LI-COR Ll-600N Instruction Manual
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LI-COR Ll-600N Instruction Manual

Porometer/fluorometer
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Ll-600N Porometer/Fluorometer
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Summary of Contents for LI-COR Ll-600N

  • Page 1 Using the Ll-600N Porometer/Fluorometer Instruction Manual...
  • Page 2 Regional Offices LI-COR Biosciences GmbH Siemensstraße 25A 61352 Bad Homburg Germany Phone: +49 (0) 6172 17 17 771 envsales-gmbh@licor.com LI-COR Biosciences UK Ltd. St. John’s Innovation Centre Cowley Road Cambridge CB4 0WS United Kingdom Phone: +44 (0) 1223 422102 envsales-UK@licor.com LI-COR Distributor Network: www.licor.com/envdistributors...
  • 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

    Contents Section 1. The LI-600N Components Parts and accessories kit Support Power and battery Section 2. Using the LI-600N interface Select Configuration and Matching Measurement Data labels and remarks Scan Barcode Settings Info Section 3. Taking Measurements Precautions and techniques Precautions Techniques Gaskets...
  • Page 7 Connection Overview Home screen Toolbar Drop-down menu Buttons Configuration Management Data Management Live View Offline Mode 4-10 Barcode generator 4-12 Barcode generator screen 4-12 Print preview screen 4-14 Section 5. Configurations Configuration settings Creating custom configurations General Data labels Stability Criteria Remarks Measurement Settings Display Layout...
  • Page 8 Section 7. Troubleshooting Instrument issues Instrument will not power on Instrument will not seal on a leaf or needle The display layout is blank Software warning when connecting the LI-600N Software warning when updating the firmware The new RH sensor serial number has not updated The RH values and sample RH are high Instrument warnings Matching.
  • Page 9 Changing the RH sensors serial number 8-20 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 9-12...
  • Page 10 Appendix A. FlashAnalysis App Standard Terms and Conditions Index...

  • Page 12: Section 1. The Li-600N

    Section 1. The LI-600N The LI-600N Porometer/Fluorometer is a lightweight hand- held instrument that takes combined stomatal con- ductance and Pulse Amplitude Modulation (PAM) chlorophyll a fluorescence measurements of a needle or leaf in seconds. It delivers precise, high-throughput stress evaluations over the same needle or leaf area and can quickly survey many conifer needles, narrow leaves, and grass blades under ambient conditions.

  • Page 13: Components

    LI-600N Porometer/Fluorometer Instruction Manual Components The LI-600N components are as shown below. Figure 1-1. LI-600N Components. Chamber. Surrounds the needle/leaf gasket, the site of the active measurement. Clamp. Closes onto the needle/leaf. Fluorometer. Takes PAM chlorophyll a fluorescence meas- urements. Quantum sensor. Measures ambient light level. Accelerometer / Magnetometer (internal).

  • Page 14: Parts And Accessories Kit

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

  • Page 15: Support

    FAQs, and other resources are avail- able online at licor.com/600Nsupport. This manual can be downloaded as a PDF. To contact LI-COR environmental support, go to https://www.licor.com/env/contact/ Power and battery The LI-600N is powered by a rechargeable lithium ion battery.
  • Page 16 The LI-600N 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. The exclamation point label on the exterior and a warning label on the interior indicate the location of the lithium ion battery...
  • Page 17 LI-600N Porometer/Fluorometer Instruction Manual 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. Many localities have battery recycling facilities that accept lith- ium ion batteries.

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

    Section 2. Using the LI-600N interface The LI-600N 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-600N on, selects highlighted options, and initiates or logs a measurement.

  • Page 19: Measurement

    LI-600N Porometer/Fluorometer Instruction Manual Figure 2-1. The Select Configuration (left) and Matching screens. Select Configuration is the Home screen in the nav- igation, and from it you access Settings and Info with the arrow buttons. After a configuration is selected, the LI-600N will go into Matching.
  • Page 20 Section 2. Using the LI-600N interface includes the variables and layout set in the con- figuration (see Display Layout on page 5-7). The bottom includes navigation to labels and remarks, and indicates whether to initiate a New measurement, or to Log it with the Enter button.

