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Measuring Chlorophyll Fluorescence with the CFM 

 

CIRAS-2 Operator's Manual Version 2.04 

- 96 - 

Measuring Chlorophyll Fluorescence with the CFM 

 

Getting Started with the CFM 

It is assumed that you are already familiar with operation of the CIRAS-2 Portable Photosynthesis System.  
If  not,  we  strongly  suggest  that  you  familiarize  yourself  with  the  basic  operation  of  the  CIRAS-2  system 
and  refer  you  to  the  CIRAS-2  Portable  Photosynthesis  System  Tutorial  and  earlier  sections  of  this 
Operator‟s Manual. 
 
The Chlorophyll Fluorescence Module (referred to as CFM throughout this manual) consists of two main 
pieces of hardware: 
 

1. 

Light Unit

.  The chlorophyll fluorescence detector and light sources are built directly into the PP 

Systems‟ LED light unit. 

 
2. 

Signal conditioning board

.  This is fitted beneath the PP Systems‟ User Interface (U/I) in a 

rugged, aluminium enclosure. 

 

Warning: The light unit and signal conditioning board are a matched pair and are 

not interchangeable. 

 
At this stage, it may be advantageous to visit the back of this manual to review the information relating to 
chlorophyll fluorescence measurements.  To learn more about chlorophyll fluorescence in general (theory, 
measurement techniques, etc.), refer to 

Brief Introduction to Chlorophyll Fluorescence

 on page 119.  For a 

full list and description of the various chlorophyll fluorescence parameters (measured and calculated), go 
to 

Glossary of Fluorescence Terms

 on page 125. 

Firmware & Software Requirements 

To operate the CFM with the CIRAS-2, the following CIRAS-2 firmware and software must be in place: 
 

Firmware (EPROM) 

Version 1.77 or greater 

To check this with your system, run the 
CIRAS-2 software and click on 

View -  

Quick Info

.  This is shown under 

“Hardware Information” at the top of the 
window next to the serial number of your 
instrument. 
 

Software 

Version 1.06 or greater 

To check this with your system, run the 
CIRAS-2 software and click on 

Help - 

About

.   

 
New systems will be supplied with the required firmware and software.  For CFM upgrades, PP Systems 
will supply the proper hardware, firmware and software along with full instructions on how to upgrade your 
system. 

Software Installation 

All  the  software  for  both  the  integral  PC  (User  Interface)  and  external  PC  are  supplied  on  the  CD  ROM 
supplied with your system.  Make sure that you keep this CD in a safe place.   
 

 
 

Содержание CIRAS-2

Страница 1: ...or Remote Control Software RCS Version 1 07 or greater 2010 PP Systems All Rights Reserved 12 th May 2010 PP Systems Inc 110 Haverhill Road Suite 301 Amesbury MA 01913 U S A Tel 1 978 834 0505 Fax 1 9...

Страница 2: ...This page is left intentionally blank...

Страница 3: ...electrical and gas connections 19 CIRAS 2 gas electrical connection panel detailed view 19 Step 4 Connect leaf cuvette power cable to external 12V DC Power Supply 20 Step 5 Inspect absorber columns an...

Страница 4: ...p Details 32 Graphing 32 Preferences 32 Reset 32 Utilities Menu 32 Zero 32 Diff Bal 33 Measure Quit 33 Initialise 33 Pulse Alarm 34 Simultaneous Measurements With CIRAS 2 and FMS2 34 Diagnostics 34 St...

Страница 5: ...ry 43 Add Custom Accessory 44 Light Type 45 Leaf Temperature Tleaf 45 Leaf Temperature Determination Explanations 45 Energy Balance 45 Thermistor 46 Direct Leaf Temperature Measurement Common Problems...

Страница 6: ...esponse 53 Customized Operation of CIRAS 2 with Ambient CO2 53 Customized Operation of CIRAS 2 at Humidity Levels Above Ambient 54 CIRAS 2 Time 54 Analog Outputs 54 CO2 Analog Outputs 55 H2O Analog Ou...

Страница 7: ...Type 73 H2O Control Type 73 Light Type 73 Temperature Control 73 Batch Response Curves 76 Enable Batch Response Levels 76 Batch Level Options 76 Show Prompt 76 Force Zero and Automatic Settle 76 Repe...

Страница 8: ...xternal PC 99 Stand Alone Operation User Interface 100 CFM Operation 101 Default Adaptation 102 Dark Adaptation 102 Far Red Adaptation 102 No Adaptation 102 CFM Recording Options 102 Dark Period Minut...

