PP Systems CIRAS-3 Operating Manual
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PP Systems CIRAS-3 Operating Manual

Portable photosynthesis system
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CIRAS-3
Portable Photosynthesis System
Operation Manual
Version 1.09
2017 PP Systems. All Rights Reserved
th
7
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@ppsystems.com
URL:
www.ppsystems.com

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Summary of Contents for PP Systems CIRAS-3

  • Page 1 CIRAS-3 Portable Photosynthesis System Operation Manual Version 1.09 2017 PP Systems. All Rights Reserved 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@ppsystems.com URL: www.ppsystems.com...

  • Page 2: Table Of Contents

    Inspect desiccants ..........................16 Insert a fresh CO cartridge ......................... 17 Connect the PLC3 Universal 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 ..........................
  • Page 3 Power Supply Adapter ......................... 44 Battery Pack ............................45 Battery Pack Installation ........................46 Charging Batteries inside the CIRAS-3 Console ................. 47 CIRAS-3 Rear Console ........................... 48 USB Flash Drive Ports ......................... 48 Battery Charging Socket (EXT PWR) and LED ................... 49 Power ..............................
  • Page 4 Checking Stability - Before You Place a Leaf in the Chamber ............70 Survey Measurements – Some Tips ....................71 Additional Filtering in Dirty/Dusty Environments .................. 72 Section 7. Basic Functions - Viewing and Controlling CIRAS-3 ..............73 Settings (F2) ............................73 Settings Graph Set (F5) ........................78 Controls (F3) ............................
  • Page 5 Power (F5) ............................111 APA (F6) ............................112 Report (F7) ............................113 Firmware Upgrade ..........................114 Section 9. CIRAS-3 Console and PC Utility Software ................116 CIRAS-3 Console Software ........................116 Installation Instructions for Main CIRAS-3 Console ................116 Uninstall Instructions .......................... 116 PC Utility Software ..........................
  • Page 6 Electrical and Pneumatic Connection between the CIRAS-3 and SRC-1 / CPY-4 ......142 Electrical and Pneumatic Connection between the CIRAS-3 and SRC-2 / CPY-5 ......144 Configuring the CIRAS-3 console for measurement of Soil Respiration or Canopy Assimilation ..144 Settings (F2) ............................145 Do I Use Linear versus Quadratic ......................
  • Page 7 Photosynthesis Data ..........................153 Photosynthesis and Chlorophyll Fluorescence Data ................155 Closed System Operation Data ......................158 Summary of the Gas Exchange Equations Used in CIRAS-3 ............... 159 Mass Flow Equation ........................... 159 Transpiration ............................159 Leaf Temperature ..........................160 Saturation Vapor Pressure ........................
  • Page 8 Cuvette Gaskets ..........................193 Checking For Leaks Associated With the PLC3 ................194 PLC3 Leaf Cuvette Head Adjustment ....................195 PLC3 Pneumatic Connector ......................196 Environmental Sensors ......................... 196 Temperature ............................196 PAR ..............................196 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 9 Section 15. Consumables/Spares ......................202 Desiccants and Absorber Columns ....................... 202 Pumps & Air Filters ..........................202 O Control ............................ 203 Batteries & Power Supplies ........................203 Cables/Data Storage ..........................203 Leaf Cuvette Accessories ........................203 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 10: Welcome

    PLC 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 firmware, future software and firmware updates can be made locally without the need to return the system to our factory.

  • Page 11: User Registration

    Otherwise, damage may be caused which is not covered under our normal warranty policy. User Registration It is very important that ALL new users register with us. If you are a PP Systems’ user, please go to www.ppsystems.com and click on Customer Registration in the upper left hand corner.

  • Page 12: Service & Warranty

    PP Systems or an authorized agent for repair or replacement of the defective part(s). Prior to returning equipment to PP Systems for service, you must first get in contact with our Service Manager (service@ppsystems.com) to request a case number for reference and tracking purposes.

  • Page 13: Contact Information

    Please also note the following: · We strongly recommend using UPS “door to door” service for all returns. PP Systems is not responsible for any unnecessary shipping related charges caused by incorrect preparation of shipment documentation. If you have any questions regarding the return of your equipment please consult with PP Systems.

  • Page 14: Unpacking And Storage Of Your Equipment

    ACCOUNTED FOR. WE RECOMMEND THAT YOU RETAIN THE ORIGINAL PACKING FOR FUTURE USE. If you suspect that any of the items listed 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 location.

  • Page 15: Ciras-3 Tutorial & Basic Operation

    CIRAS-3 Tutorial & Basic Operation After being in business for over 30 years we have learned that one thing is for certain. Very few people have the time to read operation manuals from cover to cover. With that in mind we strongly encourage you to take the time to step through this quick and easy tutorial to learn about the general operation of the system.

  • Page 16: Let's Get Started

    We recommend charging the batteries the night prior to use. Connect the power supply adapter supplied 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 secure connection and that the internal batteries are being charged.

  • Page 17: Insert A Fresh Co 2 Cartridge

    CO O control column on the CIRAS-3 console. The empty soda lime column will ensure that ambient air is used for your reference air and the column will simply act as a smoothing volume.

  • Page 18: Connect The Plc3 Universal Leaf Cuvette To The Ciras-3 Console

    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 CIRAS-3 console. Be careful to align the arrow on the black signal plug with the top center console socket on the CIRAS-3 console.

  • Page 19: Power Up The Ciras-3 System

    Press the ON/OFF switch in the upper left hand corner on the back of the console. A blue ring around the switch should illuminate. After approximately 30 seconds the “Welcome screen” 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.

  • Page 20: Setting Up The Ciras-3 System

    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 Cuvette, 18x25mm window) and all associated settings, options and environmental controls for that accessory.

  • Page 21: Setting Up The Graphical Display For Data Plots

    So by this time you will have everything up and running with the proper system settings and will now be in a great position to establish a baseline to determine that everything is good to go. After about 3-4 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 22 Press Toggle View (F4) to view the graphical display which should look like this below after several minutes. Note the stability of the CO2r, CO2d and Flow. This display will be based on the settings you created in Graph Set (F5). CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 23: Let's Have A Look At The Environmental Controls

    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 flow rate and leaf area from this screen. This is ideal when you want to change any of the values quickly and easily for rapid measurements without having to go back to Settings.
  • Page 24 Controls (F3) as shown below. Let’s try this again making some additional changes to the environmental controls. Press Controls (F3) and tab from field to field making changes exactly as shown below. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 25: It's About Time We Start Taking Some Data On A Real 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 Operations (F1) > Rec Options (F2) to create a data file where all readings will be saved to. Data can be recorded manually (by default), timed or as part of a response curve.
  • Page 26 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 at 00 and count up from there (i.e. 01, 02, 03, etc.) unless changed by the user.

