PP Systems CIRAS-3 User Manual Download

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CIRAS-3

Portable Photosynthesis System

Operation Manual

Version 1.09

August 2017

PP Systems

110 Haverhill Road, Suite 301

Amesbury, MA 01913 U.S.A.

Tel: +1 978-834-0505 Fax: +1 978-834-0545

Email:

[email protected]

URL:

www.ppsystems.com

Summary of Contents for CIRAS-3

Page 1: ...m Operation Manual Version 1 09 2017 PP Systems All Rights Reserved 7 th August 2017 PP Systems 110 Haverhill Road Suite 301 Amesbury MA 01913 U S A Tel 1 978 834 0505 Fax 1 978 834 0545 Email support...

Page 2: ...al Leaf Cuvette to the CIRAS 3 console 18 Connect light unit to PLC3 Universal Leaf Cuvette 18 Power up the CIRAS 3 System 19 System Warm up 19 Setting up the CIRAS 3 System 20 Setting up the graphica...

Page 3: ...IRAS 3 Console 47 CIRAS 3 Rear Console 48 USB Flash Drive Ports 48 Battery Charging Socket EXT PWR and LED 49 Power 49 Mini USB PC 49 PLC Connections 49 CO2 Cartridge Holder 49 CO2 Cartridges 50 How d...

Page 4: ...and Control Variables 62 Section 6 Startup Routine and System Stability Checks 66 Before You Power Up CIRAS 3 66 Startup and Warm up 67 CO2 Cartridge Status 68 Changing a CO2 Cartridge 70 Checking Sta...

Page 5: ...ion Setup 99 CO2 Calibration 99 H2O Calibration 100 Find Max C 101 Store Diff Bal 102 LED Calibrate 105 PAR Calibrate 106 Diagnostics 107 IRGA F2 107 PLC F3 108 Flow F4 110 Power F5 111 APA F6 112 Rep...

Page 6: ...130 CFM 3 Set Up 131 CFM 3 Settings 132 CFM 3 Controls 135 Measurement of Fm with CIRAS 3 137 Section 11 Closed System Measurements 140 Soil CO2 Efflux and Net Canopy CO2 Flux 140 Theory 140 FCO2 Unit...

Page 7: ...Net Photosynthesis 161 Intercellular CO2 Concentration 162 Physical Constants Used in Equations 163 Definition of Symbols 163 Section 13 Troubleshooting Diagnosis 165 System Power 165 CO2 Measurement...

Page 8: ...Air Inlet Filter Assembly Part Number STD558 184 Desiccants and Absorber Columns 184 Zero Column Assembly 185 CO2 H2O Control Column 186 Soda Lime 187 Drierite 187 Molecular Sieve 188 Molecular Sieve...

Page 9: ...Changing PLC3 Universal Head Plates 200 Replacement of PLC3 Glass Window For Use with CFM 3 201 Section 15 Consumables Spares 202 Desiccants and Absorber Columns 202 Pumps Air Filters 202 CO2 H2O Con...

Page 10: ...C Version V 3 14 and above To check which software and firmware versions are currently installed on your CIRAS 3 go to Help F8 About F2 For users running V 1 09 console software along with latest firm...

Page 11: ...e equipment must be checked for correct operation and calibration at intervals appropriate to the circumstances The PP Systems equipment warranty is limited to replacement of defective components and...

Page 12: ...Service Manager service ppsystems com to request a case number for reference and tracking purposes Returning equipment to PP Systems Before returning equipment to PP Systems it is very important that...

Page 13: ...ning Li ion batteries There is also no need to return the power supply adapter or any cables Remove the CO2 cartridge from the CO2 cartridge holder To save on weight and shipping costs you can remove...

Page 14: ...on the packing list or checklist are not included or damaged you must contact PP Systems or your authorized distributor immediately Storage We highly recommend storing your equipment in a safe dry lo...

Page 15: ...and become more familiar with the user interface Store and retrieve data from memory This tutorial is based on the following system configuration If you have our CFM 3 Chlorophyll Fluorescence Module...

Page 16: ...with the system to the EXT PWR socket on the CIRAS 3 console to charge the internal batteries Make sure that the connection is secure The indicating LED should be steady green in color indicating secu...

Page 17: ...s which are manufactured by a company called ISI https www isi com They can easily be sourced from many different suppliers around the world If you have any questions or problems related to these CO2...

Page 18: ...rial we will be controlling H2O using the Drierite Connect the PLC3 Universal Leaf Cuvette to the CIRAS 3 console Connect the black 4 pin electrical plug from the PLC3 to the Signal socket on the CIRA...

Page 19: ...will appear on the LCD Press Continue F1 to start the CIRAS 3 software System Warm up We recommend allowing the system to warm up for at least 15 30 minutes It normally takes the system approximately...

Page 20: ...us in the lower right hand corner of the display Setting up the CIRAS 3 System Press Settings F2 This is where you select the accessory being used with the CIRAS 3 in this case PLC3 Universal Leaf Cuv...

Page 21: ...nces Tab from field to field and set your graph settings exactly as shown below Press Clear F5 OK Accept F2 Accept F2 Again when you are in any field you can press the Expand List F4 to see all availa...

Page 22: ...b and Tleaf should be the same 0 2 o C The environmental controls in red are based on your Settings file Do not worry about the Photosynthesis Data at this point These calculated values do not matter...