Страница 9: ...7 Settings 128 Soil Respiration Operational Settings 128 Chamber Properties 129 Volume cm 3 129 Area cm 2 129 System Type 129 Recording Parameters 129 CO2 Change 129 Maximum Time 129 System Temperatur...

Страница 10: ...140 Current Battery Power Source 140 Report 140 Quick Report 140 Extended Report 140 Calibration 143 External connections for CO2 Calibrations 143 CO2 calibrations using the internal standard 143 CO2...

Страница 11: ...Definitions 159 Measured Parameters 159 Calculated Parameters 159 Physical Constants Used in Equations 160 Saturated Vapor Pressure of Water from Air Temperature 160 References 161 Addendum 162 Corre...

Страница 12: ...sed which is not covered under our normal warranty policy This manual and the information contained within are copyright to PP Systems No part of the manual may be copied stored transmitted or reprodu...

Страница 13: ...or an authorised agent for repair or replacement of the defective part s Contact Information PP Systems Inc 110 Haverhill Rd Suite 301 Amesbury MA 01913 USA Tel 978 834 0505 Fax 978 834 0545 Sales sa...

Страница 14: ...he top and bottom caps of the absorber columns Close the leaf cuvette to allow successful LED tuning Always operate CIRAS 2 in a vertical position Important Precautions Do not use substitute battery c...

Страница 15: ...ing and Servicing Maintenance Calibration Visit the Registered Users Area of our website to download the Technical Manual The Operator s Manual is designed to guide you through the various menus displ...

Страница 16: ...r Safe Mode Please note that your Display may look different i e lower resolution Use Windows Explorer to locate the setup exe file and proceed with the installation 3 When completed restart your comp...

Страница 17: ...aved for you The most recently used preferences and settings will load each time that the RCS program is subsequently started and the login procedure will be circumvented The New User option facilitat...

Страница 18: ...and CIRAS 2 There are 99 COM port options currently available to the user By default the COM port on the UI is set to COM1 To select the appropriate COM port see the Windows Device Manager instructio...

Страница 19: ...be described in detail later Click at any time for On line help While working with CIRAS 2 from your PC or notebook you have access to compiled Windows Help Files through the buttons associated with m...

Страница 20: ...timal results This is best achieved by connecting the batteries to their respective chargers the night prior to measurements This ensures that the battery packs are fully charged and ready to power th...

Страница 21: ...entries AN IN REF IN AIR OUT at the top of the panel CIRAS 2 gas electrical connection panel detailed view Note that it does not matter which leg of the tubing marked R is connected to the REF IN or A...

Страница 22: ...Molecular Sieve 2 3 rd Envirogel White Non Indicating Orange White Non Indicating Green 2 Soda Lime Green Brown 3 Soda Lime Green Brown 4 1 3 rd Molecular Sieve 2 3 rd Envirogel White Non Indicating O...

Страница 23: ...end of a CO2 cylinder between your fingertips to lightly lubricate it Slide the new cylinder into the holder with the narrow cylinder neck facing out towards the open end of the holder Thread the reg...

Страница 24: ...l pressure If the CO2 value achieves or comes close to 1 500 ppm and remains stable the CO2 cylinder should NOT be removed as it remains pressurized You can begin measurements without changing the CO2...

Страница 25: ...CIRAS 2 Switch on CIRAS 2 by pressing the red On Off button on the back panel When powered the switch should illuminate bright red The cuvette fans and CIRAS 2 s internal pumps should be running at t...

Страница 26: ...nch the PC version of RCS from your computer s Start Menu or Desktop shortcut icon Once you have established a connection CIRAS RCS will automatically load default settings and begin LED tuning Within...

Страница 27: ...ocedure when first entering into the Measurement mode This process takes approximately 30 seconds and cannot be interrupted During this time CIRAS 2 drives the light unit to a range of different level...

Страница 28: ...observing gas exchange click on the button for the Setpoint s that you wish to change and the Ciras Control Values dialog appears With this dialog open you can change one or all of the Control Setpoi...

Страница 29: ...min 1 Ap Atmospheric Pressure mb RH Relative Humidity Calculated Calculated Variables Description Unit Ci Substomatal CO2 Concentration ppm E Transpiration Rate mmol m 2 s 1 gs Stomatal Conductance mm...

Страница 30: ...atches the plot color of the variable Clicking on this button will toggle through your maximum of four selected Time Plot variables See Graphing Preferences on page 57 for details Status Bar Errors an...