  • Page 27: Placing The Leaf Inside The Cuvette

    After approximately 45-60 seconds you should start to see the CO2d and H2Od values stabilize indicating that the leaf has reached equilibrium. At this stage the Photosynthesis Data should also be very stable as shown below. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 28 Assuming that you are seeing the same thing then now would be a good time to record a measurement. Press Record (F6) on the CIRAS-3 console or the “R” key on the PLC3 to record data and then proceed to record 5 more measurements on the same leaf. After the 5 record press End Recording F5.
  • Page 29 On the CIRAS-3 console press Operations (F1) > Rec 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 Flash Drive. You should now see the data file on your USB flash drive as shown below.
  • Page 30 It is now safe to remove the USB flash drive from the CIRAS-3. Most customers like to use Microsoft ® Excel to import and review data. We will do the same here. Insert your USB flash drive into a USB port on your PC.

  • Page 31: Quick Start

    CIRAS-3 main console (this will help to preserve the battery). 2. 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 (F1).
  • Page 32 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 If everything looks like this you should be good to go. Good luck! CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 33: Section 1. Technical Specification

    Data Storage 512 MB flash memory for programming and data storage. Unlimited data storage using USB thumb drives (memory sticks). Microprocessor Speed 800 MHz Display 7.0” WSVGA transflective, color LCD User Input 27 tactile keys CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 34 PLC3 Universal – 2 miniature, silicon photodiode sensors PLC3 Narrow and Conifer – 1 miniature, silicon photodiode sensor · Response: 400-700 nm · Range – 0-3000 µmol m · Precision – 10 µmol m CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 35 4.5 cm · PP Systems is a registered trademark of PP Systems, Inc. · PP Systems is continuously updating its products and reserves the right to amend product specifications without notice. · All brand names are trademarks of their respective owners.

  • Page 36: Section 2. What's New With Ciras-3

    Much has changed since we introduced the CIRAS-1 Portable Photosynthesis System back in 1992. What you will find in CIRAS-3 is not only a simple repackaging of existing designs and concepts, but in many cases a complete rethinking of both the form and function available through CIRAS-3’s hardware and software.
  • Page 37 · CIRAS-3 now has a Li-ion one-battery system (potential field operation time up to 12 hours), replacing the two NiMH batteries. PLC3 Series Leaf Cuvettes The new PLC3 Universal cuvette has several new improvements and features: ·...

  • Page 38: Changes To Ciras-3 Software

    The new user-friendly and intuitive software is easy to navigate, involving no programming or complicated software language. Basically, navigating CIRAS-3 menus is performed by way of clearly labeled function keys to move between menus and screens, then a TAB key moves you among entry fields, where selections are entered or selected from dropdown lists.
  • Page 39 SRC-1/SRC-2 Soil Respiration Chamber– soil collar volume/area input is a new Settings input, display and graph ∆CO2, FCO2, evaporation, Tsoil CPY-4/CPY-5 Canopy Assimilation Chamber– collar volume/area input is a new Settings input, display and graph ∆CO2, canopy Assimilation/Respiration, transpiration rate, Tchamber, PAR CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 40: Section 3. Summary Of System Design

    O gasses. CIRAS stands for Combined Infra-Red Analysis System. Its open-path design allows for continuous, unattended air sampling, as the pumps introduce fresh sample gas to the essential components, the IRGAs. CIRAS-3, like previous generations of CIRAS, has four non-dispersive IRGAs (Infra-red Gas Analyzers) – CO...
  • Page 41 CIRAS-3’s IRGAs are quite stable owing to their construction, calibration and thermal environment, but various circumstances can cause apparent changes over time. Some changes may require recalibration, although one of the strengths of CIRAS-3 is that recalibration is not a routine (annual) maintenance task. The factory calibration ranges of 0-2000 µmol mol and 0-75 mb water vapor are ideally suited for most typical applications.
  • Page 42 Reference and Analysis cell pair is real and not artificial. An overview of the gas circuit design of CIRAS-3 configured for leaf-level photosynthesis is shown in the schematic on the following page. Sample air, denoted as AIR IN, entering the console and is first pumped and its flow rate metered, then directly “conditioned”...
  • Page 43 REF and AN gases from source to IRGA are accounted for, and with only a very small delay in response time, the displayed console REF and AN readings are nearly instantaneous. In addition, Zero valves are periodically activated for Zero or Diff Bal functions, diverting the gas streams from their normal paths. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 44: Section 4. System Components And Assembly

    System Power Power Supply Adapter An AC power supply adapter (120/240 VAC / 50/60 Hz) is included with the CIRAS-3. If mains power is available the system can be operated continuously using the power supply adapter. This same adapter is also used to charge the internal battery packs.

  • Page 45: Battery Pack

    For field use the system is powered by internal, rechargeable battery packs. Up until June 2017 the CIRAS-3 was powered by a single, internal rechargeable 7.2V Li-ion battery pack (Aved) providing system operation up to 8 hours. Starting in July 2017 we began supplying instruments with two 7.2V (8.7 Ah, 63 Wh) Li-ion battery packs (Inspired Energy) improving system operation for up to 12 hours (actual operation time will vary depending on environmental control settings).

  • Page 46: Battery Pack Installation

    180 for more details. If you have an older CIRAS-3 system using the old battery pack (Aved type) and are interested in updating your system to the latest battery technology (Inspired Energy) please get in contact with PP Systems.

  • Page 47: Charging Batteries Inside The Ciras-3 Console

    When all 5 bars are dark it indicates that the pack is fully charged (see below). Please note that the CIRAS-3 also reports the state of the battery packs in the lower right hand corner of the display when the instrument is powered on.

  • Page 48: Ciras-3 Rear Console

    CIRAS-3 Rear Console The CIRAS-3 rear console contains all of the essential components including power, gas and electrical connections, USB ports, charger socket, desiccants and CO cartridge holder. USB flash Battery charging drive ports socket and LED Power Mini USB...

  • Page 49: Battery Charging Socket (Ext Pwr) And Led

    The Mini-PCB socket (PC) is a communication port for connection to a laptop or desktop computer and is commonly used with the PC Utility program for CIRAS-3 remote operation and display. A suitable USB cable is included with the CIRAS-3.

  • Page 50: Co 2 Cartridges

    CO cartridge you will observe a very rapid escape (and loud pop) of gas from the cartridge when you slowly unscrew the cartridge holder from the CIRAS-3. You will also observe that the cartridge will be quite cold. How do I determine the state of the CO...