Page 23: ...ols You will be amazed at how easy it is to dynamically control all environmental parameters with your CIRAS 3 system Press Controls F3 In addition to controlling the environment you can also set the...

Page 24: ...utomatic Diff Bal as the CO2r approaches its target value of 500 followed by very stable results for CO2r and CO2d over several minutes as shown above If not perform a manual Diff Bal by pressing Z Di...

Page 25: ...al plant Now that we ve established that everything is working well and you are a bit more comfortable with the CIRAS 3 it is time to get set up to begin taking measurements on a real plant Press Oper...

Page 26: ...ile is provided by default Note that the default data file always starts with C3XXXX_YYYYMMDD_00 where C3XXXX The serial number of your CIRAS 3 console YYYYMMDD Year Month Day 00 All data files start...

Page 27: ...h your leaf to eliminate time consuming post leaf area analysis and recalculation of results If the leaf fills the window completely then leaf area is clearly defined and there will be no need to reca...

Page 28: ...ecord a measurement The actual equilibration time varies based on the state of the plant at time of measurement and environmental controls Having said that normal healthy leaves tend to equilibrate an...

Page 29: ...Options F2 Transfer Data F6 Under Internal Memory arrow down to your data file and press OK to select the file Note the check box next to the file Press Export F3 to transfer the file to your USB Flas...

Page 30: ...a file in the Ciras 3 Data folder Follow the instructions to open the file in Excel Once retrieved your data should look similar to the following Some variation may apply depending on the Excel softwa...

Page 31: ...Connect the PLC3 Leaf Cuvette gas and signal connectors to the CIRAS 3 main console close the cuvette with no leaf present and press the CIRAS 3 On Off switch to power up the system and then Continue...

Page 32: ...following All measured data match up well with the environmental controls and they are stable The CO2d is close to 0 0 5 ppm and H2Od is also close to 0 0 5 mb Tamb and Tleaf is reading similarly 0 2...

Page 33: ...0 75 mb H2O Precision 0 015 mb at 0 mb 0 020 mb at 10 mb 0 030 mb at 50 mb H2O Control Range 0 Dewpoint or 0 100 Ambient Pressure Range 65 115 kPa Air Sampling User adjustable from 50 100 cc min 1 us...

Page 34: ...cm D x 24 cm H Weight 4 3 kg including 1 battery pack 4 5 kg including 2 battery packs PLC3 Leaf Cuvettes Construction Handle Aluminum Leaf Gasket Closed cell foam Impeller Aluminum fan blade Window P...

Page 35: ...ent Accuracy 0 5 o C at 25 o C PLC3 Narrow and Conifer Precision thermistor Accuracy 0 5 o C at 25 o C Dimensions General 32 cm L x 3 8 cm Handle diameter Weight PLC3 Universal 0 750 kg PLC3 Narrow an...

Page 36: ...main console has been significantly redesigned it is now exceptionally light at 4 5 kg including 2 battery packs with new more compact dimensions of 28 cm Width x 15 5 cm Depth x 24 cm Height footprin...

Page 37: ...ilicon photodiode sensors beneath the cuvette window PLC3 Universal and 1 silicon photodiode sensor beneath the cuvette window PLC3 Narrow and Conifer LED Light Unit RGBW Outwardly the LED light unit...

Page 38: ...ing and data recall For example you can make changes to dynamic Controls e g CO2 H2O light temperature with as few as three key presses Below are several new software highlights Toggle to view either...

Page 39: ...uorescence Module You now have the option to run and record complete fluorescence measurement sequences on their own with or without combining photosynthesis measurements Calculated fluorescence param...

Page 40: ...s system eddy covariance soil CO2 efflux etc Non dispersive infra red NDIR refers to the transmission of broad band infra red wavelengths from the IRGAs source lamps A single IRGA consists of four bas...

Page 41: ...por also causes an increase in infra red absorption which is detected as an apparent increase in CO2 This is of a similar magnitude but opposite to the dilution effect and CIRAS 3 automatically correc...

Page 42: ...ou can have confidence that a reported differential between the Reference and Analysis cell pair is real and not artificial An overview of the gas circuit design of CIRAS 3 configured for leaf level p...

Page 43: ...ing you to determine and set an optimal flow rate of air to the cuvette and leaf air supply pump as well as the sampling rate by the IRGAs reference and analysis pumps We also ensured that the differe...

Page 44: ...nterface with its 30 display and keypad group used to navigate the CIRAS 3 console menus Access to the Li ion battery pack s and internal mechanical and electrical components is achieved by loosening...

Page 45: ...r 41526 1 Battery Pack Inspired Energy Part Number 41535 1 ALWAYS MAKE SURE THE BATTERY PACKS ARE FULLY CHARGED THE NIGHT BEFORE USE Please note that batteries are shipped only partially charged due t...

Page 46: ...on time in the field See External Battery Pack For extended operation in the field on page 180 for more details If you have an older CIRAS 3 system using the old battery pack Aved type and are interes...

Page 47: ...and the battery removal black tab should be on the top of the battery pack 5 Secure in place with the retaining bracket in the Run position 6 Close battery compartment Charging Batteries inside the C...

Page 48: ...e holder USB Flash Drive Ports There are two USB flash drive ports labeled USB1 and USB2 These are used for downloading uploading stored data files and for transfer of settings and response script fil...

