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Measuring Chlorophyll Fluorescence with the CFM

CIRAS-2 Operator's Manual Version 2.04

- 100 -

Stand-Alone Operation (User Interface)

After 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:

Switch the “CFM” slide switch to On.

Switch the “CFM Control” slide switch to CIRAS.

The correct COM ports will be automatically selected by default.

Summary of Contents for CIRAS-2

Page 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...

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

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

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

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

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

Page 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...

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

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

Page 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...

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

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