Страница 31: ...C Power Source E External Power Supply Connected L Left Battery in Use R Right Battery in Use Left and Right Battery Power Status Color Battery Voltage Is Battery is Green OK Fully Charged Blue 10 2 V...

Страница 32: ...see Recalculate Data on page 81 Export Data Exports all stored CIRAS 2 Data Files to your desktop PC in a user specified format for importing into spreadsheet applications such as Microsoft Excel Plea...

Страница 33: ...are but working off line this function will be unavailable grayed out To connect to the Chlorophyll Fluorescence Module CFM click Connect Add On CFM For further information about operating the CFM see...

Страница 34: ...clude Plot Type plotted variables and parameters font size display scales of variables time scale Refer to Graphing Preferences on page 57 for details Reset Clears the current Time and Data Plots and...

Страница 35: ...s thicker to differentiate between normal running and DIFF BAL cycle A letter code DB representing the event appears on the currently plotted variable When completed the Status Bar returns to its prev...

Страница 36: ...visible light When simultaneous gas exchange and fluorescence measurements are performed this must be replaced with a plain glass window that transmits infrared radiation resulting in an increased hea...

Страница 37: ...er to Calibration on page 143 for more details Calibration Check Used to verify the current CIRAS 2 CO2 and H2O calibration settings Refer to Calibration Check on page 145 for details Calibration Rese...

Страница 38: ...to starting the CO2 Midpoint setting Refer to Max C Determination on page 149 for further details LED Tuning Allows manual LED tuning automatic LED Tuning performed during start up and recalls Tuning...

Страница 39: ...page 127 for more details Begin Opens the Select Recording Options dialog to name a new file or select an existing file edit treatment descriptions and select type of recording End Select to terminat...

Страница 40: ...dialog Plugin Record Not currently assigned View Menu Quick Info Opens the CIRAS 2 Received Setting dialog Provides information such as the serial number of the instrument eprom version and technical...

Страница 41: ...s detected by CIRAS 2 such as changing A D Zero values can be viewed from this menu Time Plot To view measurements as color coded plots over time select View Time Plot Alternatively if Data Plot is cu...

Страница 42: ...About to see which version of the CIRAS 2 Remote Control Software you are running Diagnostics Contains information related to the 6 CIRAS 2 Diagnostics topics Calibration Stored Diff Bal Contains topi...

Страница 43: ...will load each time that the RCS program is started and the login procedure will be circumvented Set File Options Set Entry Name Click on Setup in the CIRAS main menu bar to open the Settings dialog...

Страница 44: ...hing Options button to change various options associated with graphical presentation of data in the Graph Preferences dialog The same dialog is available by selecting Setup Graphing Preferences from t...

Страница 45: ...other options will automatically be set to defaults for this Accessory The table below lists several current and older style cuvettes and chambers supported by CIRAS 2 Accessory Cuvette Chamber Type C...

Страница 46: ...ccessories If you have any questions as to which cuvette or probe type you have refer to the original paperwork i e invoice from PP Systems the Appendix at the back of this manual or contact PP System...

Страница 47: ...ranspiration the air inside the leaf is assumed to be saturated at the leaf temperature Tleaf is determined by the balance between energy absorbed by the leaf from incident radiation visible and short...

Страница 48: ...mperature Heat conduction along the wires that are in the air to from the sensor also has a significant effect IR photography of leaves also shows significant patchiness in leaf temperature Infrared I...

Страница 49: ...d 2 are fresh and that the reference CO2 concentration is steady when the Diff Bal is performed Manual with Warnings Perform manual Zeroes and Diff Bal if desired CIRAS 2 will prompt you when it deter...

Страница 50: ...from previous 79 2 If more than 4 sets of Stored Zeros are present CIRAS 2 checks the slope of the data If the slope falls out of an acceptable range an Error Code 78 is generated Zero Showing Progre...

Страница 51: ...al cuvette air supply unit on and off Setting the Air Supply pumps to Off will result in the setting of CO2 and H2O set points being disabled as the flow is assumed to come from a separate source i e...

Страница 52: ...nder the current Set and Parameters files and whenever you exit the Recording Mode where you may be using different values Control values associated with Cuvette Environment may be changed at any time...

Страница 53: ...the concentration stabilizes In both cases measurements should be suspended until the system is stable as these data will be invalid H2O 0 100 or 0 mb Dewpoint Selections available from the H2O Contr...

Страница 54: ...leaf chamber are wholly artificial from a physiological standpoint and measurements should be suspended until stable conditions prevail Control Types 3 4 5 are dynamic responding to feedback from the...