  • Page 51: Gas Ports And Link Pipe

    CARTRIDGES ARE THE SAME AND SOME MAY EVEN CAUSE DAMAGE IF USED WITH THE CIRAS-3. They come in all different sizes, shapes and contents (some even have oil) and are commonly used for things like pellet guns, soda siphons, etc. If you have any questions whatsoever regarding the CO cartridges you are urged to get in contact directly with PP Systems.

  • Page 52: Co 2 /H 2 O Control Columns And H

    Go to Settings (F2) and set the CO2 reference to 0. The CO2r and CO2a values should drop close to 0 (± 2 ppm) after a few minutes with a 0 CO2d (± 0.5 ppm). CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 53: Plc3 Series Leaf Cuvettes

    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 connections are made and that the appropriate PLC is selected under Accessory in the Settings dialog.

  • Page 54: Plc3 Temperature Control

    We recommend the energy balance method. Temperature Control Type PLC3 Universal – Five control options are available: · Set leaf temperature · Track leaf to ambient · Cuvette temperature · Track cuvette to ambient · Disable temperature control CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 55: Lcd On Leaf Cuvette

    All PLCs include an LCD for display of parameters. Press the S button located on the cuvette open/close lever to toggle between displays to view additional parameters. Press R to record a measurement if in record mode. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 56: Par Measurement

    PLC3 Universal Leaf Cuvette PLC3 Conifer and Narrow Leaf Cuvette PARe PARe PARi PARi The PARi sensor will normally read about 10% lower than the PARe sensor due to attenuation of the cuvette window. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 57: Light Control (Optional)

    Please note. Maximum light intensity and range of temperature control is dependent on RGBW settings. The PLC3 Universal LED light unit is designed to mate quickly and easily with the PLC3 Universal leaf cuvette. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 58: Plc3 Narrow And Conifer Led Light Unit

    0-2000 µmol m (ranges are dependent on selection of red-green-blue-white LEDs). Caution: do not look directly at illuminated LEDs, even with the light unit set to lower intensity control levels. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 59: Chlorophyll Fluorescence Module

    Attachment and connection to the PLC3 Universal Leaf Cuvette is identical to that described above with the PLC3 Universal LED Light Unit. See PLC3 Universal LED Light Unit (RGBW) on page 57. The CFM-3 can also be used as an actinic light source for gas exchange measurements if required. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 60: Section 5. Ciras-3 Console Software

    Section 5. CIRAS-3 Console Software Overview The CIRAS-3 console software is the most user-friendly and intuitive software we have designed to date. All CIRAS-3 functions are accessed and implemented by the same easy-to-understand software structure – Settings, Controls, Recording, Data Transfer, Diagnostics, Calibrations and other useful functions. The CIRAS-3 Console software is the system’s command interface, based on function keys linked to first level...

  • Page 61: Basics Of Navigating Console Screens And Menus

    Several default setting files are included, representing the standard applications that can be run with CIRAS-3. Use the Arrow keys or Expand List (F4) to select PLC3 from the Settings File list. Press the TAB key to move to the next field, Accessory, and choose the appropriate cuvette window size, such as 18 x 25 mm shown above.

  • Page 62: Numeric View Of Data And Control Variables

    Numeric View of Data and Control Variables As you familiarize yourself with CIRAS-3 you will begin to establish your own preferences of how and what you would like to see on the console for differing circumstances of data collection and various applications.
  • Page 63 O Analysis (mb) H2Od O Differential (mb) PARi PAR internal (µmol m PARe PAR external (µmol m Relative Humidity inside leaf chamber (%) Tamb Temperature ambient ( Tcuv Temperature in cuvette ( Tleaf Leaf temperature ( CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 64 Leaf to air vapor pressure deficit (kPa) Photosynthetic water use efficiency (mmol CO Environmental Controls Reference (µmol mol O Reference (mb) PARi PAR internal (µmol m Flow Cuvette flow rate (cc min Tleaf Temperature control method Area Leaf Area (cm CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 65 Photochemical quenching, lake antenna model (Kramer) ϕNO Non-photochemical quenching, non-regulatory (Kramer) ϕNPQ-K Non-photochemical quenching, down-regulatory (Kramer) ϕfD Non-photochemical quenching, non-regulatory, lake or puddle models (Genty, Hendrickson) ϕNPQ-G non-photochemical quenching, down-regulatory lake or puddle models (Genty,Hendrickson) CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 66: Section 6. Startup Routine And System Stability Checks

    Before You Power Up CIRAS-3 The time required to be up and running from when you power on CIRAS-3 to when you make your first measurement is reasonably short. Much of the pre-operation phase depends on the how well you maintain chemicals.

  • Page 67: Startup And Warm Up

    (temp) should be close to ambient temperature °C. Note that the initial temperature depends on the ambient temperature where CIRAS-3 is located. Warm up time to the required 55 °C 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 environment.

  • Page 68: Co 2 Cartridge Status

    Assume that we want to enter the Numeric View screen, press Continue (F1). The Numeric View screen will appear as below (at this point CIRAS-3 is in its warm up phase, so live data is not displayed): When the warm up phase is completed you will begin to hear a clicking sound from the CO mixer valves, switching at a rate of 4 Hz.
  • Page 69 CO cartridge will be low and it is safe to change out. If the CIRAS-3 is operating for just a short period of time throughout the day (i.e. less than 4 hours in total) and at approximate ambient CO concentration (i.e.

  • Page 70: Changing A Co 2 Cartridge

    24 hours after it was inserted and with the CO regulator assembly fitted to the CIRAS-3 console. If you do, the pressurized cartridge will make a loud popping noise and the pressure may cause the internal tubing...

  • Page 71: Survey Measurements - Some Tips

    Approach the leaf from its side margin, not the leaf tip, to avoid crushing it in the rear section of the leaf chamber. Try to orient the cuvette to the leaf and do not severely twist the petiole. Use a tripod if CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 72: Additional Filtering In Dirty/Dusty Environments

    Additional Filtering in Dirty/Dusty Environments If working in extreme dirty/dusty environments, we strongly recommend using the external air in filter (included in your CIRAS-3 spares kit). It easily connects to the CIRAS-3 “AIR IN” port as shown here. CIRAS-3 Operation Manual V. 1.09...

  • Page 73: Section 7. Basic Functions - Viewing And Controlling Ciras-3

    Controlling CIRAS-3 Settings (F2) Settings are essentially defined as operational environments that are recreated each time that CIRAS-3 is powered on. The options that you choose here could be your typical working options in many cases, but it is also likely that you will need to change and adapt for different leaf samples, species and environmental conditions, as well as for imposing experimental conditions on the leaf.
  • Page 74 (within 1-2 minutes). Exact reference air. The CO supplied to the leaf chamber from CIRAS-3’s internal CO source will be within 2 µmol mol from the actual set value within the control range of 0-2000 µmol mol...
  • Page 75 H Please Note. It is very easy to increase the humidity of the air above ambient if required. Please contact PP Systems for the application note that was prepared for this feature. CIRAS-3 Operation Manual V. 1.09...
  • Page 76 Remember that the CIRAS-3 controls water vapor, chamber humidity and VPD through the desiccants and not by increasing or decreasing flow rate.
  • Page 77 PP Systems can ®...

