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LI-COR LI-600, Instruction Manual

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LI-COR LI-600 Instruction Manual Download Page 118

A-1

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 6-10.)

FlashAnalysis was built on Windows

®

10 and macOS

®

Catalina 10.15.6 with Python 3.8, with limited testing on
other operating system versions. The macOS

®

version of

the app is not signed by Apple, so you have to allow the
system to open the app by going to System Preferences >
Security & Privacy > General to allow the system to open
the application.

For more information on the FlashAnalysis application,
and for links to the download, go to:

licor.com/flash-analysis

Summary of Contents for LI-600

Page 1: ...Using the Ll 600 Porometer Fluorometer Instruction Manual ...

Page 2: ...U S and Canada envsales licor com LI COR Distributor Network www licor com envdistributors 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 ...

Page 3: ... part of this doc ument may be photocopied reproduced or translated to another language without prior written consent of LI COR Inc Windows is a trademark of Microsoft Inc macOS is a trade mark of Apple Inc registered in the US and other countries Drierite is a registered trademark of the W A Hammond Drier ite Company Excelon Bev a line is a registered trademark of Thermoplastic Processes Inc All ...

Page 4: ...rkings The product is marked with this symbol when it is necessary for you to refer to the manual or accompanying doc uments 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 damage to your equipment Manual markings Warning Warnings must be followed carefully to avoid bodily inju...

Page 5: ...mits 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 ...

Page 6: ...5 Instrument Settings 2 5 Info 2 6 Section 3 Taking Measurements Measurement precautions and techniques 3 1 Precautions 3 1 Techniques 3 2 Taking a measurement 3 3 Taking a measurement in Auto Mode 3 3 Taking a measurement in Manual Mode 3 4 Using the barcode scanner 3 5 Viewing measurement data on screen 3 6 Section 4 Using the computer software Download the software and connect the LI 600 4 1 Co...

Page 7: ...Measurement Settings 5 7 Display Layout 5 9 Preview 5 10 Save Configuration 5 10 Section 6 Data files Downloading data from the LI 600 6 1 Exporting data files from the computer software 6 2 Data file structure 6 2 Variables units and equations 6 3 Groups labels and descriptions 6 3 Section 7 Troubleshooting Instrument issues 7 1 Instrument will not power on 7 1 Instrument will not seal on a leaf ...

Page 8: ...Storing the LI 600 8 1 Cleaning the LI 600 8 1 Removing the instrument head shells 8 3 Removing and inserting a battery 8 5 Replacing the air intake filter 8 6 Calibrating the sensors 8 8 RH sensors 8 8 Flow sensors 8 16 Fluorescence detector 8 17 Changing the RH sensors serial number 8 17 Section 9 Theory of operation Leaf porometer 9 1 Derivation of equations 9 2 Boundary layer conductance 9 5 I...

Page 9: ...dapted measurements 9 15 Steady state fluorescence 9 16 Logged Variables 9 17 Porometry group 9 18 Fluorometry group 9 19 Leaf angle and GPS 9 20 Accelerometer Magnetometer 9 20 GPS 9 21 Leaf angle software calculations 9 22 Clocks 9 24 References 9 25 Section 10 Specifications General 10 1 Porometer 10 2 Fluorometer 10 3 GPS Receiver 10 3 Appendix A FlashAnalysis App Appendix B Warranty Appendix ...

Page 10: ...users to track return to and map locations The LI 600 includes a magnetometer accelerometer that measures the pitch roll and heading of a leaf 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 1 The LI 600 computer software is available for both Win dows and macOS It is used to create and up...

Page 11: ...r escence measurements 4 Quantum sensor Measures ambient light level 5 Accelerometer Magnetometer internal Measures pitch roll and heading 6 Display Shows measurement workflow instrument set tings and variables data 7 Navigation arrows Moves up down right and left through options and screens 8 Enter button Powers on the instrument and selects options 9 Handle Encloses the rechargeable battery 10 M...

Page 12: ...tion Quantity Part Number Aperture clamp 2 6360 350 Face seal O rings 2 192 17935 Filters1 2 301 19838 Foam swabs 6 610 16093 Leaf gasket 2 6360 356 Microfiber cloth 1 229 16069 Radial seal O rings 4 192 18368 Scrub tube zero kit 1 9968 258 Spare screws 20 150 14386 Charging adapter 1 591 19074 Charger prong kit 1 591 19075 USB cable 1 392 19077 Wrist strap 1 610 19076 Zero adapter assembly 1 9960...

Page 13: ...https www licor com env contact Power and battery The LI 600 is powered by a rechargeable lithium ion bat tery The LI 600 is shipped partially charged Before using it the first time charge the battery to 100 fol lowing the instructions below 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 ...

Page 14: ...ring 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 If the LI 600 is not responding and the settings cannot be accessed power off the instrument by pressing and hold ing the Enter bu...

Page 15: ...e 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 Many localities have battery recycling facilities that accept lith ium ion batteries Contact your local dis tributor or the loc...