Страница 55: ...ing Supply Ref Approximate ppm for CO2 and either Supply Ref Ambient or Supply Ref Set mb 0 Ambient for H2O If performing a Light Response 1 Set the CO2 to a high non limiting value 2 Set the light to...

Страница 56: ...r paper and reattach it to the manifold In very hot dry conditions you can also cover the filter paper in clear plastic wrap to minimize evaporation CIRAS 2 Time CIRAS 2 can be set to match the exact...

Страница 57: ...000 ppm Difference 25 999 ppm H2O Analog Outputs Low 0 75 mb High 0 75 mb Difference 5 75 mb For differential values both CO2 and H2O an output of 2 5V corresponds to a 0 differential Output values be...

Страница 58: ...5 50 x 2 5 2 5 3 75 V Example 4 If H2O Reference 25 56 mb Low H2O 10 mb High H2O 50 mb Then H2O Reference Voltage Output 25 56 10 0 50 10 x 5 0 V 1 945V Automatically Update CIRAS If checked after cli...

Страница 59: ...ect Plot Type list choose Time Plot Select Variables Choose up to four variables to display as continuous colored plots in the Time Plot At least one variable must be displayed The list of variables a...

Страница 60: ...ist You will see a message if you set the scale outside of the min max range Time Span Choose your desired X axis time span 10 20 or 30 minutes Data Plot From the Select Plot Type drop down list selec...

Страница 61: ...eral minutes a display similar to the one below should be observed assuming the system has been adequately warmed up and all steps in Preparations for Use on page 18 have been carefully followed Pleas...

Страница 62: ...Precise CO2 control is available to within 1 ppm of the set value by using the Supply Ref Set ppm Control Type The system is functioning properly if the above conditions are observed If not please re...

Страница 63: ...sion Treatment Editor See detailed information below Treatment Editor Treatment files extension trt are provided to help identify records associated with a particular experimental or sampling level su...

Страница 64: ...e Select data file dialog box as above will appear for you to name the data file In the Select Recording Options dialog you can choose from three file saving options Append to Data File Overwrite Data...

Страница 65: ...ing the leaf from the side with the open cuvette to avoid accidentally injuring the leaf in this way The cuvette tension screw is located beneath the cuvette open close lever Use a small hex wrench to...

Страница 66: ...a highly shade adapted plant that is suddenly exposed to strong light intensities in the leaf chamber In this case delayed gas exchange responses can be expected compared to a plant or leaf accustome...

Страница 67: ...inate measurements Keypress Recording For many leaf gas exchange measurements such as those made in the field and under dynamic light conditions this method of recording is most practical Using this m...

Страница 68: ...leaves Again select Recording Begin from the CIRAS 2 main menu In the Select Recording Options dialog click in the circle next to Timed and then click OK There are two Timed Recording Options 1 Record...

Страница 69: ...eselect it Steady Pn Value Enter an acceptable value for Pn variability before data can be recorded Recording at Pre set Intervals In this mode a record is taken after the elapse of the Interval and o...

Страница 70: ...nue button to resume recording To terminate Timed Recording click the Stop button Response Curve This option allows you to design highly individualized leaf chamber conditions for experiments in which...

Страница 71: ...Each Response File rsp extension can contain up to 10 Response Curves The options for each are saved with the Response Curve Definition Editing Response Variable Values Editing All the Values in a Ro...

Страница 72: ...nt to bear in mind that changing CO2 concentrations etc may result in time delays of variable length in order to propagate through the system Therefore it is advisable to test the Response Curve prior...

Страница 73: ...ve state of the 30 Response Levels To change the number of active levels in the response curve click on the cell in the Enable row where your response curve will end Level 11 in the example below The...

Страница 74: ...completion Repeat Beneath the Repeat field click the button to choose the number of measurements to be recorded at each level Later this will be important for producing means when you process your dat...

Страница 75: ...trol option Refer to CO2 0 2000 ppm on page 51 for more details H2O Control Type Refer to H2O 0 100 or 0 mb Dewpoint on page 51 for more details Light Type Defaults to Auto Light Unit See Light Type o...

Страница 76: ...Settle times The end of Response Levels are marked by a light green vertical line In the example 15 Response Levels have been completed note Settling for Level 16 1 14 of 1 30m in upper left of displ...

Страница 77: ...Observing and Recording Leaf Gas Exchange CIRAS 2 Operator s Manual Version 2 04 75 Time Plot Data Plot...