  • Page 78: Settings Graph Set (F5)

    Graph1 as described above and select None for both Graph2 and Graph3, you will see a single large graph. Select None for Graph3 to display two graphs only, etc. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 79: Controls (F3)

    Press Controls (F3) to enter control mode and make changes then press Accept (F2). The status bar in the lower left corner will display the message “Updating Environmental Control values…” and the plot data displayed in Graph View will refresh. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 80: Controls Graph Set (F5)

    Toggle View if there is a variable that you would like to monitor, but it is not currently displayed in Graph View. One of many possible configurations of Graph View can be seen below with the control steps of an A/Ci curve displayed in the upper graph. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 81 The second example (below) features 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 axis) between 0 and 2000 µmol m CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 82: Reviewing And Transferring Data Files

    Reviewing and Transferring Data Files Transfer Data (F6) Retrieving your .xml data files from CIRAS-3 internal memory is a routine operation that is accomplished with a few easy steps. Importantly, we allow two-way transfer of three file types: data, settings and scripts.
  • Page 83 USB Memory by pressing Delete Ext Files (F5). To transfer CIRAS-3 settings files, from the Numeric or Graph View screens select Settings (F2) > Transfer (F3), then follow the instructions above. To transfer CIRAS-3 response curve scripts, press Operations (F1) >...

  • Page 84: Section 8. Operations

    Select the desired recording option at the top of the screen by using the Left or Right arrow keys – the first option is Manual recording. For most leaf gas exchange measurements in the field, this method of recording is most common. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 85 The next field is Start recording data file: where a default filename using the serial number of the CIRAS-3 and current date appears, e.g. 0000_20130131_00. The date format is yyyymmdd. Each new data file you create will be sequentially numbered, beginning with that day’s date, such as 0000_20130131_00.

  • Page 86: Timed Recording

    The status bar at the bottom of the screen will indicate Next record in mm:ss, counting down to the next automatic recording interval. Timed recording continues indefinitely at the selected recording interval unless paused. This can introduce unnecessary and irrelevant data into your data file. To suspend CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 87: Response Curves

    There are multiple options available to create and edit your own response curve protocols to automatically run response curves. This can be done on the CIRAS-3 Console, on a computer using the PC Utility Software supplied with the system and also with any external xml editor. You can also find Help on how to edit these files outside of the console on your own computer, and then transfer the files to the console.
  • Page 88 The following selections are available: Response Curve Scripts Editor Response Script Several scripts are included with CIRAS-3 by default. You can use them as templates to edit on the console, or export them for external editing and renaming. Level These fields are the starting and ending points of your response curve, representing the total number of steps.
  • Page 89 Press CFM Settings (F6) to access settings associated with chlorophyll fluorescence measurements (only if you have purchased the CFM-3 Chlorophyll Fluorescence Module). Also make sure that you have this accessory properly selected under “Settings File” and “Accessory” in Settings. See Settings (F2) page 73. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 90 If you previously selected CFM-3, Chlorophyll Fluorescence Module, the Calc Fluorescence box will be checked (enabled) and Photosynthesis will be unchecked (disabled). Both will be grayed out, indicating that only fluorescence data will be written to the data file. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 91 This will be influenced by your choice of Measurement Recording mode (Manual, Timed, or Response Curve). None. If selected, there will be no chlorophyll fluorescence measurements performed after a photosynthesis measurement has been recorded. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 92 This defines the final measurement to be recorded after the last Fluorescence photosynthesis measurement. Measurement None. If this is selected, there will be no concluding chlorophyll fluorescence measurement and the sequence will terminate after the last photosynthesis measurement. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 93 Settings (F2) on page 73 and that you perform a stored Diff Bal Store Diff Bal on page 102). This will allow you to execute faster response curves without Diff Bal interruptions between levels. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 94: Z-Diff Bal (F7)

    Zero and Diff Bal will otherwise be performed automatically at regular 31 minute intervals by CIRAS-3. Diff Bal will help ensure that detectable Analysis gas differentials are real, and not simply artifacts of unbalanced IRGA cells.

  • Page 95: Set Clock

    Use the Tab key to move through the selections and when finished press Accept F2. It is very important to have the correct date and time set on the CIRAS-3 as the default data files use this information as part of the file name. See Manual Recording on page 84.

  • Page 96: View Saved (F4)

    Press Operations F1 > View Saved (F4) to view data stored on internal memory or on the USB. This feature of CIRAS-3 allows almost immediate review of recorded data on the console, in both tabular and graphical formats. To enter the View Saved Data screen press Operations (F1) and View Saved (F4).
  • Page 97 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 98: Calibration

    IRGA calibration and long term stability for many, many years. It is important that you properly maintain the desiccants to ensure that they are fresh in order for the CIRAS-3 to perform Auto-Zero. Simple, periodic checks of all CO...

  • Page 99: Calibration Setup

    1. Ensure that all chemicals are fresh. 2. Connect the CO calibration mixture 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.

  • Page 100: H 2 O Calibration

    1. Ensure that all chemicals are fresh. 2. Connect the H O calibration mixture 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.

  • Page 101: Find Max C

    Find Max C Press Find Max C (F3). This process determines the maximum CO level that can be achieved with the CIRAS-3. This should be performed prior to using “Approximate reference air” for CO reference (See Settings (F2) for optimal control. Prior to starting this process, make sure that you have inserted a fresh cartridge and that all chemicals are fresh.

  • Page 102: Store Diff Bal

    Stored Diff Bal process. When complete and ready, press Start (F2). The process is automated taking approximately 20 minutes to complete beginning with an initial Zero before proceeding through 6 levels. The status bar for each level will be highlighted when complete as shown below. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 103 The user can choose to Accept the results (OK then Accept (F4), which will allow the new Stored Diff Bal Coefficients to be used when the CIRAS-3 is in Stored Diff Bal mode. The user can also choose to reject the results (OK then Cancel (F1), and return to the Stored Diff Bal Calibration Screen for another attempt at the Stored Diff Bal Calibration.
  • Page 104 This message is more relevant when performing measurements on live plants when chamber humidity can get quite high depending on the environmental conditions and state of the plant. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 105: Led Calibrate

    It normally takes approximately 4-5 minutes for this automated calibration to take place. If the calibration is not successful and you receive a “test failed” message in the lower left hand corner, contact PP Systems. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 106: Par Calibrate

    PAR sensor (± 2%) then there is no need to recalibrate. If it is outside this range, press Calibrate External Sensor (F2). 5. A new calibration factor (New factor) will be displayed and the Observed PAR should now match the Reference PAR Sensor. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 107: Diagnostics

    If you are unsure about your calibration, 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 CO O, leaf environment, signals from external probes and gas flow through the instrument. The Diagnostics function collects the signals from each of these sensors and summarizes them.