Page 16: ...powers the LI 600 on selects highlighted options and initiates or logs a measurement The LI 600 instrument display has four parts GPS map pin time and battery percentage on the top headings and prompts options or information in the main portion of the screen and navigation icons and text at the bottom Select Configuration Select Configuration appears when the LI 600 is powered on and lists the con...

Page 17: ...ration has been selected the Meas urement screen appears The screen headings include a prompt measurement status and how many meas urements have been logged The main part of the dis play includes the variables and layout set in the configuration see Display Layout on page 5 9 The bot tom includes navigation to labels and remarks and indicates whether to log or initiate a new measurement with the E...

Page 18: ...a measurement with the LI 600 Porometer 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 in manual mode it is Log then New The right arrow is either Mark or Prompt The left arrow navigates back to Select Configuration Data labels and remarks Data labels and remarks are configured in the LI 600 computer software s...

Page 19: ... on log is enabled in the configuration If Prompt on log is not enabled the options are accessed with the right arrow before taking a measurement When accessed and selected manually data labels and barcodes apply to subsequent measurements until a new label or barcode is selected Done takes you back to Meas urements See Data Labels on page 5 5 Remarks are accessed with the right arrow after loggin...

Page 20: ...sing the barcode scanner on page 3 5 and Data Labels on page 5 5 Instrument Settings Settings options include Shut Down Match Instru ment Settings and Warning s Navigate to Settings with the left arrow from Select Configuration l Shut Down powers off the LI 600 l Match manually match the RH sensors to the envir onment it will beep when complete l Instrument Settings to set the time or clear all da...

Page 21: ...n the instru ment l Back go back to Select Configuration l Warning s shows instrument warnings see Instru ment warnings on page 7 5 Info From Select Configuration navigate to Info with the right arrow button The information lists porometer and fluorometer settings for the active configuration ...

Page 22: ...carrying case Before using the LI 600 take the following precautions l Charge the battery A fully charged battery provides approximately 8 hours of active use See Charging con siderations on page 1 4 for charging time l Attach and use the wrist strap To protect the LI 600 attach the wrist strap to the instrument and adjust it to your wrist size Use the wrist strap at all times or risk being the pe...

Page 23: ... the leaf you measure is in the light ensure that the quantum sensor is also in the light If the leaf you measure is in shade ensure that the quantum sensor is also in the shade l Avoid measuring a leaf with water on it If the leaf you plan to measure has water or condensation on it gently and thoroughly dry the top and bottom of the leaf l Avoid clamping onto the veins of the leaf The uneven surf...

Page 24: ...settings in the active con figuration whether the measurements are taken in Auto mode or Manual mode and whether Prompt on log is enabled for optional data labels Taking a measurement in Auto Mode In Auto Mode the LI 600 automatically logs a meas urement when the stability criteria set in the con figuration are met To take a measurement in Auto Mode 1 Power on the LI 600 2 Select a configuration w...

Page 25: ...nt is taken you can add an optional remark to the measurement by pressing the right arrow key Mark Remarks are set in the computer software when editing or creating a configuration 6 Press Enter to start a new measurement Press the left arrow key Home to go back to the Select Configuration screen Taking a measurement in Manual Mode In Manual Mode the instrument does not search for stability or aut...

Page 26: ...ne taking measurements go back to the Select Configuration screen press the left arrow to Settings Select Shut down and press the Enter but ton to safely turn off the instrument Using the barcode scanner To enable the barcode scanner for a configuration see Data Labels on page 5 5 You will scan a barcode either before or after a meas urement is logged depending on whether Prompt on log is enabled ...

Page 27: ...code When it reads the barcode the LI 600 will beep and return to the Measurement screen The barcode scanner will time out after a few seconds If this happens go back to Data labels and repeat the pro cess 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 F...

Page 28: ...to your computer 1 Install the computer software which is downloaded at licor com 600software 2 Press and hold the Enter button to power on the LI 600 3 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 If the software and firmware are not up to date the c...

Page 29: ...erview screen you will receive one of the following prompts upon starting the com puter software LI 600 connected An LI 600 is powered on and has been discovered by the computer software l Select Explore LI 600 to access Configuration Man agement Data Management Live View Connection Overview and Barcode Generator l Select Offline Mode to access the Configuration Management Data Management Connecti...

Page 30: ...d LI 600 Home screen When the LI 600 is connected select Explore LI 600 to access the Home screen The Home screen includes a toolbar a drop down menu and tiles for accessing Con figuration Management Data Management Live View Connection Overview and Bar Code Generator Toolbar The Toolbar on the home screen includes a drop down menu in the upper left corner and three buttons in the upper right Drop...

Page 31: ...ow Factory Calibration is checked in Prefer ences Fluorometer Intensity Flow In Flow Out IRT 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 down loaded file Select RH in the left menu to change the RH sensor serial number and to calibrate Preferences select the text delimiter for data and log ...

Page 32: ... buttons Configuration Management When an LI 600 is connected the Configuration Man agement menu shows two configuration lists LI 600 Configurations those stored on the instrument and Local Configurations those stored on the local com puter LI 600 Configurations Figure 4 3 Configurations loaded onto the LI 600 LI 600 Configurations is the list of configurations loaded onto the connected LI 600 Thi...