Страница 78: ...h Response Curve Instructions for setting up storing and running Batch Response Curves is very similar to those described in the section Response Curve starting on page 68 Enable Batch Response Levels...

Страница 79: ...pear Click on the Enable Internal Recording box and enter the value required in the Record Interval box Please note The value you enter will be that value x 10 In other words if you want to record eve...

Страница 80: ...normally be saved to the following location on the PC unless otherwise specified Program Files Ciras2 Users PPSystems DataFiles Clear CIRAS Memory To clear internally stored CIRAS 2 records click the...

Страница 81: ...e must be present The measurement screen will then be displayed and initially CIRAS 2 will zero CIRAS 2 will then be set to the first set of values When the graph shows that the readings have stabiliz...

Страница 82: ...offsets The results are displayed showing the measured values and offsets and the calculated offsets You then have the option of accepting or rejecting the offsets If accepted CIRAS 2 will use the ca...

Страница 83: ...e automatically given a mod extension The original file dat extension will remain unaltered Click Save to continue The CIRAS 2 Photosynthesis Recalculation dialog will appear Initially data from the f...

Страница 84: ...line read automatically However the software will pause depending if Pause when Treatment Comment Changes See below is selected Pause when Treatment Comment change Regardless of the Step by Step optio...

Страница 85: ...stomata on the upper and lower surface of the leaf Please note that the ratio is in terms of the upper leaf During recalculation the value should be entered as a percentage of 1 i e 50 Stomata on top...

Страница 86: ...ssion date and time file name and information related to the CIRAS 2 and user information The General tab will open first when Session is selected as described above Probe To view information related...

Страница 87: ...rsion 2 04 85 Recording View the recording type selected i e keypress timed response curve and associated settings Treatments To view treatment descriptions as they pertain to different plots records...

Страница 88: ...or off by clicking it Data ranges Maximum and Miniumum are calculated by the software To switch between Data and Plot view type click on the Plot or Data button in the upper left hand corner In Data...

Страница 89: ...d what additional data to export Export options for data dumped data and closed system data are treated individually Shared Options Stores fields from the data file are displayed in the preview graph...

Страница 90: ...ly in the program selected Please note Please contact PP Systems see Contact Information on page 11 if the above options do not work properly on the UI Export Data This feature allows you to export al...

Страница 91: ...i e CIRAS type serial number of instrument probe type etc Export Fields There are numerous fields of data that can be output to suit your needs Check To All Fields Export all fields i e measured and c...

Страница 92: ...live session you must first deselect All Fields and select Calculate VPD and Cuvette RH Then check All Fields again After selecting the appropriate fields to be exported click on Export You will be p...

Страница 93: ...integral PC Pencentra or User Interface UI over to your desktop PC To do this you can use ActiveSync the RS232 Null Modem or by moving them from the UI to a Flash Card via the PCMCIA drive Records can...

Страница 94: ...splay Settings and Control Panel Next double click on PC Connection and ensure the following A Make sure that Enable direct connections to the desktop computer is ticked off B Make sure that 19200 com...

Страница 95: ...r files from the integral PC Pencentra to your PC To transfer stored files open Windows Explorer on your PC and navigate to Mobile Device on your PC and locate the subdirectory where the data files ar...

Страница 96: ...ing a different PC with your CIRAS 2 Establishing An ActiveSync Connection For Data Transfer from UI To PC 1 Turn off the CIRAS 2 and disconnect the USB cable from the UI 2 On your PC start ActiveSync...

Страница 97: ...f the connector not the body of the connector or the wire Remove the reference R and analysis A gas connectors from CIRAS 2 by pulling back on the sleeve around the front of the connector not the body...

Страница 98: ...relating to chlorophyll fluorescence measurements To learn more about chlorophyll fluorescence in general theory measurement techniques etc refer to Brief Introduction to Chlorophyll Fluorescence on p...

Страница 99: ...ss window which must be fitted to the cuvette in place of the CALFLEX window If you have received a complete new CIRAS system including the CFM the plain glass will already be fitted to the leaf cuvet...

Страница 100: ...on the end of the light unit to the small screw protruding from the end of the leaf cuvette head until snug B 3 Connect the shorter grey LED electrical cable on the light unit into the 5 pin socket on...

Страница 101: ...able on your PC go to Start Control Panel System Hardware Device Manager and open Ports COM LPT You will need to remember which COM ports are being used when logging in and setting up CIRAS 2 with the...