  • Page 21: Data Labels And Remarks

    LI-600N Porometer/Fluorometer Instruction Manual Figure 2-3. Inverted variables on the Measurement screen. Depending on which size gasket is in the clamp, the leak_pct variable may or may not be inverted when the chamber is empty. Data labels and remarks Data labels and remarks are configured in the LI-600N computer software (see Configurations on page 5-1 and Remarks on page 5-5) and correspond to Prompt and Mark on the instrument.
  • Page 22 Section 2. Using the LI-600N 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: Scan Barcode

    LI-600N Porometer/Fluorometer Instruction Manual Scan Barcode Scan Barcode prompts you to scan a barcode when a barcode data label is selected and the onboard barcode scanner on the bottom of the instrument is activated. See Using the barcode scanner on page 3-9 and Con- figurations on page 5-1.

  • Page 24: Info

    Section 2. Using the LI-600N interface Info From Select Configuration, navigate to Info with the right arrow button. The information lists porometer and fluorometer settings for the active configuration.

  • Page 26: Section 3. Taking Measurements

    Section 3. Taking Measurements This section describes precautions, techniques, and pro- cedures for taking measurements with the LI-600N. Precautions and techniques Observe these precautions and practice these techniques before and while taking measurements with the LI-600N. Precautions To protect the LI-600N when not in use, turn it off and place it in the carrying case.

  • Page 27: Techniques

    Maintain unblocked vents on the instrument. Do not cover any of the vents on the instrument when taking measurements. This is referred to as a "Madsen Error" within LI-COR.

  • Page 28: Gaskets

    Section 3. Taking Measurements Turn GPS off when not in use. GPS uses more power when it is searching for satellites. If you're indoors or in an area with poor satellite fix, turn off GPS to save battery power. GPS can be turned off on the instrument by going to Settings (left arrow from Select Configuration), or can be turned off in a con- figuration by leaving "Use GPS and Leaf Angle"...
  • Page 29 LI-600N Porometer/Fluorometer Instruction Manual The diameter or thickness of the needle or leaf to be measured determines which clamp gaskets to use. The 0 gasket is for needles or leaves of up to 2.6 mm in dia- meter/thickness, and the 1 and 2 gaskets are for needles or leaves of up to 2.8 mm in diameter/thickness.

  • Page 30: Aperture Gasket

    Section 3. Taking Measurements Changing clamp gaskets Remove the installed gaskets from the clamp. The mater- ial is pliable, and you can pull one side out of its notch and lift the gasket out. Store them in the ziplock bag. Tip: Bring your patience;...
  • Page 31 LI-600N Porometer/Fluorometer Instruction Manual Figure 3-5. The aperture gasket on the instrument. To remove the aperture gasket from the instrument, gently pull on one of the outside ends to slightly stretch the gasket over the edge of the aperture, then lift it off. To install the new gasket, place one end of the gasket over an outer edge of the aperture, and stretch slightly to pull the other end over the other edge.

  • Page 32: Taking A Measurement

    Section 3. Taking Measurements Figure 3-7. A cross-section view of the aperture gasket fitted onto the aperture. For information on cleaning the gaskets, see External Cleaning on page 8-1. Taking a measurement The workflow for taking a measurement on the LI-600N will vary depending on two settings in the active con- figuration: whether Prompt to edit during meas- urements is enabled for leaf area or width, and...

  • Page 33: Measurement Workflow

    LI-600N Porometer/Fluorometer Instruction Manual 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 waits 10 seconds and computes the match adjustment without the valve.

  • Page 34: Using The Barcode Scanner

    Section 3. Taking Measurements scan a barcode. Select Done and press Enter to return to the Measurement screen. Add remark (optional). Press the right arrow (Mark) to add a remark. Select the remark and press the Enter button. You will go back to the Measurement screen. Press Enter (New) to initiate a new measurement.

  • Page 35: Viewing Measurement Data

    LI-600N Porometer/Fluorometer Instruction Manual 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 36: Section 4. Using The Computer Software

    Section 4. Using the computer software The LI-600N computer software is the interface for man- aging configurations and data, performing user cal- ibrations, and for generating custom barcodes. The software can be used with or without an LI-600N con- nected. Download the software and connect the LI-600N Take the following steps to download the software and...
  • Page 37 LI-600N Porometer/Fluorometer Instruction Manual here, you can proceed with or without a connected LI-600N or safely eject a connected instrument. The software may display warning messages. See Soft- ware warning when connecting the LI-600N on page 7-2 and Software warning when updating the firmware on page 7-3.