Page 33: ...ct The author name LI COR Default cannot be used for any other configurations Download To Computer Downloads the configuration to Local Configurations Select Download on the con firmation prompt to finish Remove From Instrument Removes the configuration from the LI 600 Select Remove on the confirmation prompt to finish Table 4 2 Buttons to download and remove data from the instrument Local Configu...

Page 34: ... be re uploaded to the LI 600 Upload To Instrument Uploads a configuration to LI 600 To replace a configuration select Replace Select Upload to complete Export To File Exports the configuration as a PSAC file Delete Configuration Removes the configuration from the Local Configurations list Table 4 3 Configuration management buttons Data Management Data Management includes two data lists Data on LI...

Page 35: ...stored on the computer software You can sort the files by Config Name Config Author Date Taken Porometer Fluorometer or Downloaded At Each data file includes the Number of Observations or number of measurements taken Flash Files Con figuration Last Updated Firmware Version and RH Sensor Serial Number Export Selected Files Downloads the selected data files to the computer s local file system Toggle...

Page 36: ...layout from the top of the screen Navigate through the five variable screens by selecting one of the five squares or by using the arrows Drag and drop the desired variables into graph boxes not all boxes need to be filled Select CLEAR ALL to remove all variables and reset the graph boxes If screen does not adequately display units select the graph titles to toggle between chart title and units Edi...

Page 37: ...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 Connection Overview Connection Overview returns to the computer soft ware startup screen Offline Mode Offline Mode can be accessed with or without a con nected LI 600 It includes access to Configuration Man agement Data Management Connection Overview Bar...

Page 38: ...r 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 Figure 4 8 The barcode generator screen Barcodes Text Type paste or import delimited text into this field Each barcode is limit...

Page 39: ...he bottom portion of the window The length of the text determines the width of the barcode PRINT PREVIEW View the barcodes with text as they will appear on a printed page REMOVE ALL Clear the generated barcodes You can continue to add barcodes in either format until you re ready to print or save them as a PDF Once generated barcodes can be edited or removed indi vidually by using the icons in the ...

Page 40: ...ank page plain paper U S Letter Avery 5163 labels 10 per page A4 Avery L7992 labels 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 see Groups labels and descriptions on page 6 3 ...

Page 41: ...4 14 ...

Page 42: ...ftware see Using the computer 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 General General settings specify the name and author of the con figuration and the fluorometer option If the fluo...

Page 43: ...ity criteria When Auto Mode is enabled the LI 600 determines when to log a data point It computes stability criteria and compares it to the settings 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...

Page 44: ...cates how often a match of the RH sensors is triggered specified in minutes Flash indicates whether the measurements are light or dark adapted type of flash flash intensity and flash length in milliseconds Fluorescence Constants are Leaf Absorptance abs and Fraction Abs PSII PS2 1 Modulation modrate is the modulation rate of the LEDs used to take the fluorescence measurement The input Actinic Modu...

Page 45: ...gurations use the green plus icon to Create New Configuration You can also open a default con figuration and save it as a new one General Figure 5 2 The General configurations screen In General name your configuration First add a Con figuration Name and an Author For the LI 600 with a fluorometer check Include Fluorometer Options fluorometer options are hidden if unchecked For the LI 600 with leaf...

Page 46: ...t On Log is not checked you set data label values prior to taking a meas urement Enabling Prompt On Log is useful when meas uring a variety of leaves that require individual labeling for example when screening different genetic strains Leave Prompt On Log unchecked to add a label or bar code to a set of measurements before taking those meas urements Each label selected prior to taking a measuremen...

Page 47: ...options At least one variable must be selected to enable Auto Mode Figure 5 4 Automode Setup screen Then select the variables gsw F or both then a Preset Fast Medium or Custom If selecting Fast or Medium the Stability Limit gsw specific option Slope Limit F specific option and Period over which to cal culate the change are automatically determined If select ing Custom you can set Stability Limit S...

Page 48: ...by observing those variables on the instrument display see Display Layout on page 5 9 Remarks In Remarks you can create an optional comment e g Poor Clamp or Chlorotic Leaf that can be added to a measurement to help exclude outlier data during ana lysis Select Add Remark and add text You can create up to three remarks to choose from Figure 5 5 Remarks setup screen Measurement Settings In Measureme...

Page 49: ... in Flash and Modulation automatically set to default 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 Flash fluorometer sets the flash to light default or dark adapted and whether the flash will be rectangular ...

Page 50: ...Layout you can customize the layout and variables that are visible on the LI 600 Measurement screen Figure 5 7 Select a 2 or 8 panel layout for the Logged screen or the Flash Complete screen To change variables click into the variable box then select the desired variable from the list Not all variable boxes need to be filled Select CLEAR to leave a variable box blank Clear All to remove all variab...

Page 51: ...w Figure 5 9 Preview of data labels Save Configuration Save Configuration to save the configuration To load the configuration to the instrument go to Connection Overview from the drop down menu and connect your instrument Select the Upload button under Local Con figurations to add it to the LI 600 Up to four con figurations can be loaded onto the instrument at a time ...