Страница 102: ...all electrical and pneumatic connections are made as described in the section Connecting the CFM to CIRAS 2 perform the following to operate the system from the PP Systems User Interface 1 Switch the...

Страница 103: ...xternal PC or the User Interface Ensure that the leaf cuvette is closed in order for the system to perform LED Tuning and CFM Tuning on startup Power on CIRAS 2 by pressing the red On Off switch Execu...

Страница 104: ...l calculation results Far Red Adaptation For this selection the sample does not require dark adaptation Instead an Fo is performed under Far Red Light to determine only phiPSII calculations However qN...

Страница 105: ...should adapt further no record will be taken until the End DA or End LA button in the Recording window is clicked In Keypress and Manual Responses this prompt is displayed regardless The Adaptation p...

Страница 106: ...ty mol m 2 s 1 Pulse Width seconds Recovery Time seconds Fo Duration seconds Far Red Adaptation Parameter Setup Options Fo Duration seconds Recovery Period seconds Time allowed for leaf to recover dep...

Страница 107: ...can also perform a phiPSR at the end of measurement If this is desired click on Setup for the Calculation Options dialog Default Adaptation Calculations Performed Dark Adaptation phiPSR Fo Far Red Ada...

Страница 108: ...ay is shown place your leaf sample in the cuvette and close it You want to see a steady fluorescence signal similar to this before proceeding with fluorescence measurements If the signal is too high l...

Страница 109: ...ay one of four possible parameters that can be selected Span Fluorescence data can be displayed over 2 3 and 4 minute time intervals In all cases the last 1 minute is discarded when the full span has...

Страница 110: ...chlorophyll fluorescence measured and calculated data They are not superimposed because of the differing time scales of the two processes gas exchange and chlorophyll fluorescence though it is possibl...

Страница 111: ...ation The user can intiate the adaptation required at any time if this option is available Button Result Minimizes the Chlorophyll Fluorescence CFM display D Data Plot Fluorescence data can be shown o...

Страница 112: ...CIRAS CFM Display CIRAS 2 Operator s Manual Version 2 04 110...

Страница 113: ...easurement based on the CFM settings described earlier The following sections describe the two most common types of measurements Keypress and Response Curve Recording Keypress Recording with CFM Click...

Страница 114: ...Recording Chlorophyll Fluorescence CIRAS 2 Operator s Manual Version 2 04 112 CFM Recording Options Fv Fm Options phiPSII Options...

Страница 115: ...tton During dark adaptation the LED light unit is automatically turned off During this period you should witness a fluorescence signal green line of 0 on the lower display and your photosynthesis calc...

Страница 116: ...he dark adaptation period will be extended There are event markers in the display showing exactly when the measurement was recorded If you would like to view the chlorophyll fluorescence data and trac...

Страница 117: ...nt In addition to measurement of photosynthesis a phiPSII is calculated followed by a recovery period in seconds set by the user under CFM Recording Options to allow the sample to recover from the lig...

Страница 118: ...he photosynthesis readings will be based on the settings in the Response Curve Editor Following the dark adaptation period the CIRAS 2 will perform an Fv Fm and the chlorophyll fluorescence measuremen...

Страница 119: ...s to all CFM measurements and calculation phases Unlike CIRAS 2 gas exchange data raw CFM data dat files are not written to output with headings CFM data files are complex and can be difficult to inte...

Страница 120: ...Fo Low 1 Fluorescence Origin Low Fm Low 2 Fluorescence Maximum Low Fm Fo 4 Fluorescence Maximum less than Fluorescence Minimum Fo Low 8 Fluorescence Origin Prime Low Fm Fs 16 Light adapted Fluorescen...

Страница 121: ...into two groups Photochemical processes Electron donation from the pigment to an acceptor molecule occurs The energy is then used in the carbon fixation cycle Non photochemical processes Energy is re...

Страница 122: ...from Krause and Weiss 1984 Therefore accurate determination of fluorescence requires a detection system that is sensitive to the fluorescence wavelengths yet blind to the actinic or excitation light...

Страница 123: ...tracking electronics amplify and measure ambient and non pulsed fluorescence signal are discarded C Figure 1 2 Figure 1 2 Fluorescence signal detected by the CFM under modulating beam only conditions...

Страница 124: ...on fluorescence analysis procedures The most widely accepted parameter definitions used by main stream workers are presented in a glossary with alternative nomenclatures There are two common types of...

Страница 125: ...see parameters glossary Changes in the magnitude of the J peak following multiple pulse tests are currently thought to provide a particularly sensitive indicator of photosynthetic stress Determination...