  • Page 38: Home Screen

    Section 4. Using the computer software No LI-600N detected! Connect the instrument to the computer via USB, then wait for the LI-600N con- nected! prompt to appear, or select Offline Mode to proceed. Home screen When the LI-600N is connected, select Explore LI-600N to access the Home screen.

  • Page 39: Buttons

    RH, and Miscellaneous values can be edited. Perform a factory reset, download a calibrations file from the LI-COR website, or perform a manual reset using a downloaded file. Select RH in the left menu to change the RH sensor serial number and to calibrate.

  • Page 40: Configuration Management

    Section 4. Using the computer software Table 4-1. Toolbar buttons. (...continued) View Help: Goes to the LI-COR support website. Battery Level: Displays the percent battery charge of the connected instrument. Configuration Management When an LI-600N is connected, the Configuration Man-...
  • Page 41 LI-600N Porometer/Fluorometer Instruction Manual LI-COR Default cannot be used for any other con- figurations. Table 4-2. Buttons to download and remove con- figurations from the instrument. Download To Computer: Downloads the configuration to Local Configurations. Select Download on the con- firmation prompt to finish.

  • Page 42: Data Management

    Section 4. Using the computer software Table 4-3. Configuration management buttons. (...- continued) Export To File: Exports the configuration as a PSAC file. Delete Configuration: Removes the configuration from the Local Configurations list. Data Management From Data Management, you download data from a connected instrument to the software, and export it to your computer as text and Excel files.
  • Page 43 LI-600N Porometer/Fluorometer Instruction Manual Local Files Figure 4-4. 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 44: Live View

    Section 4. Using the computer software Table 4-5. Data file buttons. Export Selected Files: Downloads the selected data files to the computer’s local file system. Toggle Selected Metadata: Shows or hides selected metadata for the selected file. Delete Selected Files: Removes the selected data files from the Local Files.

  • Page 45: Offline Mode

    LI-600N Porometer/Fluorometer Instruction Manual boxes; not all boxes need to be filled. Select CLEAR ALL to remove all variables and reset the graph boxes. If the screen does not adequately display units, select the graph titles to toggle between chart title and units. Table 4-6.
  • Page 46 Section 4. Using the computer software When you launch the software without an instrument connected, you go to the Connection Overview screen, where you choose the instrument you're working with. Figure 4-7. The Connection Overview screen in offline mode. After you select an instrument, you're taken to the Off- line Mode Home screen.

  • Page 47: Barcode Generator

    LI-600N Porometer/Fluorometer Instruction Manual 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. The functionality of these features is the same as when an instrument is connected, with the exceptions of not being able to upload configurations, download data, or view live measurements.
  • Page 48 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 49: Print Preview Screen

    LI-600N Porometer/Fluorometer Instruction Manual Print preview screen The Print Preview screen displays barcodes as they will appear on a page, with options for paper size and page template. Figure 4-11. The Print Preview screen. Paper Size: U.S. Letter (8.5 x 11") or A4 (8.25 x 11.75") Page Template: Blank page: plain paper;...

  • Page 50: Section 5. Configurations

    Section 5. Configurations The LI-600N Porometer/Fluorometer comes with two default configurations preloaded: gsw+F and gsw+F+- prompt. Configurations are uploaded to the instrument from the computer software (see Using the computer soft- ware on page 4-1). Figure 5-1. Default configurations on the LI-600N. Configuration settings Configurations include settings for porometer and fluoro- meter options, measurement settings, data labels, remarks,...
  • Page 51 LI-600N Porometer/Fluorometer Instruction Manual at least one label must be a barcode to enable the bar- code scanner on the instrument. Remarks Remarks are optional comments that can be added to each measurement. You can create up to three remarks; one of those remarks can be applied to each meas- urement.

  • Page 52: Creating Custom Configurations

    Section 5. Configurations Display Layout Display Layout determines the layout of the instru- ment display. The options include a 2- or 8-panel layout that displays selected variables after a measurement is taken. Creating custom configurations Custom configurations can be created in the LI-600N computer software with or without an LI-600N con- nected.