Page 52: ...ware and connect the instru ment Select Data Management 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 off the instrument or Cancel Clearing removes all data from the LI 600 not from the computer software It is a good practice to clear the data fr...

Page 53: ...here the comma is used as a decimal separator Select Toggle Selected Metadata to view a data file s metadata Metadata is also recorded in the exported data file for each measurement Select Export Selected Files to save the selected data files to the computer s local file system Select Delete to delete the data from the software after exporting it This will not delete the exported files All data fi...

Page 54: ...mation in the fluorometer configuration group Figure 6 1 Variables and their equations and units in the fluorometer configuration 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 10 for information on flash files The tables are organized as follows Group label Description System The System g...

Page 55: ...ent on page 3 3 for adding them to measurements At least one label must be formatted as a barcode 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 600 porometer See Porometry group on page 9 18 PORO gsw Stoma...

Page 56: ...mum fluorescence in light Fm Maximum fluorescence in light PhiPS2 Quantum efficiency in light PS2 1 Ratio of PSII to PSII absorptance abs Leaf light absorptance ETR Electron transport rate Sensor The Sensor group contains the values recorded by the relative humidity temperature flow pressure and PAR sensors as well as the battery voltage The output in the SENSOR group is calculated from the SENSOR...

Page 57: ...r magnetometer LEAF_ANGLE pitch Slope from horizontal roll Rotation from horizontal heading Rotation from North angle_inc_ leaf Angle of incidence between the leaf and the sun direct_pct Proportion of direct irradiance incident on leaf slope_leaf Leaf inclination from horizontal az_leaf Leaf rotation from south dec_solar Angular position of sun with respect to equator az_solar Solar rotation zenit...

Page 58: ...rement on page 3 3 MATCH match_time Match time match_date Match date rh_adj Relative humidity sensor correction Stability The Stability group records the measurement stability of stomatal conductance gsw and slope and fluorescence flr at 1 2 and 4 seconds See Taking a measurement on page 3 3 step 6 and Stability criteria in auto mode on page 9 9 for the equations STABILITY gsw1sec Stomatal conduct...

Page 59: ...imit 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 Phase 1 maximum fluorescence P2_ramp Phase 2 ramp depth P2_slp Phase 2 regression slope P3_Fmax Phase 3 maximum fluorescence P3_Pred Phase 3 predicted fluorescence P3_DeltaF Phase 3 measured phase 3 pre dicted Sensor voltage The Sensor Voltage group reports the vol...

Page 60: ...8 8 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 m_rhs Sam RH sensor zero slope poro span_rhs Sam RH sensor span poro z_flowIn Flow in zero poro z_flowOut Flow out zero poro z_quantum Quantum sensor zero poro z_flr Fluor zero optional fluor Metadata The metadata...

Page 61: ... 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 3 Rectangular flash on page 9 16 and Multiphase flash on page 9 16 Flash Files flashId Flash file ID time HHMMSS date YYYYMMDD lciSerialNumber Instrument serial lcpSerialNumber Porometer serial ...

Page 62: ...ss them Instrument will not power on If the instrument will not power ensure that your battery is charged and the power supply is adequate when char ging the power supply needs to source at least 1 Amp at 5 VDC Ensure that your cable and battery are functioning prop erly see Removing and inserting a battery on page 8 5 Instrument will not seal on a leaf If the instrument will not seal on a leaf wh...

Page 63: ...Stability criteria in auto mode on page 9 9 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 Selected the desired variables for the layout in con figuration management in the software see Display Lay out on page 5 9 A blank layout will appear on the display...

Page 64: ...h Software An LI 600 is powered on and has been discovered by the com puter software via USB but the instrument firmware is incompatible with the computer software Select Install Bundled Firmware to update the firmware and pro ceed to the LI 600 connected screen Select Offline Mode to access the Configuration Management Data Management and Connection Overview menus without updating the firmware So...

Page 65: ...ial number The RH sensor serial number does not automatically update and must be updated in the computer software to obtain the correct calibration information If a new RH sensor is installed without updating the serial number the LI 600 will continue logging data using the previous RH sensor serial number Ensure that the new RH sensor serial number has been updated in the computer software see Ch...

Page 66: ...ct Warnings Matching Do not clamp on leaf Matching happens automatically when the LI 600 is powered on and when you select Match on the Instru ment Settings screen Always allow the instrument to match before clamping onto a leaf Low memory The Low Memory warning appears then there is less than 10 of data storage space remaining Stop using the instrument download the data then clear all data from t...

Page 67: ...ists replace the pump see Support on page 1 4 No GPS map pin If no GPS map pin appears in the top of the instrument display go to Settings and make sure GPS is enabled If enabled and still no map pin go to GPS settings from Instrument Settings on the device and check NumSats if 3 move to a location away from buildings and wait to see if GPS can get a satellite lock If you are working inside you ma...

Page 68: ...orometer option and re uploads the configuration to the same spot on the instrument and continues taking measurements Orphaned Flash ID Detected This error occurs when the fluorometer option is dis abled on the fly The user picks a configuration with the fluorometer enabled takes measurements then con nects the instrument to the computer The user then dis ables the fluorometer option and uploads t...