  • Page 108: Plc (F3)

    Reset Zeros (F7) Press Reset Zeros (F7) to reset the stored Zeros. PLC (F3) Press PLC (F3) to view readings associated with the PLC Leaf Cuvette. To further test temperature control settings, press Temperature (F2). CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 109 Note that the box will be empty again after hitting OK. In the table above you should see the entered value for “Temperature control mode”. General (F3) Simply refers to the opening dialog showing readings associated with the PLC3. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 110: Flow (F4)

    32000 to open the valve completely. Values that are in between 0 and 32000 are based on the currently set H O control value. When the H valve is set to 0 or 32000, there should not be any clicking of the H O valve. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 111: Power (F5)

    Press Power (F5) to view readings associated with the system power. Power Readings External voltage Displays the voltage from an external power source (i.e. CIRAS-3 AC Adapter/charger). When the CIRAS-3 power supply adapter is connected to the console EXT/PWR socket, this should read approximately 15V. When disconnected, it should read 0.00V...

  • Page 112: Apa (F6)

    C) from the sensor on the accessory (if applicable). Our latest SRC-2 Soil Respiration Chamber and CPY-5 Canopy Assimilation Chamber (introduced in February 2016) can connect directly to the 4 pin “AUX” connector on the CIRAS-3 console (No APA required). CIRAS-3 Operation Manual V. 1.09...

  • Page 113: Report (F7)

    CIRAS-3 display: Press OK to complete the transfer. The file will be saved as a .xml file which can then be emailed directly to PP Systems for further analysis to assist in troubleshooting and diagnosis. CIRAS-3 Operation Manual V. 1.09...

  • Page 114: Firmware Upgrade

    “OK” to view both the currently installed firmware versions and available versions on the USB thumb drive. If you have not yet inserted the USB thumb drive into the CIRAS-3 console, you can do so now and then press Scan USB (F7) to view the available files. To upgrade or downgrade (depending on your requirements) to a new firmware version for a particular CIRAS-3 module, arrow to the module, press “OK”...
  • Page 115 IRGA – Firmware associated with the optical bench (infrared gas analyzers) · APA – Firmware associated with the Auxiliary Probe Adapter (APA) If you have any questions related to firmware compatibility, please get in direct contact with PP Systems. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 116: Section 9. Ciras-3 Console And Pc Utility Software

    Installation Instructions for Main CIRAS-3 Console 1. Insert the USB thumb drive (memory stick) provided by PP Systems into the USB port on the CIRAS-3 main console (we recommend USB slot 2). The USB thumb drive is included with the CIRAS-3 spares kit.

  • Page 117: Pc Utility Software

    The CIRAS-3 PC Utility Software is provided as a “Setup.exe” file and a MSI file named “Ciras3_PC_Utility_vxxx.msi”. 1. Insert the USB thumb drive (memory 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.

  • Page 118: Pc Utility Operation

    If the CIRAS-3 PC Utility software 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. The following should be displayed.

  • Page 119: Create/Edit Response Scripts

    Click on File>Open Scripts Folder, browse to the location C:\Program Files (x86)\PP Systems\CIRAS-3 PC Utility\Response on your computer, and click OK. This opens the Script window where you can select, create or edit response scripts which can then be easily transferred to your CIRAS-3 main console.
  • Page 120 Click the arrow button to expand the dropdown list at the Script File item. Edit the script just as you would if you were working from the CIRAS-3 Console. Then click 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: Create/Edit Settings Files

    Settings File and Accessory. Edit the script just as you would if you were working from the CIRAS-3 Console. You can also click on the Graph View tab for graph settings. Then click File >Save, or Save As to rename it.
  • Page 122 Press 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 export the files to a USB thumb drive.

  • Page 123: Remote Display

    Now the file is available for use on the CIRAS-3 console. Remote Display This feature allows the user to view all screens of the CIRAS-3 using an external device such as a PC computer or projector. This can be very useful when presenting information to a large group or for teaching applications.
  • Page 124 To start remote viewing of a CIRAS-3 console on an external device, 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”.
  • Page 125 Next, select click the CIRAS-3 PC Utility to attain focus on that window and select OK in the original message window. If you have previously connected the USB cable before starting the software, there is no need to wait for the Windows Mobile Device Center window just select OK in the original message window to continue.
  • Page 126 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 Windows 10 Operating Systems The Windows Mobile Device Center (WMDC) replaces ActiveSync. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 127: Section 10. Measuring Chlorophyll Fluorescence With Cfm-3

    Rev. Plant Biol. 59: 89-113 When performing measurement of chlorophyll fluorescence you MUST make sure that the glass window (supplied by PP Systems) is fitted to the leaf cuvette head. This window will have the letter “P” etched in the lower left hand corner.
  • Page 128 - non-photochemical quenching, correlates to heat dissipation via xanthophyll cycle and PsbS protein calculated - photochemical quenching coefficient, correlates to proportion of open PSII Ꞌ (Kramer calculation) reaction centers in lake antenna mode, requires F CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 129: Calculations Used For Chlorophyll Fluorescence Parameters

    �� �� �� ′ �� �� � ∙ � = �� ∙ NPQ = �� ′−�� �� ′ �� ′ �� �� �� �� �� �� ′−�� ′ �� �� �� �� �� �� CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 130: Chlorophyll Fluorescence Measurements - Setup And Operation

    Chlorophyll Fluorescence Measurements – Setup and Operation With CIRAS-3 there is a new option available to record complete fluorescence measurement sequences with or without combining simultaneous photosynthesis measurements. We have also included updated calculated fluorescence parameters, representing both lake and puddle models of PSII reaction centers - their detailed descriptions and calculations are provided above.