  • Page 53: Data Labels

    LI-600N Porometer/Fluorometer Instruction Manual Data labels Figure 5-3. The Data Labels screen. This configuration would enable the barcode scanner and have a list of three labels to choose from. 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.

  • Page 54: Stability Criteria

    Section 5. Configurations Select New Data Label. Add a Data Label Name, then select Number, List, or Barcode. 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.

  • Page 55: Measurement Settings

    LI-600N Porometer/Fluorometer Instruction Manual analysis. Select Add Remark and add text. You can cre- ate up to three remarks to choose from (e.g. "Poor clamp"). Figure 5-5. Remarks screen. Measurement Settings In Measurement Settings, you can select values for Flow Rate, Leaf Area or Leaf Width, and Match Fre- quency for the porometer, and Flash, Fluorescence Con- stants, and Modulation values for the fluorometer.

  • Page 56: Display Layout

    Section 5. Configurations multiphase (light-adapted measurements), and sets flash intensity and flash length. If the Dark Adapted box is checked or the Rect- angular or Multiphase Flash options are selected, val- ues in Flash and Modulation automatically set to default. Fluorescence Constants include Leaf Absorptance and Fraction Abs PSII.

  • Page 57: Preview

    LI-600N Porometer/Fluorometer Instruction Manual All variables are recorded in the data files; this setting only indicates the variables seen in the display. Preview In Preview, you can view a simulation of the Meas- urement and Data labels screens. Figure 5-7. Display preview. Figure 5-8.

  • Page 58: Upload Configuration To Instrument

    Section 5. Configurations Upload configuration to instrument 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.
  • Page 59 5-10...

  • Page 60: Section 6. Data Files

    Section 6. Data files Getting data from the LI-600N onto your computer for use in a spreadsheet application is done in two steps: download the data from the instrument to the soft- ware, then export it from the software to your computer. Downloading data from the LI-600N To download data from the LI-600N to the computer soft- ware, launch the LI-600N software and connect the instru-...

  • Page 61: Exporting Data Files From The Computer Software

    LI-600N 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. To export Excel files with embedded equations, check the box next to Excel Files.

  • Page 62: Data Dumps

    Section 6. Data files the files are in directories organized by configuration and date. Data dumps Data dump files are data that have been unsuccessfully imported to the software. These are useful in the event of download errors. They are stored in the following loc- ations: Windows OS C:/Users/Username/AppData/Roaming/licor-li600/data_...

  • Page 63: Groups, Labels And Descriptions

    LI-600N Porometer/Fluorometer Instruction Manual 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. See Flash files on page 6-11 for information on flash files.
  • Page 64 Section 6. Data files urements. At least one label must be formatted as a bar- code to enable the barcode scanner. USERDEF remark Mark reason -alphanumeric barcode Label 1 barcode, list, or number Label 2 barcode, list, or number Label 3 barcode, list, or number Porometry The Porometry Group contains the data collected from the LI-600N porometer.
  • Page 65 LI-600N Porometer/Fluorometer Instruction Manual FLUORO 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 Electron transport rate TRANS Transmission factor Sensor The Sensor group contains the values recorded by the relative humidity, temperature, flow, pressure, and PAR sensors as well as the battery voltage.
  • Page 66 Section 6. Data files 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 az_leaf Leaf rotation from south Angular position of sun with respect to...
  • Page 67 LI-600N Porometer/Fluorometer Instruction Manual 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(g ), and slope and fluorescence (flr) at 1, 2, and 4 seconds. See Taking a measurement on page 3-7, step 6.
  • Page 68 Section 6. Data files Fluorometer configuration See Measurement Settings on page 5-2. 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 MPF phase 1 duration P2_dur MPF phase 2 duration P3_dur MPF phase 3 duration P1_Fmax...
  • Page 69 LI-600N Porometer/Fluorometer Instruction Manual SENSOR_V De-modulated fluorescence (fluoro) i_LED LED current (optional) (fluoro) User calibrations See Calibrating the sensors on page 8-11 and Drop-down menu on page 4-3. USERCAL b_rhr Ref RH sensor zero intercept (poro) m_rhr Ref RH sensor slope (poro) span_rhr Ref RH sensor span (poro) b_rhs Sam RH sensor zero intercept (poro)
  • Page 70 Section 6. Data files 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. See Meas- urement Settings on page 5-2.
  • Page 71 6-12...

