section 8. Maintenance Figure 8-7. The RH sensors board. Never touch the RH sensors or H O buffer material in the instrument head, as oils on the skin and scratches can affect the instrument’s performance. Removing and inserting a battery Removing and inserting the battery is only required when the battery no longer functions and needs replace- ment.

  • Page 87: Replacing The Air Intake Filter

    Replacing the air intake filter The air intake filter serves to remove solid particles from air before it is drawn through the LI-600 porometry sys- tem. A 0.45 micron filter (part number 301-19838) is a direct replacement for the original 1.0 micron filter (part number 301-16918).

  • Page 88: Calibrating The Sensors

    Replace the filter cover and instrument head shells. Calibrating the sensors The LI-600 includes sensors whose calibration para- meters can be adjusted by the user: relative humidity (RH) sensors, flow sensors, and a fluorescence detector.

  • Page 89: Rh Sensors

    This section describes the process of setting the available parameters for each sensor. To view user calibration coefficients and change the user-adjustable parameters, connect the LI-600 to the computer software. In the drop-down menu on the Tool- bar, select Instrument Calibration. (For sensor equa- tions, see Theory of operation on page 9-1)
  • Page 90 O buffer material. Use gloves or tweezers to remove the H O buffer material, as oils on the skin and scratches can reduce its buffering efficacy. Alternatively, turn the LI-600 over a container to col- lect the H O buffer material. 8-11...
  • Page 91 To seal the leaf aperture, clamp on a plastic bag or similar material. Open Instrument Calibration. Power on the LI-600. Connect it to a computer via USB then open the computer software. Click the drop-down menu on the Toolbar then select Instru- ment Calibration.
  • Page 92 Prepare the LI-600. Power on the instrument. Open Instrument Calibration. Connect the LI-600 to a computer via USB then open the computer software. Click the drop-down menu on the Toolbar then select Instrument Calibration. Power off the pump.
  • Page 93 LI-600 Porometer/Fluorometer Instruction Manual Select RH Zero then click Begin RH Zero Cal- ibration to view the RH Ref and RH Sample. Click TURN PUMP OFF. Remove the leaf clamp. Gently but firmly pull on the leaf clamp to remove it from the instrument.
  • Page 94 Section 8. Maintenance Figure 8-14. Attach a tank of ultrapure dry air to the cal- ibration clamp. Figure 8-15. Visual representation of an attached air tank Dry the RH sensors. Deliver an airstream across the RH sensors for 30 minutes to 1 hour. Do not allow maximum airflow to exceed 0.25 LPM.
  • Page 95 Using a user-supplied airstream on page 8-13. If delivering air- flow across the sensors via the LI-600 pump only, see Using the LI-600 pump on page 8-10. If the resulting RH is <1% and trending down after several minutes, the zero does not require resetting.
  • Page 96 Section 8. Maintenance Prepare the LI-600. Power on the instrument. Open Instrument Calibration. Connect the LI-600 to a computer via USB then open the computer software. Click the drop-down menu on the Toolbar then select Instrument Calibration. Set the H O input.

  • Page 97: Flow Sensors

    Take the following steps to reset the flow sensors. No disassembly is required. Open Instrument Calibration. Connect the LI-600 to a computer via USB then open the computer software. Click the drop-down menu on the Toolbar then select Instrument Calibration.

  • Page 98: Fluorescence Detector

    Take the following steps to reset the fluorescence detector. Open Instrument Calibration. Connect the LI-600 to a computer via USB then open the computer software. Click the drop-down menu on the Toolbar then select Instrument Calibration.
  • Page 99 Take the following steps to change the RH sensors serial number. Open Factory Calibration. Connect the LI-600 to a computer via USB then open the computer software. In Explore the LI-600, select the drop-down menu on the Toolbar then select About Instrument.

  • Page 100: Section 9. Theory Of Operation

    Section 9. Theory of operation 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.