Page 69: ...7 8 ...

Page 70: ...ake when storing the LI 600 l Power down and store it in the carrying case when not in use this will keep dust insects and other con taminants out of the aperture l Store it in an air conditioned environment l Charge the battery to 60 capacity prior to long term storage l Disconnect the power supply Cleaning the LI 600 The following are basic cleaning procedures for main taining the LI 600 to ensu...

Page 71: ...or if a shift in RH zero is noted see RH sensors on page 8 8 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 Never touch the RH sensors or H2O buffer material in the instrument head as oils on the skin and scra...

Page 72: ...and any additional enclosure parts l Avoid water entering the cuvette Water can damage the cuvette and the flow path If the leaf you plan to measure has water or con densation on it gently and thoroughly dry the top and bottom of the leaf If water enters the cuvette disassemble the instrument and remove the water using a foam swab Removing the instrument head shells Internal maintenance procedures...

Page 73: ...meter Instruction Manual 8 4 Figure 8 2 Remove the shell on the left side 2 Remove the five screws on the right of the instru ment Set the shells and screws aside for safekeeping Figure 8 3 Remove the shell on the right side ...

Page 74: ...shells on page 8 3 3 Unplug the battery connector On the right side of the instrument head locate the cable clip Push down on the clip and disconnect the battery connector 4 Remove the coverings on the instrument handle Remove the six screws nearest the USB port on the handle using a Phillips screwdriver do not remove the two hex screws at the end of the handle Gently spread apart the left and rig...

Page 75: ...ace the instrument head shells After a battery replacement or any other repair verify the safe state of the instrument by checking that the dis play is and the fan are powered off 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 f...

Page 76: ...e the filter Figure 8 6 Filter part number 301 19838 is a direct replace ment for the original filter part number 301 16918 4 Install the replacement filter Insert the replacement filter from the accessories kit Always use gloves or tweezers as oils on the skin and scratches can damage the filter 5 Replace all parts in reverse order Replace the filter cover and instrument head shells ...

Page 77: ...ent Calibration For sensor equa tions see Theory of operation on page 9 1 All calibration coefficients can be viewed in Factory Calibration if enabled in the software Preferences See Drop down menu on page 4 3 RH sensors RH sensor parameters include Zero or the sensor s response to dry air and Span or the sensor s response to a known dew point or H2O mole fraction Using the LI 600 pump Take the fo...

Page 78: ...r part number 301 16918 4 Remove the pump cover and pump Remove the four screws on the pump cover then remove it Using gloves remove the pump to gain access to the H2O buffer material Handle the black plastic corners only 5 Remove the H2O buffer material Use gloves or tweezers to remove the H2O buffer material as oils on the skin and scratches can reduce its buffering efficacy Alternatively turn t...

Page 79: ...fer material removed 7 Connect the zero kit Attach the zero kit to the air inlet next to the tripod mount via the 10 32 fitting Figure 8 9 Attach the zero kit 8 Seal the leaf aperture To seal the leaf aperture clamp on a plastic bag or similar material 9 Open Instrument Calibration Power on the LI 600 Connect it to a computer via USB then open the computer software Click the ...

Page 80: ...12 Reinstall all parts in reverse order Reinstall the H2O buffer material pump pump cover filter filter cover and instrument head shells Using a user supplied airstream Follow these steps when drying the RH sensors using a user supplied airstream from an air tank Alternatively you can use a user supplied pump and the zero kit P N 9968 258 with chemicals to dry the RH sensors If using an external p...

Page 81: ...f and RH Sample Click TURN PUMP OFF 4 Remove the leaf clamp Gently but firmly pull on the leaf clamp to remove it from the instrument Figure 8 10 The leaf clamp 5 Attach the calibration clamp Gently but firmly attach the calibration clamp The calibration clamp is equipped with a 10 32 hose barb for tube connection P N 9960 327 6 Attach the air tank Connect a tank of ultrapure dry air to the calibr...

Page 82: ...airstream across the RH sensors for 30 minutes to 1 hour Do not allow maximum airflow to exceed 0 25 LPM The Flow or inlet flow sensor will read negative values i e approximately 30 to 100 µmol s 1 due to the airflow toward both the air exhaust and air inlet Flow_s will read positive values i e approximately 100 to 200 µmol s 1 RH sensor zero Follow these steps when zeroing the RH sensors ...

Page 83: ...sing the LI 600 pump on page 8 8 If the resulting RH is 1 and trending down after several minutes the zero does not require resetting 2 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 3 Power off the pump and power on the blower Select RH Zero then click Begin RH Zero Cal...

Page 84: ...nu on the Toolbar then select Instrument Calibration 3 Set the H2O input Select RH Span then click Begin RH Span Cal ibration to view the RH Ref and RH Sample Select either Dew Point or Mole Fraction then enter the desired H2O input 4 Power off the pump Select Utility then click TURN PUMP OFF 5 Remove the leaf clamp Gently but firmly pull on the leaf clamp to remove it from the instrument Figure 8...