Page 49: ...on the PLC3 connects to the port labeled GAS and the 4 pin black electrical connector connects to the socket labeled SIGNAL Both the reference and analysis gas lines are built into the single pneumat...

Page 50: ...artridge holder from the CIRAS 3 You will also observe that the cartridge will be quite cold How do I determine the state of the CO2 cartridge It is very easy to determine if you have a highly pressur...

Page 51: ...Ports and Link Pipe AIR IN is the entry port for ambient air or introduced air from an external gas cylinder i e experimental air containing 2 oxygen A short link pipe connects AIR OUT with REF IN Thi...

Page 52: ...mation related to this column and management of desiccants TIP Always change the Molecular Sieve weekly during use See Desiccants and Absorber Columns on page 184 We also strongly recommend performing...

Page 53: ...Cuvette For measurement on conifers and short needle vegetation All 3 PLC3s connect to the PLC Gas and Signal connectors on the CIRAS 3 console Prior to use make sure that the gas and signal connectio...

Page 54: ...ower light intensities leaf temperature control is wider and at high light intensities it is much tighter We recommend that when using Set leaf temperature as the Temperature Control Type under Settin...

Page 55: ...nsor will represent an approximate temperature to ambient for reference purposes only Tamb may vary 1 3 o C from actual ambient depending on local conditions and orientation of the cuvette LCD on Leaf...

Page 56: ...is somewhat attenuated approx 10 attenuation by the window This affects the amount of light reaching the leaf if the light source is ambient sunlight but not if our LED light unit is the source This...

Page 57: ...e colors in any proportion to recreate the spectral distribution of a specific natural or artificial light source With full power available to the cuvette the normal intensity output range will be 0 2...

Page 58: ...it for the PLC3 Narrow and Conifer leaf cuvettes feature 96 LEDs 24 each of RGBW red green blue white color You are able to set any single color from 0 100 of the light source or you can combine color...

Page 59: ...er internal PAR sensor maximum light intensity may be lower than 2000 mol m 2 s 1 depending on mixture of red green blue and white LEDs CFM 3 Chlorophyll Fluorescence Module The CFM 3 Chlorophyll Fluo...

Page 60: ...rom the dialogs that you open The 8 function keys form the top level for menu selections Function keys are context sensitive so as you go deeper into a menu their assigned functions may change Once a...

Page 61: ...ose the appropriate cuvette window size such as 18 x 25 mm shown above Move down through the fields to make other changes to CO2 water vapor light temperature control etc Holding down the TAB key will...

Page 62: ...ssages with time stamps Press Display Help F6 to return to the Help file Numeric View of Data and Control Variables As you familiarize yourself with CIRAS 3 you will begin to establish your own prefer...

Page 63: ...l mol 1 CO2d CO2 Differential mol mol 1 H2Or H2O Reference mb H2Oa H2O Analysis mb H2Od H2O Differential mb PARi PAR internal mol m 2 s 1 PARe PAR external mol m 2 s 1 RH Relative Humidity inside leaf...

Page 64: ...gs Stomatal conductance mmol H2O m 2 s 1 E Transpiration mmol H2O m 2 s 1 VPD Leaf to air vapor pressure deficit kPa WUE Photosynthetic water use efficiency mmol CO2 mol 1 H2O Environmental Controls...

Page 65: ...iency J Thylakoid electron transport rate mol e m 2 s 1 Fv Fm PSII operating efficiency far red qP Photochemical quenching qNP Non photochemical quenching NPQ Non photochemical quenching qL Photochemi...

Page 66: ...e is sufficient battery power for field operation For optimal performance we recommend charging the internal CIRAS 3 Li ion battery s the night prior to field measurements using the power supply adapt...

Page 67: ...IRGA temperature can vary based on ambient temperature The warm up period can be only several minutes in a mild or warm environment in the laboratory and longer if it has been stored in a colder envi...

Page 68: ...data fields in the Numeric View screen are now updating with live data approximately every 2 seconds Data will update and be displayed in the fields except when the system is performing a Zero or Diff...

Page 69: ...ould reach 2000 If the CO2r reaches 2000 you can proceed with measurements without having to change out the CO2 cartridge Note keep an eye on the CO2r during your measurements and if you observe the C...

Page 70: ...mbly removed from the console place a new CO2 cartridge in the holder and put it back into the console and turn the holder a quarter turn clockwise to lock it in place and then continue until snug You...

Page 71: ...also that CO2 in air surrounding the cuvette is more likely to enter the Analysis gas stream if strong gradients exist For example suppose your CO2 control value is 390 mol mol 1 and the test locatio...

Page 72: ...af ontogeny reduced rates of metabolism can often be expected despite year round plant culture in artificial indoor environments Note that some physiological variables especially A gs stomatal conduct...

Page 73: ...Settings files are provided based on the Accessory selected later you will learn how to edit Settings files outside of the console on your own computer and then transfer those files to the console Pre...

Page 74: ...For response curves or in situations that require frequent large changes in CO2 levels this option is recommended because it settles near the set value very quickly within 1 2 minutes Exact reference...

Page 75: ...ot go away you should reduce the incoming RH until you get below 70 Fixed reference mb Allows you to choose a specific saturation partial pressure value of chamber air from 0 mb to dewpoint depending...