  • Page 131: Cfm-3 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 appropriate PLC3 Universal window size (Under Accessory) used for chlorophyll fluorescence measurements. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 132: Cfm-3 Settings

    If you previously selected CFM-3, PLC3 18x25 mm window (or any combination of CFM-3 and PLC3 cuvette window), the Calc Fluorescence box will be checked and Gas exchange will be checked (combined fluorescence/gas exchange enabled). CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 133 20 minutes, since longer dark adaptation periods did not result in higher F values. Note that prior light exposure (intensity, duration) significantly affects the minimum effective dark adaptation period required to fully re-oxidize (open) PSII photochemistry in the leaf sample. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 134 None. If this is selected, there will be no concluding chlorophyll fluorescence measurement and the sequence will terminate after the last photosynthesis measurement. FoP (Fo’). If selected, far-red light will be applied to the leaf sample. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 135: Cfm-3 Controls

    However, some active controls and functions are available for sample calibration and to make slight adjustments prior to or during measurements. At either the Numeric View or Graph View screens select Controls (F3) > CFM Control (F7). The following selections are available: CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 136 CFM Settings or CFM Control. Mod Lt Off (F6) and Mod Lt On (F7) toggle the modulating lights off or on. After making changes press Back (F1) to return to the Controls dialog and Accept (F2) to finalize the modifications. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 137: Measurement Of Fm' With Ciras-3

    Under high actinic light conditions, Fm’ measured using a single saturation pulse may be underestimated due to the rapid turnover rate of PSII reaction centers. The Multi-Pulse sequence with CIRAS-3 (Console software V. 1.08 and above), based on a method developed by Earl et al. (2004), allows for a more accurate estimate of Fm’...
  • Page 138 6. Start a measurement operation as described in previous sections of the manual. Our testing of CIRAS-3 CFM Multi-Pulse function on light-adapted, fully expanded tobacco leaves suggest that 5 saturating pulses at widely-spaced Q’ intensities (for example, 5000, 4000, 3000, 2000, 1000 μmol m...
  • Page 139 Loriaux SD, Avenson TJ, Welles JM, McDermitt DK, Eckles RD, Riensche B, Genty B (2013) Closing in on maximum yield of chlorophyll fluorescence using a single multiphase flash of sub-saturating intensity. Plant Cell Environ 36: 1755-1770 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 140: Section 11. Closed System Measurements

    Soil CO Efflux and Net Canopy CO Flux The SRC-1 and SRC-2 Soil Respiration Chambers can be used with the CIRAS-3 Portable CO Gas Analysis System for closed system measurement of soil CO efflux. The CPY-4 and CPY-5 Canopy Assimilation Chamber can also be used with the CIRAS-3 for closed system measurement of net canopy CO flux.

  • Page 141: Fco Units For Measurement Of Soil Co Efflux

    Time Simulated Soil Respiration Measurements With the CIRAS-3 software a quadratic relationship (y = a + bx + cx ) is fitted between the cuvette concentration (C=y) and time (T=x) from the start of measurement. Note that there is a delay after the chamber is first placed on the soil to allow for the establishment of stable gradients before the measurements begin.

  • Page 142: References

    In order to use the SRC-1 and CPY-4 with the CIRAS-3, an Auxiliary Probe Adapter (APA) is required. The APA connects electrically to the CIRAS-3 via the 4 pin socket labeled “AUX” in the lower left hand corner of the CIRAS-3 console. The SRC-1 and CPY-4 (and STP-1 Soil Temperature Probe if used) connect to either of the 15 pin sockets on the other end of the APA.
  • Page 143 “AIR OUT” which is only used when using the leaf cuvettes with the CIRAS-3. 1. Connect the 4 pin plug on the APA to the “Aux” socket on the CIRAS-3 console. Line the arrow up on the black APA connector with the top middle of the “Aux” connector.

  • Page 144: Electrical And Pneumatic Connection Between The Ciras-3 And Src-2 / Cpy-5

    PP Systems introduced the SRC-2 Soil Respiration Chamber and CPY-5 Canopy Assimilation Chamber in March 2016 for use with the CIRAS-3. Both can connect electrically directly to the “AUX” port on the CIRAS-3 console (Auxiliary Probe Adapter not required). All pneumatic connections are identical as described in the previous sections.

  • Page 145: Settings (F2)

    Settings (F2) Settings are essentially defined as operational environments that are recreated each time that CIRAS-3 is powered on. The options that you 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 SRC-2 Soil Respiration Chamber or CPY-4 or CPY-5 Canopy Assimilation Chamber.
  • Page 146 Also, it is important to take note of the measurement units that you have selected for Soil Evaporation, FCO2, Transpiration and Assimilation, Respiration for later data analysis. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 147: Do I Use Linear Versus Quadratic

    Do I Use Linear versus Quadratic The CIRAS-3 system automatically collects data based on both a linear or quadratic fit for the assimilation data. In the past quadratic fitting was most popular but at the request of some customers we have now also introduced a linear fitting.
  • Page 148 C). The default value is 25 but this should be set to your actual surface temperature for accurate results when using the SRC-1. This is not displayed when using the SRC-2 and Tsoil is replaced with Tsurface. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 149 Relative humidity based on Tsurface (%). Water use efficiency (Assimilation/Transpiration). Note that WUE can only be calculated if the Transpiration Units are set to mmol m Assimilation, Respiration units set to µmol m under Settings. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 150: Measurement Sequence

    1. Begin CPY/SRC 2. Hold Chamber in Air to Flush – Data collection begins in x Sec 3. Position Chamber on Soil 4. Chamber equilibrating 5. Data Collection Started 6. Sequence complete. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 151: Initial Test Measurement Sequence

    When you are happy with the named data file, press Start (F2) to begin the measurement sequence and then Back (F1) to the Numerical or graphical screen. Press Begin CPY/SRC (F6) to begin measurement sequence. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 152 At the end of a measurement sequence during manual recording, a message “Sequence complete. Press F6 to start a new sequence.” appears in the status bar. Additional measurements can be recorded by pressing Begin CPY/SRC (F6) and to end recording, press End Recording (F5). CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 153: Section 12. Data Output

    Photosynthesis and Chlorophyll Fluorescence Data · Closed System Data (Soil Respiration and Canopy Assimilation) Photosynthesis Data When one of our leaf chambers (Universal, Conifer, Narrow) is used with the CIRAS-3 for measurement of photosynthesis only, the stored data is output as follows: µmol µmol µmol...
  • Page 154 CFM-3 Chlorophyll Fluorescence Module Ambient. No light unit in use. PLC3 Used PLC3 Universal Leaf Cuvette PLC3 Conifer Leaf Cuvette Ambient. No light unit in use. Analyzer only. Probe (Accessory) PLC3 Universal Leaf Cuvette with CFM-3 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 155: Photosynthesis And Chlorophyll Fluorescence Data

    Photosynthesis and Chlorophyll Fluorescence Data When our PLC3 Universal Leaf Cuvette is used with the CIRAS-3 for measurement of photosynthesis and/or chlorophyll fluorescence, the stored data is output similar to the following (May vary slightly depending on measurement configuration): µmol µmol...
  • Page 156 665 0.359 0.454 phiNO phiNPQK phifD phiNPQG 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 10.332 0.638 0.638 0.680 0.520 0.449 0.305 0.449 0.338 15.078 0.792 0.198 0.112 0.675 0.548 0.093 0.576 0.369 CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 157 Data associated with a ϕPSII-SP measurement. Note the “phiPSII-SP in the Status column. Data associated with Fs (fluorescence signal). Note the “Fs” in the Status column. Data associated with a ϕPSII-MP (Apparent Fm’) measurement. Note the “phiPSII-MP in the Status column. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 158: Closed System Operation Data

    Closed System Operation Data When the SRC-1/SRC-2 Soil Respiration Chamber and CPY-4/CPY-5 Canopy Assimilation Chamber are used with the CIRAS-3, the stored data is output as follows (23 columns): µmol µmol mol Date/Time Seconds RecType ExcelTime deltaTime CO2r deltaCO2 H2Or...