  • Page 72: Section 7. Troubleshooting

    This section describes how to identify possible issues with the LI-600N and any warnings that may appear on the instrument display. If you cannot find a solution in this section, contact your local distributor or LI-COR support (see Support on page 1-4). Instrument issues This section describes the potential issues with the LI-600N and how to address them.

  • Page 73: The Display Layout Is Blank

    LI-600N Porometer/Fluorometer Instruction Manual The display layout is blank A blank layout will appear on the display if no variables have been selected for the configuration. A meas- urement can still be taken if the display layout is blank. Select variables for the layout in configuration man- agement in the software (see Display Layout on page 5-7).

  • Page 74: Software Warning When Updating The Firmware

    Section 7. Troubleshooting 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-600N connected! screen. Select Offline Mode to access the Configuration Management, Data Management, and Connection Overview menus without updating the firmware.

  • Page 75: The Rh Values And Sample Rh Are High

    LI-600N Porometer/Fluorometer Instruction Manual The RH values and sample RH are high If the RH values on the display are 95% or above, water may have entered the cuvette (see External Cleaning on page 8-1). If the sample RH (RH Sample) value on the display is 95% or above, clamp onto a stable object, such as a piece of printer paper, and flush the instrument’s system until the sample RH value drops to match the...

  • Page 76: Low Battery

    Section 7. Troubleshooting Low battery The Low Battery warning appears when there is less than 10% of battery charge remaining. Stop using the instrument and charge the battery. Blower off The Blower Off warning appears when the blower is off. To turn the blower on, power on the LI-600N and select a configuration;...

  • Page 77: Data Download Errors

    LI-600N Porometer/Fluorometer Instruction Manual away from buildings and wait to see if GPS can get a satellite lock. If you are working inside, you may not have the necessary reception. GPS can be turned off to conserve battery power. Data download errors Data download error messages pop up with "Data Download Failed!"...
  • Page 78 Section 7. Troubleshooting disables the fluorometer option, and uploads the updated configuration to the same spot on the instru- ment 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...

  • Page 80: Section 8. Maintenance

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

  • Page 81: Barcode Window And Quantum Sensor

    LI-600N Porometer/Fluorometer Instruction Manual Barcode window and quantum sensor Regularly check that the barcode window and quantum sensor are clean, as dirt and debris may accumulate after 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.
  • Page 82 Section 8. Maintenance Figure 8-2. The aperture gasket. Remove the clamp gaskets. The material is pliable, and you can push one side out of its notch and lift out the gasket. Figure 8-3. The clamp gaskets. Do not clean the gaskets while they are on the instru- ment as water can damage the parts.

  • Page 83: Fluorometer

    LI-600N Porometer/Fluorometer Instruction Manual Avoid water entering the cuvette. Water can damage the chamber and the flow path. If water enters the cuvette, disassemble the instrument and remove the water using a foam swab. Fluorometer Figure 8-4. The fluorometer LEDs and fluorescence detector. Regularly check that the fluorometer LEDs and fluor- escence detector are clean.

  • Page 84: Removing The Instrument Shells

    Section 8. Maintenance Removing the instrument 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. Figure 8-5. Remove the shell on the left side. Remove the five screws on the right of the instrument.

  • Page 85: Irt Sensor

    LI-600N Porometer/Fluorometer Instruction Manual 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. To put the instrument head shells back on the instru- ment, reverse the removal steps.

  • Page 86: Rh Sensors

    Section 8. Maintenance Lift out the chamber insert. You don't need to remove the o- rings around and next to the IRT sensor. Figure 8-8. The IRT sensor. Use a foam swab and isopropyl alcohol (IPA) to carefully clean the IRT sensor. Do not touch the sensor, and skin oils and scratches can damage it.

  • Page 87: Removing And Inserting A Battery

    LI-600N Porometer/Fluorometer Instruction Manual Use a squeeze bottle with deionized (DI) water to carefully rinse the RH sensors. Do not touch the active side of the sensors with your fingers or a swab. Do not use IPA. Dry them with compressed air, then bake them for 6 hours at 100 to 120 °C.
  • Page 88 Section 8. Maintenance On the right side of the instrument head, locate the cable clip. Push down on the clip and disconnect the battery connector. Remove the coverings on the instrument handle. Remove the six screws nearest the USB port on the handle using a Phillips screwdriver;...