Страница 126: ...ssary Measurement of the full range of light adapted fluorescence parameters requires the following instrumentation features Saturating Light Source Capable of delivering at least 2 500 mol m 2 s 1 to...

Страница 127: ...n Kautsky terms Maximum fluorescence signal from the dark adapted leaf following application of a saturating light pulse which fully reduced the PSII electron acceptors preventing photochemistry Dark...

Страница 128: ...lated PSII Y Yield Genty Parameter Quantum efficiency of light use by PSII i e number of PSII reaction events no photons absorbed Derived from Fm Fs Fm Measure steady state fluorescence signal Fs appl...

Страница 129: ...he SRC 1 Soil Respiration System Operators Manual for CIRAS 2 ver 4 03 or greater Soil Respiration Measurement Display Prompt Gives instructions to the user i e flushing the cuvette etc or displays th...

Страница 130: ...cm 2 Soil Respiration Operational Settings Go to the Setup Settings menu to open the CIRAS 2 Settings dialog Click on the Setup button to view current settings The following menu will appear Select S...

Страница 131: ...fixed 78 5 and can not be changed Please note If soil collars or similar devices are used with our SRC 1 chamber the total area will be larger than the default value In that case you will need to open...

Страница 132: ...prompt for new Data File Every time you start a new measurement a window will appear asking you to enter a new data file name Append to Data File If selected all measurements will be appended to the e...

Страница 133: ...amber fan should run at a noticeably higher speed during this period After approximately 15 seconds you will be instructed to Place on Soil Ready to continue The SRC 1 fan speed should be running at a...

Страница 134: ...he selected file is correct If you need to change the Plot Number or wish to add a comment between measurements click on the T button in the upper left hand corner of the display At any time during th...

Страница 135: ...fferent dialogs associated with Diagnostics Analyser A D Reads CIRAS 2 Temperature and Atmospheric Readings CO2 and H2O readings depending on valve settings and CIRAS 2 Stored Zeros Temperature PLC St...

Страница 136: ...os Clears the stored zeros If the zero reads are outside the normal range normally due to exhausted chemicals in the zero columns then after replacing the absorbers click on this to reset the stored z...

Страница 137: ...Flows Reference Refers to the flow rate of the reference pump Should read approximately 98 105 and stable Analysis Refers to the flow rate of the analysis pump Should read approximately 98 105 and st...

Страница 138: ...om IR sensor If the sensor base temperature is identical to the leaf temperature then this value will be set to 512 If leaf is warmer then the value will be greater and vice versa Cuvette State PLC Op...

Страница 139: ...s Contact Information on page 11 Apply Associated with the Probe type selected above Button caption is Apply Auto Cuvette in this example After selecting Probe connected above click this box to get di...

Страница 140: ...cuvette air supply Flow mls min Click on this so that a new value can be entered Flow Requested Flow Rate that CIRAS 2 has been set to Flow Measured Flow rate that is being delivered Control Setting...

Страница 141: ...rol Apply Lamp 1 LEDs To check Lamp 1 or an LED light unit after entering values click on the button to verify that they are working properly Lamp 2 only applies to the quartz halogen light source sma...

Страница 142: ...ful for technical support purposes It contains important information such as CIRAS 2 serial number hardware eprom version date and time analyzer reference and analysis A D reads etc A file may also ge...

Страница 143: ...Analyser Test and connecting a Leaf Cuvette during the Leaf Cuvette Tests Requires i external CIRAS 2 Power Supply ii External Zero Column iii fresh chemicals iv external power supply to Leaf Cuvette...

Страница 144: ...hen the automated tests have completed the following CIRAS 2 Extended Diagnostics summary dialog will be available You can view any section of the diagnostics by selecting it from the expandable list...

Страница 145: ...ut they may be done consecutively in any order The procedure for checking or calibrating is similar The contents of the absorber columns must NOT be exhausted The analyzer must have been switched on f...

Страница 146: ...of the H2O calibrator can be found in the CIRAS 2 Technical Manual PP Systems Water Vapor Calibrator The calibrator consists of an insulated container filled with ferrous sulphate salt FeSO4 7H2O The...

Страница 147: ...click the corresponding button After calculating the calibration factors the existing and new factors will be displayed The option is then given to use the new factors retain the existing factors or r...

Страница 148: ...r Please Note Initially only make electrical connection so that the CIRAS 2 can confirm that the salts in the Calibrator are at an acceptable temperature If the salts are too hot and ambient air tempe...