  • Page 159: Summary Of The Gas Exchange Equations Used In Ciras-3

    Mass Flow Equation Calculate the mass flow of air (W) entering the cuvette per unit leaf area (1.1) The CIRAS-3 mass flowmeter is calibrated to read the volume flow (V ) at 0 °C and 1013.25 mb. The Ideal Gas molar volume is 22.414 L mol at 0 °C and 1013.25 mb (STP).

  • Page 160: Leaf Temperature

    H is calculated from the photon flux incident on the cuvette (I), taking into account the ratio of infra-red to PAR in the light source, transmission through the cuvette window (Trans), and reflection/absorption by the leaf: (H = I x Trans). CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 161: Saturation Vapor Pressure

    �� � = × ���� −�� −�� �� �� �� �� Net Photosynthesis Determine the rate of net photosynthesis (A) from the difference between CO concentrations entering ) and exiting (C ) the cuvette CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 162: Intercellular Co 2 Concentration

    − �� ) × ��� + ( �� × �� ) � ������ ���� ������ CIRAS-3 calculates and displays the CO difference (C ). As relates to the calculated values in the CIRAS-3 display: = ( ������ ) = ������...

  • Page 163: Physical Constants Used In Equations

    µmol m Total conductance to CO transfer mmol m concentration of sub-stomatal cavity µmol mol * Detected by IRGAs, temperature and pressure corrected, effects of foreign gas broadening (water vapor effects) on measurement corrected. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 164 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. Farquhar 1981. Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves. Planta, Vol. 153:376-387. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 165: Section 13. Troubleshooting & Diagnosis

    The EXT/PWR indicating LED on the CIRAS-3 console is flickering It is possible that the CIRAS-3 was not powered off when the battery was extremely low and it continued to drain beyond normal levels. If this happens the batteries may require a longer charging period to get back to full charge status.

  • Page 166: Co 2 Measurement And Control

    Check that both absorber column assemblies are firmly fitted to the CIRAS-3 console and check all “O” rings to ensure that they are all firmly seated and not pinched off or cracked. · Did you store the CIRAS-3 console in the black transport case with a partially pressurized CO cartridge? See Storage on page 14.
  • Page 167 My CO2d readings are always reading positive even with an empty cuvette and the head closed · You most likely stored your CIRAS-3 in the black transport case with a pressurized CO cartridge. If so you will need to allow the system to equilibrate for a period of time before proceeding with measurements.

  • Page 168: H 2 O Measurement And Control

    Usually this is associated with the absorber columns and the result of a recent desiccant change. Check that both absorber column assemblies are firmly fitted to the CIRAS-3 console and check all “O” rings to ensure that they are all firmly seated and not pinched off or cracked.

  • Page 169: Temperature Measurement And Control

    Usually this is associated with the absorber columns and the result of a recent desiccant change. Check that both absorber column assemblies are firmly fitted to the CIRAS-3 console and check all “O” rings to ensure that they are all firmly seated and not pinched off or cracked.

  • Page 170: Par Measurement And Control

    My PARe readings do not seem accurate · The sensor likely requires recalibration. Check the calibration against another PAR sensor that you trust and believe to be calibrated. Recalibrate if necessary. See PAR Calibrate on page 106. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 171: Flow Control

    If that does not get it up and running and you are properly connected it likely means you have a seized pump and it requires replacement. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 172: Data Management

    You likely saved your data to the USB Flash Drive (external memory) by mistake. Not a big problem. Put the USB flash drive into the USB1 or USB2 ports on the back of the CIRAS-3 console and transfer it to internal memory if you want to keep a back-up of the file on the CIRAS- 3 (Operations (F1) >Rec Options (F2) >...

  • Page 173: Status Codes Displayed On The Ciras-3 Lcd

    Status Codes Displayed on the CIRAS-3 LCD From time to time the CIRAS-3 may send a status code (message) to either A) recommend that the user perform a certain task or B) to report a suspected problem. Some messages that get sent include just the Code or the Description (with code) as shown below.
  • Page 174 5-6 seconds perform a manual Diff Bal (Z-Diff Bal F7) > Diff Bal). If problem persists contact PP Systems. Also ensure that all desiccants are fresh and that the absorber columns are firmly seated in their respective manifolds.
  • Page 175 If the message does not disappear after 5-6 seconds perform a manual Diff Bal (Z-Diff Bal F7) > Zero). If problem persists contact PP Systems. Also ensure that all desiccants are fresh and that the absorber columns are firmly seated in their respective manifolds.
  • Page 176 Analysis Temperature > 65° [98] IRGA temperature has exceeded the normal 55 indicating a thermostat failure. Contact PP Systems. Analysis Temperature < 50° [99] IRGA temperature not reaching the normal 55 indicating a thermostat failure. Contact PP Systems. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 177: Other Status Codes/Messages

    Divide by Zero Possible corruption of system data pointers or calculation error. Download any stored data from internal memory and then clear the internal memory. If problem persists contact PP Systems. Stored DIFF BAL CO2 out of range The maximum reference CO...

  • Page 178: Section 14. Routine Maintenance

    Hydrophobic filter Battery Pack (Li-ion Battery) Up until June 2017 the CIRAS-3 was powered by a single, 7.2V Li-ion battery (Manufacturer: Aved) which is capable of delivering up to 8 hours continuous use in the field (dependent on environmental controls).

  • Page 179: Battery Removal

    To charge the internal battery(s), connect the power supply to the “EXT PWR” plug on the back of the CIRAS-3 main console. The indicating LED above the plug shows the charge status of the internal battery. It will illuminate a steady green when charging and when the battery is fully charged.

  • Page 180: External Battery Pack (For Extended Operation In The Field)

    Belt Pack Kit – Battery, Charger and Power Supply Air Sampling Pumps (Reference and Analysis) The CIRAS-3 has 2 rotary vane pumps used for sampling the reference and analysis air and should be inspected periodically. Rotary vane pump components wear with prolonged use and material from the vanes may build up over time within the pumps.