Page 76: ...No light unit RGBW Control Allows you to set your desired LED color distribution An individual color can be set to 100 or any color combination may be selected with a combined distribution of red gre...

Page 77: ...ntrol Leaf Temperature or Cuvette Temperature Enter a temperature value that is between 10 C below ambient to 15 C above ambient The absolute control range is between 0 45 C Ability to control at a st...

Page 78: ...ys the variables that will be shown and the numeric min max scaling or time scale Press the TAB key to move down to Graph1 Y Axis is the first dropdown list containing all available variables Again wi...

Page 79: ...in the Settings dialog Use Controls to establish system stability empty leaf chamber by altering CO2 H2O light factors temperature flow rate and leaf area Press Controls F3 to enter control mode and...

Page 80: ...d Leaf Area Options are identical to those described in Settings See Settings F2 on page 73 Controls Graph Set F5 Press Controls F3 Graph Set F5 to change your Graph View options You will find this es...

Page 81: ...atures a two variable scatter plot of A x PAR This graph captures a light curve with each vertical group of blue markers representing photosynthetic acclimation at subsequent increasing light levels X...

Page 82: ...r device alternatively referred to as memory stick or thumb drive into the USB port located at the back of the console Press Scan USB F7 to see the contents stored on the USB device only compatible xm...

Page 83: ...g Delete Int Files F6 You can also import data files back to Internal Memory for example to quickly review the data using Operations F1 View Saved F4 To move a copy of a data file from the USB Memory...

Page 84: ...rding Options Press Operations F1 Rec Options F2 to set up a recording session There are 3 options available Manual recording Normally used for individual leaf level gas exchange measurements Timed re...

Page 85: ...gin recording data you are automatically returned to the Operations screen The status bar indicates that you are now in Recording mode press Back F1 At this point you can use Graph Set to enter your p...

Page 86: ...es Use the Up or Down arrows to make the selection and press OK Accept the default filename or rename it and proceed back to Numeric or Graph Views screens as described above The status bar at the bot...

Page 87: ...ngs Settings F2 CFM Settings F7 must be set up and saved prior to starting the response in order to take effect There are multiple options available to create and edit your own response curve protocol...

Page 88: ...rve before you enter the specific changes you want to introduce independent variable at each successive Level Records per Level Decide how many data points you want to record at each Level Entering mo...

Page 89: ...ht intensity Light Intensity Enter a saturating light intensity held constant throughout the A Ci curve RGBW Enter your desired LED color distribution summing to 100 Press TAB to enter the table and u...

Page 90: ...measurement Gas exchange refers to gas exchange data that can be included as part of each fluorescence measurement If you previously selected CFM 3 PLC3 18x25 mm window or any combination of CFM 3 an...

Page 91: ...ired for plants that have been under high light and shorter periods for plants that have been in the dark or low light To determine the effective dark adaptation period you will need to identify the p...

Page 92: ...ady state fluorescence will be recorded after a photosynthesis measurement is recorded Enter the estimated Total Manual or Timed Repeated Records for the measurement session you will conduct For examp...

Page 93: ...ments Single Pulse Duration The time in seconds for the Single Pulse Duration saturating light to be applied Single Pulse Intensity The saturation pulse intensity 0 10000 mol m 2 s 1 Multi Pulse Measu...

Page 94: ...3 Diff Bal will help ensure that detectable Analysis gas differentials are real and not simply artifacts of unbalanced IRGA cells Be sure that CO2r is not changing at the time that you run Diff Bal Re...

Page 95: ...ture Leak around leaf chamber gaskets Exhausted chemicals particularly the molecular sieve Fluctuating CO2r Set Clock Press Operations F1 Set Clock F3 to view the system clock To change the date or ti...

Page 96: ...TAB to move to the data table use the Down arrow to scroll through the table The table column headings indicate its content which for practical reasons displays most but not all of the full xml data f...

Page 97: ...CIRAS 3 Operation Manual V 1 09 97 support ppsystems com F1 F3 F2 F4 F6 F5 F7 F8 F1 F3 F2 F4 F6 F5 F7 F8...

Page 98: ...for calibration purposes TIP All CIRAS 3 systems receive a thorough factory calibration before it is shipped and it features our innovative Auto Zero facility What does this mean You should never hav...

Page 99: ...ure to the REF IN gas port on the CIRAS 3 console as shown above We recommend using flexible tubing to easily connect to the gas port and a flow rate of 250 300 cc min Be sure to include a vent pipe b...

Page 100: ...AS 3 to avoid overpressure 3 Enter the H2O gas concentration of your calibration mixture in the H2O box and press Start H2O Cal F3 4 Monitor the H2Or and H2Oa values and when steady press Data Steady...

Page 101: ...ss is automated and you should see the CO2r value settle out just above 2000 mol mol 1 and the message calibration in progress just above the graph The system will also perform and Auto Zero If this p...

Page 102: ...d Diff Bals in advance to avoid disruptions during a response Press Store Diff Bal F4 to begin the process To begin enter the minimum and maximum ranges for both CO2 and H2O For instance if the workin...

Page 103: ...the Stored Diff Bal Calibration Screen for another attempt at the Stored Diff Bal Calibration If the new results are rejected and there was a previous set of Stored Diff Bal Coefficients labeled Old...