  • Page 101: Derivation Of Equations

    Leaf tem- perature is measured in the cuvette via a non-contact infrared thermometer (IRT). Derivation of equations Apparent transpiration and stomatal conductance from the LI-600 are both expressed on a per unit area basis...
  • Page 102 W are water vapor mole fractions into and out of the leaf cuvette (mol H O mol air Flow out of the cuvette (sample flow) in the LI-600 is not measured with sufficient precision to be used in the...
  • Page 103 LI-600 Porometer/Fluorometer Instruction Manual water vapor mass balance, and is accounted for by not- ing that: Substituting 9-3 into 9-4: Solving 9-5 for E gives the mass balance used on the LI-600: It is important to note here that the units in 9-6 for most variables are different than the measurement units on board the instrument.

  • Page 104: Boundary Layer Conductance

    ) using a temperature controlled water source where g is assumed to be the only limitation to 9-12 Table 9-2. Default boundary layer conductance coef- ficients for the LI-600, found in the P_CONFIG group in the data file. Symbol Label LI-600...
  • Page 105 LI-600 Porometer/Fluorometer Instruction Manual , %) through a unique polynomial fit determined at the factory: 9-13 9-14 Where a , and d are the factory calibration coefficients of the polynomial fit, T is the reference temperature measured by a thermistor embedded in the...

  • Page 106: Flow Sensors

    ). Mole fraction is then given from the ratio of the vapor pressure to atmo- spheric pressure (P, kPa): 9-23 9-24 Flow sensors Flow in the LI-600 is determined using a pair of flow sensors positioned to measure flow entering the cuvette...

  • Page 107: Leaf Temperature Sensor

    LI-600 Porometer/Fluorometer Instruction Manual (μ , μmol s ) and that exiting it (μ , μmol s ). Voltage output from each of these sensors is related to molar flow rate through a unique polynomial fit determined at the factory:...

  • Page 108: Vapor Pressure Deficit

    (g , F or both) and a stability limit, and the periods over which to calculate the change. Since the LI-600 is designed for rapid survey measurements, the time period is limited to 1, 2, or 4 seconds.

  • Page 109: User Calibration Procedures

    LI-600 Porometer/Fluorometer Instruction Manual The LI-600 retains up to 4 seconds of 2 Hz data to cal- culate stability criteria as follows: 9-33 9-34 9-35 where X is either the computed stomatal conductance , or the de-modulated fluorescence signal F if a fluoro- meter is used, and t is the time for a given meas- urement.
  • Page 110 The soft- ware will accept either unit and convert to the correct relative humidity at the sensor, with Press coming from the LI-600 pressure sensor and T coming from the LI-600 reference thermistor.

  • Page 111: Fluorometer

    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.

  • Page 112: Maximum Fluorescence And Saturating Flashes

    Section 9. Theory of operation light intensity. The use of both LEDs for providing the measuring beam and saturating flash has a few advant- ages over using a single LED for each purpose, includ- ing improved light uniformity from light reaching the leaf from multiple angles and increased peak intensity for the measuring beam, leading to 3) improved signal- to-noise ratio.

  • Page 113: Minimum And Steady-State Fluorescence

    LI-600 Porometer/Fluorometer Instruction Manual the modulation rate (f, Hz) and the width of each mod- ulated pulse: 9-40 Where τ is a cuvette specific transmission factor (1.0 for the LI-600) and Q (μmol photons m ) is the com- peak...

  • Page 114: Fluorescence Output Parameters

    The LI-600 calculates one of two fluorescence yields depending on the instrument configuration. Because the LI-600 uses ambient light as its actinic source, the instru- ment must be told by the user whether the fluorescence measurements will be light- or dark-adapted and meas- urements must be made in a light environment that matches the instrument configuration (e.g., don’t try to...

  • Page 115: Leaf Angle And Gps

    LI-600 Porometer/Fluorometer Instruction Manual Additionally, when configured for light-adapted meas- urements the LI-600 will make an estimate of linear elec- tron flow (ETR, μmol electrons m ) from Φ PSII 9-48 Where α (dimensionless) is light absorption by the leaf...