Page 85: ...low or inlet flow sensor will read negative values i e approximately 30 to 100 µmol s 1 due to the airflow toward both the air exhaust and air inlet Flow_s will read positive values i e approximately 100 to 200 µmol s 1 Flow sensors The flow sensors response to no active flow can alter over time and can be reset Take the following steps to reset the flow sensors No disassembly is required 1 Open I...

Page 86: ... computer via USB then open the computer software Click the drop down menu on the Toolbar then select Instrument Calibration 2 Check the fluorometer response Select FLR Zero then click Begin FLR Zero Cal ibration to view FLR Zero Click Zero then ensure that the Flr Response with an empty cuvette is approximately 5 units 3 Zero the fluorescence detector If Flr response is not approximately 5 units ...

Page 87: ...eck the Factory Calibration box then click Close Select the drop down menu again to allow the software to register the change then click Factory Calibration 2 Calibrate the RH sensor Select RH under Factory Calibration then click Cal ibrate Click OK on the confirmation prompt 3 Change the RH sensor serial number The Change RH Sensor Serial Number and Auto matic RH Sensor Calibration buttons will a...

Page 88: ...heading of a leaf Those measurements along with GPS information are used by the LI 600 software to cal culate a leaf s angle of incidence This section describes the theory and equations behind these measurements 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 a...

Page 89: ...lative humidity RH sensors on the cuvette measure the air stream before and after it interacts with a leaf Flow rates are measured before and after passing through the cuvette 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 9 1 ...

Page 90: ...2 into equation 9 1 to write 9 3 Solving equation 9 3 for E gives 9 4 Total conductance to water vapor is given by 9 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 temperature and pressure equations 9 7 and 9 9 Calculation...

Page 91: ... fractions requiring additional measurements for the temperature of the sensors Tref and the atmospheric pressure Press The vapor pressures are calculated from the relative humidity measurement and a saturation vapor function from Buck 1981 9 7 where satvap T is the saturation vapor pressure kPa at the given temperature T C 9 8 where VPx is the calculated vapor pressure kPa with x is cham ref or l...

Page 92: ...tripped by the air flow across the leaf surface The conductance of the boundary layer is measured using a source of temperature controlled water vapor where total conductance boundary layer conductance 9 10 gbw flow2 6 755E 5 0 0292302 flow where flow is the cuvette flow rate in µmol s 1 Implementation of equations in the LI 600 The equations implemented in the LI 600 are shown below Sensor calcul...

Page 93: ...culations for porometry on page 9 8 We will use the terminology of RHr and RHs to indicate sensors before the cuvette ref erence and sensors after the cuvette sample Note that a match offset is applied to the RHs value equation 9 16 9 12a 9 12b where mx and bxz are factory determined coefficients and Tref is a thermistor embedded in the block adjacent to the RH sensors Converting RH sensor voltage...

Page 94: ...ccounted for by matching them 9 15 9 16 Flow sensors Converting flow sensor voltage to a flow rate µmol s 1 requires 4 factory determined coefficients and a zero and span setting for each flow sensor 9 17a 9 17b where subscript In or Out are for the flow sensors enter ing and exiting the cuvette respectively VflowX is the sensor voltage ZflowX is the user settable sensor zero nominally 0 6 SflowX ...

Page 95: ... 19 where Vleaf is the voltage from the IRT target Tref is the reference temperature and atl to gtl are factory coef ficients PAR sensor Photosynthetically active radiation µmol m 2 s 1 is com puted from a factory calibrated photodiode response 9 20 where Vpar is the voltage measured from the sensor Zquantum is a user settable offset for when no light reaches the sensor and Qcoeff is a factory cal...

Page 96: ...criteria set in the configuration are met The software provides flexibility in allowing a user to choose when a measurement is considered stable see Automode Setup on page 5 6 A measurement is con sidered stable based on monitoring changes over time to both the computed stomatal conductance gsw and the de modulated fluorescence signal F if the fluorometer is used In a given configuration a user se...

Page 97: ... limited number of data points 2 4 or 8 are used the stability criteria is not a regression slope but represents the amount of change in the parameter over the selected time period The LI 600 continuously com putes the stability criteria and compares the value to the slope limit When two consecutive data points are below the threshold then the measurement is considered stable and is logged User ca...

Page 98: ...n equations 9 13a and 9 13b for each sensor respectively A prerequisite to starting a calibration is access to a known H2O source such as a dewpoint gen erator The known quantity might be in a dewpoint tem perature or potentially in mole fraction units The software will accept either unit and convert to the cor rect relative humidity at the sensor using equations 9 7 9 21 and 9 25 with Press comin...

Page 99: ...int on a flow sensor will alter the offset parameter for a given sensor Zflowx in equa tions 9 17a and 9 17b If you select the option to zero the flow sensors the software powers down the pump and the blower before resetting the zero The calibration procedure will need the current zero parameters Zx from equations 9 17a and 9 17b and current values for the voltage reading on the flow sensor Vflowx...

Page 100: ...r 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 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 satur...