Page 104: ...ured offsets at each point should be less than 20 ppm and 0 5 mbar 2 Measured offsets should show a trend gradually increasing or decreasing over the six points 3 The computed Stored Offsets in the 3...

Page 105: ...the lower left hand corner of the display and the calibration process will begin If the calibration is successful a message test passed will appear as shown above in the lower left hand corner of the...

Page 106: ...R sensor in the same orientation to your light source i e sun Be careful not to shade either sensor 2 Enter the PAR value from your reference sensor in the Reference PAR Sensor field on the CIRAS 3 co...

Page 107: ...libration you can always press Restore Original Calibration F7 to restore the original factory calibration factors Diagnostics Press Diagnostics F6 The CIRAS 3 contains numerous sensors to measure CO2...

Page 108: ...tween 30000 and 55000 for CO2 Ref CO2 An H2O Ref and H2O An Zero F4 Press Zero F4 to show A D readings in Zero mode Values in the Zero column should be the highest values and in the range of 50000 300...

Page 109: ...ng OK In the table above you should see the entered value for Temperature setting C Temperature Control After entering a temperature above press the Tab key to place cursor in the Temperature control...

Page 110: ...uit In the table above the Analyzer flow Reference flow and IRGA flow setting should be close to your set value CO2 valve PWM Press Tab to place cursor into this box Enter 0 to turn off the CO2 valve...

Page 111: ...Battery voltage reading Battery voltage Displays the current voltage of the internal rechargeable Li ion battery pack Battery current Displays the current status of the internal rechargeable Li ion b...

Page 112: ...ration Chamber or CPY 4 Canopy Assimilation Chamber PAR Displays the measured PAR value mol m 2 s 1 from the sensor on the accessory if applicable Temperature 1 Displays the temperature o C from the s...

Page 113: ...to send it to the USB drive a USB thumb drive must be inserted into either USB1 or USB2 on the console A message similar to below will appear on the CIRAS 3 display Press OK to complete the transfer...

Page 114: ...t into the USB1 or USB2 slot on the CIRAS 3 console By default Yes is highlighted and can be selected by pressing OK to view both the currently installed firmware versions and available versions on th...

Page 115: ...AS 3 main console Air Flow Firmware associated with pumps and flow rates PLC Firmware associated with the PLC3 series leaf cuvettes IRGA Firmware associated with the optical bench infrared gas analyze...

Page 116: ...erased when installation is complete 3 Remove the USB thumb drive from console 4 Right click on cab file and ensure it is not Write protected 5 Double click on the cab file to execute the install Acc...

Page 117: ...stick provided by PP Systems into a USB port on your desktop PC or laptop computer The USB thumb drive is included with the CIRAS 3 spares kit 2 Navigate to the folder CIRAS3_PC_Utility_SW which cont...

Page 118: ...e is already installed on your desktop PC or laptop you MUST uninstall it prior to loading new versions PC Utility Operation To run this application double click on the CIRAS 3 icon on your desktop Th...

Page 119: ...where you can select create or edit response scripts which can then be easily transferred to your CIRAS 3 main console Gas Exchange Script Settings CFM 3 Script Settings Click the CFM tab at the top...

Page 120: ...ck File Save or Save As to rename it The next step would be to Export the new or updated script file to the CIRAS 3 main console The easiest way to do this is to export the files to a USB thumb drive...

Page 121: ...the location C Program Files x86 PP Systems CIRAS 3 PC Utility Settings on your computer and click OK This opens the Settings File window where you can select create or edit settings files which can...

Page 122: ...ess the Graph View tab under Accessory to set up the graphical screen The next step would be to Export the new or updated script file to the CIRAS 3 main console The easiest way to do this is to expor...

Page 123: ...the files 6 On the CIRAS 3 console click Settings F2 Transfer F3 7 Tab over to USB Memory Files arrow down to the file s and select them by hitting OK There should now be a check mark next to the file...

Page 124: ...first select View Remote Display in the CIRAS 3 PC Utility software A message will appear to Please connect a USB cable between your desktop and the CIRAS 3 before using this function If the USB cabl...

Page 125: ...are there is no need to wait for the Windows Mobile Device Center window just select OK in the original message window to continue Next two windows will appear On the left the initial remote window is...

Page 126: ...ating Systems In Window XP and prior versions you must download ActiveSync from the Microsoft site and install it to your PC in order to run this application Windows Vista Windows 7 Windows 8 and Wind...

Page 127: ...structions on how to replace the window Overview of Chlorophyll Fluorescence The Basics In basic terms chlorophyll fluorescence is light re emitted from the chlorophylls mainly chlorophyll a chl a in...

Page 128: ...dark adapted Fv Fm calculated maximum photochemical efficiency of PSII sample dark adapted Fm measured detector maximum F yield sample illuminated Fs measured detector steady state F yield sample illu...

Page 129: ...ng due to aggregate constitutive non regulatory processes equally applicable to puddle and antenna models Genty calculation NPQ G calculated non photochemical quenching due to down regulatory pH xanth...

Page 130: ...correlations based on unique plant and treatment considerations Also new is the use of calculated Fo Oxborough and Baker 1997 in the absence of Fo measured immediately following the application of far...

Page 131: ...Set Up At either the Numeric View or Graph View screens select Settings F2 You must first select the appropriate Settings File and Accessory as shown below Note Make sure that you select the appropria...