  • Page 116: Accelerometer/Magnetometer

    Section 9. Theory of operation Figure 9-2. The angle of incidence of a leaf. Accelerometer/Magnetometer The accelerometer and magnetometer measure three aspects of a leaf's angle: Pitch: slope from horizontal in degrees (accelerometer) Roll: rotation from the horizontal in degrees (accel- erometer) Heading: rotation from North in degrees (mag- netometer)

  • Page 117: Gps

    GPS/leaf angle data. Leaf angle software calculations The LI-600/LI-600N software application combines data from GPS and rotational information to compute para- meters related to solar position and leaf angle position relative to the sun.
  • Page 118 Section 9. Theory of operation 9-49 where angle_inc is the incidence angle between the leaf leaf and direct sunlight (angle_inc = 0 for leaf plane leaf perpendicular to direct sunlight). The equation above is Equation 47 from Reda & Andreas 2004. Input para- meters are calculated from either GPS location inform- ation or accelerometer/magnetometer information as follows below.

  • Page 119: Clocks

    9-51 9-52 Clocks With the addition of GPS, the LI-600/LI-600N reports two different time stamps in the data file: a date/time stamp in the SYS group, and a date/time stamp in the GPS group. The date/time stamp in the SYS group is either set manually by the user or synced to GPS (when...

  • Page 120: References

    Section 9. Theory of operation once lock is achieved before taking measurements. In a logged data set, the SYS and GPS times can be com- pared to determine the UTC offset. UTC offset is main- tained through power cycling of the instrument. References Buck, A.L.
  • Page 121 9-22...

  • Page 122: Section 10. Specifications

    Section 10. Specifications General Measurement time: Porometer: 5 to 15 seconds typically, depending on species, leaf surface characteristics, and leaf conditions Fluorometer: 1 second Operating conditions: Temperature: 0 to 50 °C Pressure: 50 to 110 kPa Humidity: 0 to 85%; non-condensing Weight: 0.68 kg (porometer only);...

  • Page 123: Porometer

    LI-600 Porometer/Fluorometer Instruction Manual Universal charging adapter: Input: 90 to 264 VAC; 50 to 60 Hz Output: 5 VDC; 1 Amp Configuration Software: Windows® and macOS® applications Data Output: Plain text files (comma or tab delimited), and Excel files with embedded equations.