Page 101: ...on on the LI 600 TheLI 600 calculates parameters as described Calculating light intensity from LED calibration coefficients Each LED has two calibration coefficients a DAC set point DACx and a parameter relating DAC setting to light intensity Qcalx The peak intensity of each LED is calculated from these coefficients 9 41a 9 41b A given configuration provides a steady state mod ulation frequency Mo...

Page 102: ... rate during Phase 2 of an MPF PARflr is written to flash files during each log point Dark adapted vs light adapted measurements With the LI 600 fluorometer the actinic light source is provided by external sources unknown to the instru ment The instrument cannot know if a given meas urement being made is on a dark adapted leaf or not The user must decide which type of measurement is being made Tab...

Page 103: ... be re set by the user Steady state fluor escence removes the zero offset following 9 46 where vF is read from the ADC and Zflr is a factory coef ficient The measurement frequency is set in the con figuration Rectangular flash A rectangular flash delivers a user selectable flash intens ity µmol m 2 s 1 for a user selectable amount of time ms The LI 600 converts that to a frequency during the flash...

Page 104: ...ing Phase 1 l P2_slp Slope of F vs 1 Q during Phase 2 l P3_Fmax Measured Fmax during Phase 3 l P3_Pred Predicted Phase 3 F using Phase 2 regression l P3_DeltaF Difference between measured and pre dicted Phase 3 F P3_Fmax P3_Pred Additional fluorometer calculations Electron Transport Rate ETR is also calculated from all light adapted flashes from 9 47 where φPSII comes from the flash as shown above...

Page 105: ...ry layer conductance gbw mol m 2 s 1 9 10 Total con ductance gtw mol m 2 s 1 9 5 Transpiration E mol m 2 s 1 9 4 Chamber vapor pressure VPcham kPa 9 21 Leaf vapor pressure VPleaf kPa 9 23 Reference H2O mole fraction H2O_r mmol mol 1 9 25 Sample H2O mole fraction H2O_s mmol mol 1 9 26 Leaf H2O mole fraction H2O_leaf mmol mol 1 9 27 Leaf Area leaf_area cm2 NA Table 9 2 Variables logged in the porome...

Page 106: ...rk Fo NA NA Maximum Fluor escence in Dark Fm NA Section 9 Quantum Efficiency in Dark Fv Fm NA 9 44 Minimum Fluor escence in Light Fs NA NA Maximum Fluor escence in Light Fm NA NA Quantum Efficiency in light phiPSII NA 9 45 Leaf absorptance abs NA 9 47 Ratio of PSII to PSII absorptance PS2 1 NA 9 47 Electron Transport Rate ETR μmol m 2 s 1 9 47 Table 9 3 Variables logged in the fluorometry group ...

Page 107: ...af angle relative to the sun at a given time and place which is the angle of incidence 1 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 1GPS and the accelerometer magnetometer are included in models with a serial number higher than PFA 00553 ...

Page 108: ... Pitch roll and heading GPS 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 GPS information is logged into a separate variable group as follows ...

Page 109: ... compute parameters related to solar position and leaf angle position relative to the sun The angle of incidence of a surface here a leaf arbitrarily oriented with respect to the sun at a given time and place can be given by 9 48 where angle_incleaf is the incidence angle between the leaf and direct sunlight angle_incleaf 0 for leaf plane perpendicular to direct sunlight Equation 9 48 is Equa tion...

Page 110: ...e years 1950 2050 with uncertainty of 0 01 Leaf plane calculations Two parameters are needed to describe the plane of the leaf slopeleaf Inclination of a surface from the horizontal pos ition azleaf Surface azimuth angle or deviation of the normal to the surface with respect to the south The following equations are similar to those from Escribano Rocafort et al 2014 with modifications to fit the L...

Page 111: ...ident on leaf direct_pct 0 100 Leaf Inclination from horizontal slope_leaf degrees 0 90 Leaf rotation from South az_leaf degrees 180 0 south west angular position of sun wrt to equator dec_solar degrees 180 Solar rotation az_solar degrees 180 Solar zenith angle zenith_ solar degrees 0 90 Table 9 5 The leaf angle variable group Clocks With the addition of GPS the LI 600 reports two dif ferent time ...

Page 112: ... time the time reported in the SYS group will reflect the last manual update and not necessarily match the GPS clock The real time clock counting for the SYS group will drift over time typically a few seconds a month therefore it is good practice to sync with GPS once lock is achieved before taking measurements In a logged data set the SYS and GPS clocks can be compared to determine the UTC offset...

Page 113: ... yield of chlorophyll fluorescence using a single multiphase flash of sub saturating intensity Plant Cell Environ 36 1755 1770 Michalsky J J The Astronomical Almanac s Algorithm for Approximate Solar Position 1950 2050 Solar Energy Vol 40 No 3 1988 pp 227 235 USA Pfündel E E et al 2013 Deriving fluorometer specific values of relative PSI fluorescence intensity from quenching of F0 fluorescence in ...

Page 114: ...rometer only 0 73 kg with fluoro meter Dimensions 32 4 cm x 16 9 cm x 6 2 cm L x W x H Display Dimensions 6 8 cm diagonally Resolution 400 x 200 pixels sunlight readable mono chrome Keypad 5 button membrane pad Battery Built in Li ion Operating hours 8 hours typically Capacity 5200 mAh Recharging time 3 5 hours typically 2 hours with Qualcomm Quick Charge 2 0 or 3 0 Data storage 128 MB USB specifi...