Page 132: ...entire or partial list of parameters provided above Raw Fluorescence refers to the instantaneous fluorescence counts that can be written to the data file from 3 seconds before to 3 seconds after the f...

Page 133: ...in the lower part of the screen under Saturating Light Fv Fm If selected you will need to allow the plant to dark acclimate prior to measurement If performing Fv Fm measurements we recommend doing so...

Page 134: ...ght adapted leaf sample The Multi Pulse duration and intensity settings up to 5 steps can be set in the lower part of the screen under Saturating Light PSII If this is selected a saturating pulse will...

Page 135: ...Pulse Duration The time in seconds for the Single Pulse Duration saturating light to be applied Single Pulse Intensity The saturation pulse intensity 0 10000 mol m 2 s 1 Multi Pulse Measurements Multi...

Page 136: ...counts Higher levels have better signal to noise while lower levels have poor signal to noise but have no actinic effect For example greater noise due to a lower modulating frequency can have a large...

Page 137: ...the above figure Fm is plotted against 1 Q At light intensities 1000 mol m 2 s 1 Fm can be seen as linearly correlated to 1 Q It has been suggested that this relationship allows us to extrapolate bac...

Page 138: ...sec per step with an intensity of 5000 4000 3000 2000 1000 mol m 2 s 1 5 Press Accept to accept the CFM Settings and then Accept again to return to the main menu 6 Start a measurement operation as de...

Page 139: ...Research in Photosynthesis IV 279 282 Earl H Ennahli S 2004 Estimating photosynthetic electron transport via chlorophyll fluorometry without Photosystem II light saturation Photosynth Res 82 177 186...

Page 140: ...milation rate CO2 flux or moles of CO2 unit area 1 unit time 1 Co is the CO2 concentration at T 0 and Cn is the concentration at a time Tn later A is the area of soil exposed and V the total system vo...

Page 141: ...dC dT b 2cT so at T 0 dC dT b 2 A comparison of b and cT gives an indication of the leakage Within the software cT must be less than 20 of b or the Non linear error message is given This is believed t...

Page 142: ...method for measuring soil respiration in the field Journal of Applied Ecology 18 221 228 Electrical and Pneumatic Connection between the CIRAS 3 and SRC 1 CPY 4 In order to use the SRC 1 and CPY 4 wi...

Page 143: ...n the black APA connector with the top middle of the Aux connector 2 Connect the SRC 1 and CPY 4 to one of the 15 pin sockets on the APA and connect the STP 1 Soil Temperature Probe to the other 15 pi...

Page 144: ...using the SRC 2 Soil Respiration Chamber Like the SRC 2 the CPY 5 Canopy Assimilation Chamber also connects electrically directly to the AUX port on the CIRAS 3 console Other than the electrical conne...

Page 145: ...choose here are normally your typical working options which in this case is closed system measurement of soil respiration or canopy assimilation Press TAB to move down to Accessory and select SRC 1 or...

Page 146: ...ontinuously Not applicable Esoil units g m 2 hr 1 mmol m 2 s 1 Default Not applicable FCO2 units g m 2 hr 1 mol m 2 s 1 Default Not applicable Transpiration units Not applicable g m 2 hr 1 mmol m 2 s...

Page 147: ...ear response especially at high assimilation rates Generally speaking if your rates are low we recommend using the linear fit For most measurements with higher rates the quadratic fit is normally reco...

Page 148: ...soil CO2 based on linear fit g m 2 hr 1 or mol m 2 s 1 Esoil Rate of change in evaporation g m 2 hr 1 or mmol m 2 s 1 RH Relative humidity based on Tsurface SRC 1 and SRC 2 Control Settings CO2 Max A...

Page 149: ...inside the CPY 4 CPY 5 mol m 2 s 1 Time Change in time during measurement sequence Seconds Tchamber Air temperature inside the CPY 4 CPY 5 o C Tsoil Soil temperature if STP 1 is used o C Calculated Da...

Page 150: ...end Graphical Data Display SRC 1 SRC 2 and CPY 4 CPY 5 The information that is included on the graphical display is dependent on user settings under Graph Set Settings F2 Graph Set F5 Measurement Sequ...

Page 151: ...The following will be displayed until the end of measurement which is determined by user settings of CO2 Max or Time Max The sequence can be aborted at any time by hitting Abort CPY SRC F6 Note data...

Page 152: ...0611_01 xml Data is output every 1 6 seconds during the measurement sequence and saved to the file that is displayed At the end of a measurement sequence during manual recording a message Sequence com...

Page 153: ...red data is output as follows Date Time mol mol 1 mol mol 1 mol mol 1 mb mb mb RecType ExcelTime CO2r CO2a CO2d H2Or H2Oa H2Od M 12 16 13 12 40 PM 390 00 390 10 0 10 11 80 11 90 0 10 mol m 2 s 1 mol m...

Page 154: ...ensor Measurement IR Infrared Thermometry Only available with the PLC3 Universal Leaf Cuvette EB Energy Balance Available with all PLC3 leaf cuvettes TH Thermistor Only available with the PLC3 Narrow...

Page 155: ...1 mb mb mb RecType ExcelTime CO2r CO2a CO2d H2Or H2Oa H2Od m1 12 16 13 12 35 PM m2 12 16 13 12 35 PM M 12 16 13 12 40 PM 390 00 390 10 0 10 11 80 11 90 0 10 m5 12 16 13 12 40 PM m4 12 16 13 1 54 PM m...