  • Page 124: Fluorometer

    Section 10. Specifications mol m mol m mol m mmol m kPa; VP kPa; VP kPa; VPD cham leaf leaf mmol mol mmol mol samp leaf mmol mol Fluorometer Flash types: User configurable Rectangular and Mul- tiphase Flash™ (MPF) Measuring light peak wavelength: 625 nm Measuring light peak intensity: 0 to 10,000 µmol m Flash intensity: 0 to 7500 µmol m...
  • Page 125 10-4...
  • Page 126 Appendix A. FlashAnalysis App FlashAnalysis is an application to help optimize flash pro- tocol, and also to summarize and export data of interest. You can import downloaded and extracted flash files saved to your computer into the application, then plot and graph the flash variables for analysis (see Flash files on page 6-11.) ®...
  • Page 128 Products. Any such charges will be added to the product invoice or subsequently invoiced to the Buyer. In the event LI-COR is required to pay any such tax, duty or charge, Buyer will promptly reimburse LI-COR.
  • Page 129 LI-COR. Unless otherwise agreed in writing, such costs will be paid by the Buyer and will appear as a separate item on LI-COR invoice. LI-COR shall ship in accordance with LI-COR standard prac- tices.
  • Page 130 Products ordered by the Buyer will pass to Buyer at time of LI-COR delivery of Products to the carrier. The carrier shall be deemed Buyer’s agent, and any claims for damages in shipment must be filed with the carrier.
  • Page 131 LI-COR, (ii) has been repaired or altered by persons other than LI-COR, (iii) has not been installed, operated, repaired and maintained in accordance with the documentation or operated outside of the environmental specifications for the Product;...
  • Page 132 Buyer, to the extent permitted by the original manufacturer or licensor. 13. Limitation of Liability. IN NO EVENT SHALL LI-COR, ITS LICENSORS OR ITS SUPPLIERS BE LIABLE TO BUYER OR ANY THIRD PARTY FOR COSTS OF PROCUREMENT OF SUBSTITUTE...
  • Page 133 LI-COR. LI- COR may assign or transfer these Conditions to any successor by way of merger, acquisition or sale of all or substantially all of the assets relating to these Conditions. LI-COR or any successor may assign all or part of...
  • Page 134 19. Entire Agreement. These Conditions of Sale take precedence over Buyer’s additional or different terms and conditions, to which notice of objection is hereby given. Acceptance by Buyer is limited to LI-COR Conditions of Sale. Neither LI-COR commencement of performance nor delivery shall be deemed or construed as acceptance of Buyer’s addi-...
  • Page 135 Buyer’s fault or negligence. In the event of any such delay the date of delivery shall, at the request of LI-COR, be deferred for a period equal to the time lost by reason of the delay.
  • Page 136 Index accelerometer/magnetometer 1-2 angle of incidence 9-16, 9-16 pitch, roll, and heading 9-17 accessories kit 1-3 air intake filter 8-8 aperture 1-2, 3-3 clamp 1-2, 3-3 barcodes configuring 5-6 generator 4-12 scanner 1-3, 3-7 battery disposal 1-5 lithium ion 1-2 removing and inserting 8-7 calibration equations 9-10...
  • Page 137 LI-600 Porometer/Fluorometer Instruction Manual fluorescence detector 8-19 in software 4-4 resetting to factory 4-4 RH sensors 8-10 user 8-9 charging 1-4 battery warnings and disposal 1-5 qualcomm quick charge 1-4 universal adapter 1-5 clocks 9-20 configuration management 4-5 configurations 5-1...
  • Page 138 Index enter button 1-2 firmware update 7-3 flash 5-9 files 6-11 flow 5-3 theory of operation 9-7 fluorescence constants 5-9 fluorometer 1-2 fluorometer upgrade kit 1-3 GPS 1-1, 9-18 clock 9-20 configuring 5-4 troubleshooting 7-6 turning off 3-3 view satellites 2-6 instrument components 1-2 interface 2-1...
  • Page 139 LI-600 Porometer/Fluorometer Instruction Manual leaf angle 9-16 calculations 9-18 light-adapted 5-9 lithium ion battery 3-1, 7-6 maintenance 8-1 storing 8-1 user calibrations 8-9 match frequency 5-8 theory of operation 9-6 measurements 3-1 settings 5-7 taking 3-3 techniques 3-2 mode auto 3-5...
  • Page 140 Index quantum sensor 1-2, 3-2 remarks 5-2 adding 3-5 configuring 5-7 RH sensor changing the serial number 8-19 user-supplied airstream 8-13 RH sensors cleaning 8-6 shut down 1-5 software 4-1 configuration management 4-5, 5-4 connection overview 4-1, 4-10 data management 4-7 download and install 4-1 live view 4-9 offline mode 4-10...
  • Page 141 LI-600 Porometer/Fluorometer Instruction Manual theory of operation 9-1 fluorometer 9-12 leaf angle 9-18 porometer 9-1 tripod mount 1-3 troubleshooting 7-1 automatic logging 7-2 data downloads 7-7 display layout 7-2 instrument warnings 7-5 powering on 7-1 RH values 7-5 sealing 7-1...
  • Page 143 LI-COR GmbH, Germany Siemensstraße 25A 61352 Bad Homburg Germany Phone: +49 (0) 6172 17 17 771 envsales-gmbh@licor.com envsupport-eu@licor.com LI-COR Ltd., United Kingdom St. John’s Innovation Centre Cowley Road Cambridge CB4 0WS United Kingdom Phone: +44 (0) 1223 422102 envsales-UK@licor.com envsupport-eu@licor.com...

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