  • Page 181: Replacement Of Reference And Analysis Pump

    Replacement of Reference and Analysis Pump It is very easy to replace the reference and analysis pumps. First, trace the electrical connection to the pump and disconnect the 2-pin connector from the terminal on the CIRAS-3 Flow board. · Analysis Pump – Connected to connector labeled “AN PUMP”...

  • Page 182: Air Supply Pump

    When finished, run the pump in air for at least 15 minutes to allow any residual alcohol to evaporate. Ideally, let the pumps dry outside of the CIRAS-3 overnight. If the pumps are reconnected prematurely, the absorber chemicals will be exhausted quicker than usual.

  • Page 183: Air Filters

    Minimal use (once or twice per week) in dirty or dusty environments – Every 3 months Blue Reference and Analysis Air Filters (5 micron) · Once every year. Gas Blender Air Filters (25 micron) · Should not require replacement. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 184: External Air Inlet Filter Assembly (Part Number Std558)

    Filter Element, 10 um, Yellow (For severe dusty environments) STD556 Filter Element, 48 um, Blue Desiccants and Absorber Columns The CIRAS-3 has two well labeled absorber column assemblies (total of 4 absorber columns) for analyzer Zero and CO and H O control.

  • Page 185: Zero Column Assembly

    Pan hd Sealing M3 x 6mm ALWAYS change self-indicating desiccants when the column is approximately 50% exhausted. If using non- indicating desiccants, we recommend changing them out prior to each measurement campaign to play it safe. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 186: Co 2 & H 2 O Control Column

    50% exhausted. If 30118-1 Filter Foam using non-indicating desiccants, we recommend changing them out prior to each measurement 64022-1 Pan hd Sealing M3 x 6mm campaign to play it safe. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 187: Soda Lime

    Soda lime (Sodium Hydroxide) is used to remove CO from air entering the CIRAS-3. Both self-indicting and non-indicating Soda Lime can be can be used with the CIRAS-3. Soda Lime cannot be regenerated and should be discarded after exhaustion. ·...

  • Page 188: Molecular Sieve

    The ZERO absorber columns should be placed in a sealed polythene bag if the CIRAS-3 is not going to be used for an extended period (i.e. days) to preserve the desiccants.

  • Page 189: Molecular Sieve Repackaging

    Molecular Sieve Repackaging The Molecular Sieve is originally supplied by PP Systems in tin packaging. After initial opening, we strongly urge all users to repackage the Molecular Sieve in small glass containers with a screw top to seal the desiccant from room air.

  • Page 190: Absorber Filters

    See How do I determine the state of the CO2 cartridge? page 50. Depending on pressure, you may here a small hiss when loosening the cylinder holder from the regulator body which is normal. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 191 Re-Order Information Part Number Description STD549 Cartridge Holder STD546 Regulator Assembly 20577-1 Gasket CO Seal CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 192: Co 2 Calibration

    The most common cause of a drift in CIRAS-3 readings is an incorrect Zero due to either exhausted chemicals, leaks on the Zero columns from pinched or damaged O-rings or the Zero absorber assembly is not properly seated in the console manifold.

  • Page 193: H 2 O Calibration

    If you do not have a device for H O recalibration, please contact PP Systems and we will be happy to recommend some. PP Systems can also perform H recalibration services at our factory.

  • Page 194: Checking For Leaks Associated With The Plc3

    To checks for leaks, connect the cuvette simulator to the PLC Gas port on the CIRAS-3 console as shown here to the right. This will allow you to sample the same air in both the reference and analysis cells of the infrared gas analyzer.

  • Page 195: Plc3 Leaf Cuvette Head Adjustment

    To isolate the leak, take a small piece of tubing and gently breathe around the gaskets and monitor the CO2d on the CIRAS-3 console. If you see a spike or increase in CO2d you have found the leak. Replace the gaskets (see Cuvette Gaskets on page 193.

  • Page 196: Plc3 Pneumatic Connector

    If you suspect 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 commonly used with the PLC3 Narrow and Conifer leaf cuvettes.

  • Page 197: Boundary Layer Determination (R B )

    An appropriate typical value can be used temporarily, with the understanding that any data must be recalculated using the correct r value. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...
  • Page 198 Remove the LED light unit from the PLC3 and connect the CIRAS-3 to mains power using the external power supply provided by PP Systems. Go to Settings (F2) and set the following environmental controls: ·...
  • Page 199 H2Od value. As the paper dries due to evaporation the positive differential will fall back towards Zero. Open the RbCal.xls file available on the USB thumb drive (supplied by PP Systems when you first purchased your system or visit our web site and download it) and enter the required values. For Air Temperature, enter the cuvette temperature °C (Tcuv).

  • Page 200: Changing Plc3 Universal Head Plates

    To ensure an air-tight seal, we recommend putting a slight smear of silicone grease between the head plate and cuvette head prior to securing the 6 screws. A slight smear of silicone grease can also be applied to the leaf gaskets themselves for improved leak tight performance. CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

  • Page 201: Replacement Of Plc3 Glass Window (For Use With Cfm-3)

    Cuvette. However, for measurement of chlorophyll fluorescence using the CFM-3 the Calflex window must be replaced with a plain glass window. When the CFM-3 is purchased with the CIRAS-3 the glass window is already fitted to the PLC3 Universal Leaf Cuvette.

  • Page 202: Section 15. Consumables/Spares

    Section 15. Consumables/Spares The following items are common consumables and can be ordered directly with PP Systems. Desiccants and Absorber Columns Part No. Description STD006 Molecular Sieve Desiccant, 1.25 Lbs. STD007W Sofnolime, white to violet, 1.0 kg STD008 Drierite, 1 lb.

  • Page 203: Co 2 /H 2 O Control

    41526-1 Battery Pack Li-ion 7.2V (Aved) 41535-1 Battery Pack Li-ion 7.2V (Inspired Energy) STD550 External Charger for CIRAS-3 Internal Battery Pack (Part No. 41526-1) STD551 Belt Pack Kit - Battery, Charger, and Power Supply STD552 Power Supply Adapter, CIRAS-3 Cables/Data Storage...
  • Page 204 PLC3/6 (U) Plain Glass Window Assembly (for use with CFM) 10088-2 PLC3/6 (U) Calflex Window Assembly 20359-1 PLC3/6 (U) Window Plate Only 55021-1 PLC3/6 (U) Calflex Window Only 55021-2 PLC3/6 (U) Plain Glass Window Only (for use with CFM) CIRAS-3 Operation Manual V. 1.09 support@ppsystems.com...

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