  • Page 89: Replacing The Air Intake Filter

    LI-600N Porometer/Fluorometer Instruction Manual Replacing the air intake filter A 0.45 micron filter (part number 301-19838) serves to remove solid particles from air before it is drawn through the LI-600N porometry system. Follow these steps to replace the air intake filter. Remove the shells.

  • Page 90: Calibrating The Sensors

    Section 8. Maintenance scratches can damage the filter. Replace the filter cover and instrument head shells. Calibrating the sensors The LI-600N includes sensors whose calibration para- meters can be adjusted by the user: relative humidity (RH) sensors, flow sensors, and a fluorescence detector. This section describes the process of setting the available parameters for each sensor.
  • Page 91 LI-600N Porometer/Fluorometer Instruction Manual The H O buffer material is in the flow path and must be removed to zero the RH sensors. Remove the filter cover and filter using gloves or tweezers. Figure 8-12. Filter part number 301-19838 is a direct replace- ment for the original filter (part number 301-16918).
  • Page 92 Section 8. Maintenance Figure 8-13. The buffer material. Reinstall the filter cover, filter, pump cover, and pump. Reinstall the parts with the H O buffer material removed. Connect the zero kit. Attach the zero kit to the air inlet next to the tripod mount via the 10-32 fitting.
  • Page 93 LI-600N Porometer/Fluorometer Instruction Manual Power on the internal pump. Select RH Zero then click Begin RH Zero Cal- ibration to view the RH Ref and RH Sample. Click TURN PUMP ON. Dry the RH sensors. Wait for RH to stabilize at ±1% then select Zero in the computer software.
  • Page 94 Section 8. Maintenance Power off the pump. 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 95 LI-600N Porometer/Fluorometer Instruction Manual Figure 8-16. Attach a tank of ultrapure dry air to the cal- ibration clamp. Figure 8-17. 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 96 Section 8. Maintenance path. This ensures that no water remains in the sys- tem. Dry the sensors using one of two methods: using user-supplied airstream or using the LI-600N pump. If drying the sensors by delivering an airstream across the sensors using either a tank of dry gas (recom- mended) or an alternate airstream method, see Using a user-supplied airstream on page 8-14.
  • Page 97 LI-600N Porometer/Fluorometer Instruction Manual Prepare the LI-600N. Power on the instrument. Open Instrument Calibration. Connect the LI-600N to a computer via USB then open the computer software. Click the drop-down menu on the Toolbar then select Instrument Cal- ibration. Set the H O input.

  • Page 98: Flow Sensors

    Section 8. Maintenance Gently but firmly attach the calibration clamp. The calibration clamp is equipped with a 10-32 hose barb for tube connection. Attach the dew point generator. Connect a dew point generator to the calibration clamp, ensuring that the tube connection does not prevent the clamp from sealing properly.

  • Page 99: Fluorescence Detector

    LI-600N Porometer/Fluorometer Instruction Manual Zero the flow sensors. When Flow In Zero and Flow Out Zero stabilize, click Zero for Flow In Zero then again on the con- firmation prompt to reset the zero. Click Apply on the second confirmation prompt to finish. Repeat for Flow Out Zero.
  • Page 100 Section 8. Maintenance to obtain the correct calibration information. If a new RH sensors board is installed without updating the serial number, the LI-600N will continue logging data using the old sensor serial number. Connect the LI-600N to a computer via USB then open the computer software.
  • Page 101 8-22...

  • Page 102: Section 9. Theory Of Operation

    Section 9. Theory of operation The LI-600N 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 conductance. The fluorometer uses optical techniques to probe the quantum yield of photosystem II.

  • Page 103: Derivation Of Equations

    LI-600N Porometer/Fluorometer Instruction Manual Figure 9-1. Flow path and optical arrangement of the LI-600N. Relative humidity (RH) sensors on either side of the cuvette measure the air stream before and after it inter- acts with a leaf or needle. Flow rates are measured before and after passing through the cuvette, though only the flow rate of air entering the cuvette is used in the calculation of apparent transpiration.
  • Page 104 Section 9. Theory of operation are dependent on leaf width (s ). Both leaf area and leaf width therefore must be known to make a meas- urement. Either leaf area or leaf width, not both, may be input by the user (see Measurement Settings on page 5-2), and the other is calculated: Where aw is a ratio relating leaf width to projected area for a leaf crossing the full length of the cuvette.
  • Page 105 LI-600N Porometer/Fluorometer Instruction Manual Substituting 9-3 into 9-4: Solving 9-5 for E gives the mass balance used on the LI-600N: 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. Water vapor mole fractions in the LI-600N (w ) are reported in mmol H O mol air...