Page 115: ...Matrix QR Code Photosynthetically Actively Radiation PAR meas urement Units Photosynthetic Photon Flux Density PPFD μmol m 2 s 1 Calibration accuracy 10 of reading traceable to NIST Cosine correction Cosine corrected up to 60 angle of incidence Porometer Aperture 0 75 cm diameter Flow rates Low 75 µmol s 1 Medium 100 µmol s 1 High 150 µmol s 1 RH sensor accuracy 2 RH Reference temperature 0 2 C Le...

Page 116: ...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 2 s 1 Flash intensity 0 to 7500 µmol m 2 s 1 LED Risk Group Exempt group in acc with IEC 62471 2006 The LED does not pose any photobiological hazard Parameters Fo Fm Fv Fv Fm Fs Fm ΦPSII ETR GPS Receiver GPS Accuracy 2 5 m CEP circular error p...

Page 117: ...10 4 ...

Page 118: ...analysis see Flash files on page 6 10 FlashAnalysis was built on Windows 10 and macOS Catalina 10 15 6 with Python 3 8 with limited testing on other operating system versions The macOS version of the app is not signed by Apple so you have to allow the system to open the app by going to System Preferences Security Privacy General to allow the system to open the application For more information on t...

Page 119: ...A 2 ...

Page 120: ... instrument 2 The instrument has not been maintained repaired or altered by anyone who was not approved by LI COR Inc 3 The instrument was used in the normal proper and ordinary manner and has not been abused altered misused neglected involved in an accident or damaged by act of God or other cas ualty 4 The purchaser whether it is a DISTRIBUTOR or direct customer of LI COR or a DISTRIBUTOR S custo...

Page 121: ...es of merchantability or fitness for a particular purpose The foregoing constitutes LI COR Inc s sole obligation and liability with respect to damages resulting from the use or performance of the instru ment and in no event shall LI COR Inc or its rep resentatives be liable for damages beyond the price paid for the instrument or for direct incidental or consequential damages The laws of some locat...

Page 122: ...xtended warranty the terms and conditions of LI COR s Warranty still apply DISTRIBUTOR or the DISTRIBUTOR s customers may ship the instruments directly to LI COR if they are unable to repair the instrument themselves even though the DISTRIBUTOR has been approved for making such repairs and has agreed with the customer to make such repairs as covered by this limited warranty Further information con...

Page 123: ...B 4 ...

Page 124: ... 9 20 pitch roll and heading 9 20 accessories kit 1 3 air intake filter 8 6 aperture 1 2 3 2 clamp 1 2 1 3 3 2 B barcodes configuring 5 6 generator 4 11 scanner 1 3 3 5 battery disposal 1 6 lithium ion 1 2 removing and inserting 8 5 C calibration equations 9 10 flow sensors 8 16 ...

Page 125: ...sal adapter 1 5 clocks 9 24 configuration management 4 5 configurations 5 1 auto mode 5 2 custom 5 4 measurement settings 5 3 preview 5 10 settings 5 1 D dark adapted 5 9 theory of operation 9 15 data files 6 1 downloading errors 7 6 instrument 6 1 exporting 6 2 flash files 6 10 groups labels descriptions 6 3 structure 6 2 variables units and equations 6 3 data labels 5 2 5 5 configuring 5 6 displ...

Page 126: ...6 rectangular 9 16 flow 5 3 theory of operation 9 7 fluorescence constants 5 9 fluorometer 1 2 fluorometer upgrade kit 1 3 G GPS 1 1 9 21 clock 9 24 configuring 5 4 troubleshooting 7 6 turning off 3 3 view satellites 2 5 I instrument cleaning 8 1 components 1 2 interface 2 1 instrument settings 2 5 ...

Page 127: ...1 7 5 M maintenance 8 1 cleaning 8 1 storing 8 1 user calibrations 8 8 match frequency 5 8 theory of operation 9 7 measurements 3 1 settings 5 7 taking 3 3 techniques 3 2 mode auto 3 3 setup 5 6 manual 5 2 setup 3 4 5 7 modulation 5 9 P porometer 1 3 precautions 3 1 prompt on log configuration 5 5 measurements 3 3 navigation 2 4 ...

Page 128: ...ing 8 1 flow through 9 2 user supplied airstream 8 11 S sensors cleaning 8 1 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 preferences 4 4 specifications 10 1 stability criteria 9 9 auto mode 5 2 5 2 5 6 support 1 4 ...

Page 129: ...3 leaf angle 9 22 porometer 9 1 tripod mount 1 3 troubleshooting 7 1 automatic logging 7 2 data downloads 7 6 display layout 7 2 instrument warnings 7 5 powering on 7 1 RH values 7 4 sealing 7 1 U universal charging adapter 1 3 USB cable 1 3 4 1 port 1 2 port protector 3 1 W wrist strap 1 3 3 1 ...

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Page 131: ...nal 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 984 19037 04 2022 ...

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