Страница 149: ...are irrelevant If the Reset Button is clicked CIRAS 2 will be instructed to reset the Calibration Constants to the Factory Default and CIRAS 2 will then return to the measurement mode using those fac...

Страница 150: ...ored CO2 Midpoint generated by the CIRAS 2 Restore Default Set the CO2 Midpoint back to the factory default value Upon selection of the appropriate option CIRAS 2 will apply the setting return to Meas...

Страница 151: ...Utilities MaxC Determination Start and ensure that the gas connection are correct MaxC is divided into 2 parts firstly with the CO2 Valve set to 100 Fully Open and then with the CO2 Valve set to 50 A...

Страница 152: ...es should be recorded and supplied to Technical Support After completion of the 100 Step Pc Max Pressure Corrected Term BT Blender Temperature V Flow After completion of the 50 Step Pc Mid The MaxC fu...

Страница 153: ...ill help Examination of the window material its shape and size and the size of the leaf aperture that can be seen beneath it will lead to the identification of your cuvette Leaf Cuvettes fitted with a...

Страница 154: ...hese cuvettes when used with CIRAS 2 1 PLC DELTA COOL MAX COOL MAXQ RAD X LAR Rb FLOW SUN PARX SUN TR LED PARX LED TR QI PARX QI TR CIRAS 1 PLC s Adapted for CIRAS 2 AUTO PLC5 B 9 190 2000 1 0 2 5 0 3...

Страница 155: ...ment Seals STD044 2 CIRAS Forwarding Pump GAST STD075 Miniature Rotary Pump ASF STD076 Sealed Miniature Rotary Pump ASF STD002N Autozero Solenoid Valve KV Microsol STD045 Control Solenoid Valve Lee LF...

Страница 156: ...et Plate 18mm Diameter Lower 10088 1 PLC6 U Plain Glass Window Assembly for use with CFM 10088 2 PLC6 U Calflex Window Assembly 20359 1 PLC6 U Window Plate Only 55021 1 PLC6 U Calflex Window Only 5502...

Страница 157: ...erefore Where a is projected leaf area cm 2 The V20 term is calculated above using cm 3 sec 1 but displayed by CIRAS 2 as ml min 1 Step 2 0 Calculate transpiration rate E from the partial pressures of...

Страница 158: ...e stirring fans and influenced by transpirational water vapor Its partial pressure is determined by the Analysis H2O IRGA As relates to the calculated values in the CIRAS 2 display Step 3 0 Calculate...

Страница 159: ...source transmission through the cuvette window Trans and reflection absorption by the leaf H Q x Trans The following approximation is made in the program 3 2 From this we derive Step 4 0 Derive i sat...

Страница 160: ...Cout the cuvette 5 1 IRGA CO2 readings are corrected for water vapor temperature and atmospheric pressure The addition of transpirational water vapor dilutes the air leaving the cuvette Cout and this...

Страница 161: ...0 Mass flow of dry air into cuvette at STP cm 3 sec 1 a Projected leaf area cm 2 rb Boundary layer resistance to water vapor m 2 s mol 1 P Atmospheric pressure mb Q Photon flux density incident on cuv...

Страница 162: ...osynthetic Rate mol m 2 s 1 gc Total conductance to CO2 transfer mmol m 2 s 1 Ci CO2 concentration of sub stomatal cavity mol mol 1 Determined by IRGA Temperature and pressure corrected for water vapo...

Страница 163: ...2 Buck A L 1981 New equations for computing vapour pressure and enhancement factor Appl Meteorol Vol 20 1527 1532 3 von Caemmerer S and G D Farquhar 1981 Some relationships between the biochemistry of...

Страница 164: ...are uniform H2O and CO2 concentrations within the leaf Where ea and el are the water vapor pressures of the cuvette air and the leaf air spaces respectively RB is the boundary layer resistance for who...

Страница 165: ...1 Now RSl 1 RSu 1 1 RS Therefore N E RB D N E E N E RB E RB D N E N E RB E RB D N E RB D RS 2 2 2 2 2 2 Which expands to N N E RB N E RB D E N N E E RB RB N E E RB RB D E RB D D RS 4 4 4 4 2 3 If we...

Страница 166: ...on has subtracted only RB Substituting in equation 5 for E D from equation 4 RB eq RS D E ie 1 RB eq RS N N RB N N eq RS true RS 1 25 0 25 0 1 6 Magnitude of Errors in RS We can determine the magnitud...

Страница 167: ...User Notes CIRAS 2 Operator s Manual Version 2 04 165 User Notes...

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