  • Page 106: Boundary Layer Conductance

    Section 9. Theory of operation Calculation of stomatal conductance (g , mol m from g requires separating boundary layer conductance , mol m 9-11 Boundary layer conductance Boundary layer conductance in the LI-600N is char- acterized as a function of flow rate through the cuvette (μ...
  • Page 107 LI-600N Porometer/Fluorometer Instruction Manual 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 block adjacent to the RH sensors and y is the sensor voltage (V , volts) corrected for zero (Z ) and span...

  • Page 108: Flow Sensors

    Section 9. Theory of operation This adjustment is applied to the raw, uncorrected, sample RH measurement (rh ) to get the sample RH sraw ) reported by the instrument (see Match mode on page 3-7): 9-20 Water vapor mole fraction (w , mmol H O mol air ) in...

  • Page 109: Leaf Temperature Sensor

    LI-600N Porometer/Fluorometer Instruction Manual 9-25 9-26 Where a , and d are the factory calibration μx μx μx μx coefficients of the polynomial fit and y is the flow μx sensor voltage (V , volts) corrected for zero (Z ) and μx μx span (S...

  • Page 110: Par Sensor

    Section 9. Theory of operation PAR sensor Photosynthetically active radiation (Q , μmol photons ) is measured with a photodiode. Voltage output by the photodiode (V , volts) is related to Q using a single factory determined calibration coefficient (Q coeff and a user-settable zero adjustment (Z ) (see Fluorescence...

  • Page 111: User Calibration Procedures

    LI-600N Porometer/Fluorometer Instruction Manual selects which variables to monitor (g , F or both) and a stability limit, and the periods over which to calculate the change. Since the LI-600N is designed for rapid sur- vey measurements, the time period is limited to 1, 2, or 4 seconds.
  • Page 112 Section 9. Theory of operation chemical to scrub H O from the airstream. Ensure dry conditions prior to resetting a zero, which can take 30 minutes or more of flowing dry air across the sensors. Upon initiation, the calibration routine averages 10 seconds of data for T and V and then recalculate the...

  • Page 113: Fluorometer

    LI-600N Porometer/Fluorometer Instruction Manual are the current calibration values for the sensor. After calculating S , the new value is stored to memory. xnew Flow sensors zero Resetting the zero setpoint on a flow sensor will alter the offset parameter for a given sensor (Z in 9-27 and μx 9-28).

  • Page 114: Maximum Fluorescence And Saturating Flashes

    Section 9. Theory of operation One unique aspect of the design is that the saturating flash is not delivered as a constant output but is mod- ulated 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 advant- ages over using a single LED for each purpose, includ- ing improved light uniformity from light reaching the...

  • Page 115: Minimum And Steady-State Fluorescence

    LI-600N Porometer/Fluorometer Instruction Manual cept of a linear regression of F over 1/Q during the flash linear ramp in flash intensity. While the target Q is a user specified parameter in flash the configuration, reported values are calculated from the modulation rate (f, Hz) and the width of each mod- ulated pulse: 9-40 Where τ...

  • Page 116: Fluorescence Output Parameters

    Section 9. Theory of operation saturating flash is initiated. The light intensity during the modulation is calculated from the user specified modulation frequency analogously to the intensity dur- ing the flash (9-40). The de-modulated fluorescence signal (F, dimensionless) used to determine F and F can be subject to meas- urement biases that arise from imperfect discrimination...

  • Page 117: Leaf Angle And Gps

    LI-600N Porometer/Fluorometer Instruction Manual 9-47 Additionally, when configured for light-adapted meas- urements the LI-600N will make an estimate of linear electron flow (ETR, μmol electrons m ) from Φ PSII 9-48 Where α (dimensionless) is light absorption by the leaf under the measurement (actinic) lighting and p PSII/PSI (effectively dimensionless) is a proportioning coefficient that describe the partitioning of absorbed photons...