Page 156: ...raw F 0 4 50 IR LA CFM 3 UF Fv Fm 0 4 50 IR LA CFM 3 UF 0 4 50 IR LA CFM 3 UF phiPSII 0 4 50 IR LA CFM 3 UF FoP Fs F Fo Fm Fv FvFm FmP Fs phiPSII FoP FvP FvPFmP 05 562 1154 592 0 513 0 0 0 000 0 0 0...

Page 157: ...ed with photosynthesis measurement Under normal operating conditions with no errors reported this column should be empty m4 Data associated with a Fo measurement Note the FoP in the Status column m5 D...

Page 158: ...Time deltaTime CO2r deltaCO2 H2Or deltaH2O Tamb Tch M 41442 60043 0 597 4 0 20 8 0 0 0 M 41442 60044 1 6 597 5 0 20 7 0 2 0 0 M 41442 60046 3 2 597 8 0 20 7 0 2 0 0 o C mol m 2 s 1 mb g m 2 hr 1 or mo...

Page 159: ...ed leaf area cm 2 converted to m 2 V0 is converted above to cc sec 1 but displayed by CIRAS 3 as cc min 1 Transpiration Calculate transpiration rate E from the partial pressures of water vapor of the...

Page 160: ...e CIRAS 3 display Leaf Temperature Calculate leaf temperature Tleaf from the energy balance optional to IR sensor or thermistor method 3 1 From Parkinson 1983 the difference between air and leaf tempe...

Page 161: ...ing ew1 and fw1 we calculate Stomatal Conductance Calculate stomatal conductance gs 4 2 From Caemmerer Farquhar 1981 Eq B14 total leaf conductance is calculated as 4 3 Since 1 4 4 stomatal resistance...

Page 162: ...e CIRAS 3 display Intercellular CO2 Concentration Calculate CO2 concentration in the sub stomatal cavity Ci using the equation derived by von Caemmerer Farquhar 1981 6 1 The sub stomatal CO2 concentra...

Page 163: ...per unit leaf area mol m 2 s 1 ein Partial pressure of water vapor of air entering cuvette mb eout Partial pressure of water vapor of stirred cuvette air mb E Transpiration rate mmol m 2 s 1 es Satura...

Page 164: ...ation for Environmental Physiology Cambridge University Press Buck A L 1981 New equations for computing vapour pressure and enhancement factor J Appl Meteorol Vol 20 1527 1532 von Caemmerer S and G D...

Page 165: ...ecially will put a large drain on the battery especially when cooling temperatures well below ambient Old battery might be losing some juice over time and may require replacement I charged the batteri...

Page 166: ...cant is non indicating and should be replaced when replacing the Drierite in the same column The CO2 cartridge is slowly exhausting or missing The cartridge was put in use at least 1 day before and mo...

Page 167: ...soda lime Replace My CO2d readings are fluctuating Check your CO2r and CO2a readings If one of them is fluctuating this will result in a fluctuating CO2d and you should service the one that is fluctua...

Page 168: ...the Zero column Check the Drierite and replace My H2Or levels are reading lower than expected Exhausted H2O scrubber in the Zero column Replace the Drierite and Molecular Sieve My H2Or or H2Oa values...

Page 169: ...3 Check leaf cuvette gaskets and replace if necessary Cracked or missing O ring on the PLC3 pneumatic connector Replace and periodically lubricate the O rings with silicone grease See PLC3 Pneumatic...

Page 170: ...o C above ambient More than likely you are unable to cool the chamber to your set point as a result of high incident light or your batteries are getting low PAR Measurement and Control Why does my PA...

Page 171: ...iction in the gas circuit Open the battery compartment door and inspect the internal tubing for any kinked piping Also inspect for any pieces of tubing that may have slipped off one of the pumps or is...

Page 172: ...2 and select the recording type Manual Timed Response curves and create a data file and then hit Start F2 to begin a recording session Very important Always click End Recording F5 when using Manual re...

Page 173: ...form a manual Zero Z Diff Bal F7 Zero This is critical to ensure calibration stability and accuracy 10 Normal Running PLC Closed 10 No action required Indicates that the PLC3 Leaf Cuvette is in the cl...

Page 174: ...ysis gas circuit Check all gas connections and look for kinks or to see if a connection has been broken 88 Time Out on Diff Bal 88 The CO2r or H2Or concentration is fluctuating too much during DIFF BA...

Page 175: ...e common after a change in flow rate If the message does not disappear check for restrictions in the gas circuit associated with the ASU pump kinked piping 92 Zero too Low 92 Exhausted chemicals in th...

Page 176: ...rence Analysis On page 181 Also check that the Zero and CO2 H2O control manifolds are properly seated in their respective manifolds and all associated O rings are not pinched off or cracked Also check...

Page 177: ...y higher than the maximum reference CO2 recorded when you performed a Stored Diff Bal Calibration This is common when there is a change in desiccants after initial Stored Diff Bal Calibration Perform...

Page 178: ...n the door as shown below The only internal components that may require local user maintenance are as follows Li ion battery packs Air sampling pumps Reference and Analysis Hydrophobic filter Battery...