  • Page 118: 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 119: Gps

    LI-600N Porometer/Fluorometer Instruction Manual Figure 9-3. Pitch, roll, and heading. If GPS is enabled in the instrument settings and there are a minimum of 3 satellite signals, a GPS map pin will appear in the upper left of the device screen. To view the number of satellites available, go to Instrument Settings on the device, select GPS, then NumSats.
  • Page 120 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 121: Clocks

    LI-600N Porometer/Fluorometer Instruction Manual The following equations are similar to those from Escribano-Rocafort et al. 2014, with modifications to fit the LI-600/LI-600N framework. 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.

  • Page 122: 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 123 9-22...

  • Page 124: Section 10. Specifications

    Section 10. Specifications General Measurement time: Porometer: 5 to 15 seconds typically, depending on species, leaf or needle surface characteristics, and con- ditions Fluorometer: 1 second Operating conditions: Temperature: 0 to 50 °C Pressure: 50 to 110 kPa Humidity: 0 to 85%; non-condensing Weight: 0.73 kg Dimensions: 32.4 cm x 16.9 cm x 6.2 cm (L x W x H) Display:...

  • Page 125: Porometer

    LI-600N 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. Barcode scanner: 1-D and 2-D, including Code 39, Code 128, PDF417, 100% UPC, Data Matrix, QR Code...

  • Page 126: 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 127 10-4...
  • Page 128 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 130 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 131 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 132 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 133 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 134 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 135 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 relat- ing to these Conditions. LI-COR or any successor may assign all or part...
  • Page 136 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 137 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 138 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 8-10 aperture clamp 1-2 barcodes configuring 5-5 generator 4-12 scanner 1-3, 3-9 battery disposal 1-5 lithium ion 1-2 removing and inserting 8-8 calibration equations 9-10 flow sensors 8-19...
  • Page 139 LI-600N Porometer/Fluorometer Instruction Manual fluorescence detector 8-20 in software 4-4 resetting to factory 4-4 RH sensors 8-11 user 8-11 chamber 1-2 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 custom 5-3 measurement settings 5-2 preview 5-8...
  • Page 140 Index enter button 1-2 firmware update 7-2 flash 5-6 files 6-11 flow 5-2 theory of operation 9-7 fluorescence constants 5-7 fluorometer 1-2 gasket 3-3 clamp 3-3 cutting 3-4 sizes 3-3 GPS 1-1, 9-18 clock 9-20 configuring 5-3 troubleshooting 7-5 turning off 3-3 view satellites 2-6 instrument components 1-2...
  • Page 141 LI-600N Porometer/Fluorometer Instruction Manual IRT sensor cleaning 8-6 leaf angle 9-16 calculations 9-18 leaf width 3-7 light-adapted 5-7 lithium ion battery 3-1, 7-5 maintenance 8-1 storing 8-1 user calibrations 8-11 match frequency 5-6 theory of operation 9-6 measurements 3-1 settings 5-6 taking 3-7 techniques 3-2 modulation 5-7...
  • Page 142 Index quantum sensor 1-2, 3-2 remarks 5-2 configuring 5-5 RH sensor changing the serial number 8-20 user-supplied airstream 8-14 RH sensors cleaning 8-7 shut down 1-5 software 4-1 configuration management 4-5, 5-3 connection overview 4-1, 4-10 data management 4-7 download and install 4-1 live view 4-9 offline mode 4-10 preferences 4-4...
  • Page 143 LI-600N Porometer/Fluorometer Instruction Manual leaf angle 9-18 porometer 9-1 tripod mount 1-3 troubleshooting 7-1 data downloads 7-6 display layout 7-2 instrument warnings 7-4 powering on 7-1 RH values 7-4 sealing 7-1 cable 4-1 port 1-2 port protector 3-1 wrist strap 3-1...
  • Page 145 Regional Offices LI-COR Biosciences GmbH Siemensstraße 25A 61352 Bad Homburg Germany Phone: +49 (0) 6172 17 17 771 envsales-gmbh@licor.com LI-COR Biosciences UK Ltd. St. John’s Innovation Centre Cowley Road Cambridge CB4 0WS United Kingdom Phone: +44 (0) 1223 422102 envsales-UK@licor.com LI-COR Distributor Network: www.licor.com/envdistributors...

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