Page 179: ...with the measurement or graphical display on the LCD If you need to order a replacement battery pack please make sure that you are ordering the correct type as highlighted earlier Battery Removal If...

Page 180: ...es may build up over time within the pumps The risk of this situation from occurring can be minimized by regular pump cleaning with alcohol Typically the following symptoms are attributed to a worn or...

Page 181: ...ports on the pump and gently prying the pump out from the securing pump bracket Please note the gas in and out tubing to the pump To replace simply plumb the pump to the correct gas in and out tubing...

Page 182: ...is usually required Re Order Information Part Number Description 10127 1 Air Sampling Pump Thomas 10181 1 Air Sampling Pump Schwarzer If you need to order a replacement pump please make sure that you...

Page 183: ...d by separating from the gas tubing We recommend that for optimal operation that these filters are changed regularly per the following schedule Air Supply Unit Hydrophobic Filter Heavy use daily in cl...

Page 184: ...RAS 3 AIR IN port as shown below This assembly is supplied with a filter element 48 um blue Part Number STD556 as standard For severe dusty environments we recommend the filter element 10 um Yellow Pa...

Page 185: ...he Zero process the Drierite adds in a small bit of CO2 and the soda lime adds a small bit of H2O which is why Molecular Sieve desiccant is required After passing Zero air through the soda lime and Dr...

Page 186: ...moves CO2 from the air to achieve levels requested by the user This assembly also includes a water vapor equilibrator containing NAFION tubing which should not require replacement and is used to equil...

Page 187: ...ems For the latest MSDS on alternative types of soda lime please contact the manufacturer directly or contact PP Systems Take caution to wash your hands completely after handling soda lime Re Order In...

Page 188: ...e is not self indicating and there is no obvious way to see that it is exhausted It is therefore best to always change the Molecular Sieve when changing the Drierite in the ZERO column Molecular Sieve...

Page 189: ...seal the desiccant from room air This desiccant saturates very quickly in room air and if not properly stored it will cause it to go bad and subsequently affect CO2 readings and calibration To ensure...

Page 190: ...hould be checked to ensure that the O rings are seated correctly in their groove and that they are not trapped or pinched resulting in system leaks Re Order Information Part Number Description 30013 1...

Page 191: ...shown below Step 3 Insert small coin in notch in regulator and turn counterclockwise to remove inner fitting as shown below Step 4 Using small flat screwdriver remove red gasket seal and fit replaceme...

Page 192: ...oadways air conditioning ventilation systems individuals breathing etc We know that the typical ambient CO2 concentration is approximately 375 400 mol mol 1 To check the CO2 analyzers using ambient ai...

Page 193: ...re leaks are often discovered leading to fluctuations in CO2 and H2O readings Over time plant material can cause the gasket material to crack or even deform requiring replacement Leaf gaskets can easi...

Page 194: ...sult of a leak To help isolate the leak and to determine if the leak is associated with the CIRAS 3 console or the PLC3 we include a simple Leaf Cuvette Simulator Part No STD553 with each new system t...

Page 195: ...Gently blow around the absorber columns and the H2O equilibrator to isolate leaks PLC3 Leaf Cuvette Head Adjustment If the leaf cuvette head is not closing properly a minor adjustment can be made usi...

Page 196: ...a problem with any temperature measurements you are encouraged to get in direct contact with PP Systems The only replaceable sensor that may break or go missing is the Leaf Temperature Thermistor com...

Page 197: ...the resistance of the stomata to transfer of gas molecules For a thorough discussion of leaf external and internal resistances see e g P S Nobel 2009 Physicochemical and Environmental Plant Physiology...

Page 198: ...dirty filter paper or sealed on all 4 sides and discarded after a few uses The area dimensions of the sample plastic envelope shown below are 45 x 75 mm The cuvette upper and lower foam rubber gaskets...

Page 199: ...eaf chamber with a dark cloth PAR sensors read 0 You should observe a rapid rise in the cuvette water vapor differential H2Od followed by a short stability phase of perhaps 1 minute duration depending...

Page 200: ...ery similar but they are slightly different Each plate is held in place by 6 small Philips type screws Open the cuvette head to maximum position and using a long thin Philips screwdriver remove the to...

Page 201: ...replace with the plain glass window plate as shown here To ensure an air tight seal we recommend putting a slight smear of silicone grease under the head plate prior to fitting it to the leaf cuvette...

Page 202: ...nolime white to violet 1 0 kg STD008 Drierite 1 lb 30118 1 Filter Foam Gray CIRAS 3 30013 1 O ring 4 76 x 1 78 30013 19 O ring 20 8 x 2 4 10123 1 Absorber Cap Assembly 10121 1 CO2 H2O Control Absorber...

Page 203: ...nternal Battery Pack Part No 41526 1 STD551 Belt Pack Kit Battery Charger and Power Supply STD552 Power Supply Adapter CIRAS 3 Cables Data Storage STD545 USB Cable A Plug to 5p Mini B Plug 43034 1 USB...

Page 204: ...t Plate 25mm x 18mm Lower PLC3 6 20349 1 Gasket Plate 18mm Diameter Upper PLC3 6 20349 2 Gasket Plate 18mm Diameter Lower PLC3 6 10088 1 PLC3 6 U Plain Glass Window Assembly for use with CFM 10088 2 P...

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PP Systems CIRAS-3, Operating Manual

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