PP Systems CIRAS-3 User manual

CIRAS-3
Portable Photosynthesis System
Operation Manual
Version 1.09
2017 PP Systems. All Rights Reserved
7th August 2017
PP Systems
110 Haverhill Road, Suite 301
Amesbury, MA 01913 U.S.A.
Tel: [phone] Fax: [phone]
Email: [e-mail] URL: www.ppsystems.com

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Contents
Welcome .....................................................................................................................................................10
User Registration ........................................................................................................................................11
Service & Warranty.....................................................................................................................................12
Returning equipment to PP Systems ......................................................................................................12
Contact Information.....................................................................................................................................13
Unpacking and Storage of Your Equipment............................................................................................14
Unpacking............................................................................................................................................14
Storage ................................................................................................................................................14
CIRAS-3 Tutorial & Basic Operation...........................................................................................................15
Let’s Get Started......................................................................................................................................16
Charge internal battery packs..............................................................................................................16
Inspect desiccants ...............................................................................................................................16
Insert a fresh CO2cartridge.................................................................................................................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 .................................................................................................................................19
Setting up the CIRAS-3 System ..........................................................................................................20
Setting up the graphical display for data plots.....................................................................................21
Let’s check out both the numerical and graphical display...................................................................21
Let’s have a look at the environmental controls ..................................................................................23
It’s about time we start taking some data on a real plant ....................................................................25
Placing the leaf inside the cuvette .......................................................................................................27
What should I be looking for at this point?...........................................................................................27
Quick Start...................................................................................................................................................31
Section 1. Technical Specification .............................................................................................................33
Section 2. What’s new with CIRAS-3?.......................................................................................................36
General Changes to CIRAS-3 Hardware.............................................................................................36

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Changes to CIRAS-3 Software............................................................................................................38
Section 3. Summary of System Design .....................................................................................................40
Overview and Theory ..............................................................................................................................40
Section 4. System Components and Assembly.........................................................................................44
CIRAS-3 Main Console........................................................................................................................44
System Power .........................................................................................................................................44
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...................................................................................................................................................49
Mini-USB (PC) .....................................................................................................................................49
PLC Connections.................................................................................................................................49
CO2Cartridge Holder...........................................................................................................................49
CO2Cartridges.....................................................................................................................................50
How do I determine the state of the CO2cartridge?............................................................................50
Gas Ports and Link Pipe......................................................................................................................51
Auxiliary Connector..............................................................................................................................51
Zero Column ........................................................................................................................................51
CO2/H2O Control Columns and H2O Equilibrator.................................................................................52
PLC3 Series Leaf Cuvettes.....................................................................................................................53
PLC3 Universal Leaf Cuvette ..............................................................................................................53
PLC3 Narrow Leaf Cuvette..................................................................................................................53
PLC3 Conifer Leaf Cuvette..................................................................................................................53
PLC3 Temperature Control .....................................................................................................................54
Temperature Measurement .................................................................................................................54

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Temperature Control Type...................................................................................................................54
LCD on Leaf Cuvette ...........................................................................................................................55
PAR Measurement ..................................................................................................................................56
Light Control (Optional) ...........................................................................................................................57
PLC3 Universal LED Light Unit (RGBW).............................................................................................57
PLC3 Narrow and Conifer LED Light Unit ...........................................................................................58
CFM-3 Chlorophyll Fluorescence Module ...........................................................................................59
Section 5. CIRAS-3 Console Software ......................................................................................................60
Overview..................................................................................................................................................60
Basics of Navigating Console Screens and Menus.............................................................................61
Numeric View of Data 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
CO2Cartridge Status...............................................................................................................................68
Changing a CO2Cartridge.......................................................................................................................70
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)............................................................................................................................................79
Controls Graph Set (F5).......................................................................................................................80
Toggle View (F4)..................................................................................................................................80
Reviewing and Transferring Data Files...................................................................................................82
Transfer Data (F6) ...............................................................................................................................82
Section 8. Operations.................................................................................................................................84
Operations (F1) .......................................................................................................................................84

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Recording Options...................................................................................................................................84
Manual Recording................................................................................................................................84
Timed Recording..................................................................................................................................86
Response Curves ................................................................................................................................87
Z-Diff Bal (F7) ......................................................................................................................................94
Set Clock .................................................................................................................................................95
View Saved (F4)......................................................................................................................................96
Calibration................................................................................................................................................98
Recalibrate...........................................................................................................................................98
Calibration Setup .................................................................................................................................99
CO2Calibration....................................................................................................................................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
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.................................................................................................................................117

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Installation Instructions for PC Utility.................................................................................................117
Uninstall Instructions..........................................................................................................................117
PC Utility Operation ...........................................................................................................................118
Create/Edit Response Scripts............................................................................................................119
Create/Edit Settings Files ..................................................................................................................121
Remote Display..................................................................................................................................123
Section 10. Measuring Chlorophyll Fluorescence with CFM-3................................................................127
Overview of Chlorophyll Fluorescence..................................................................................................127
The Basics .........................................................................................................................................127
Calculations Used for Chlorophyll Fluorescence Parameters...........................................................129
Chlorophyll Fluorescence Measurements – Setup and Operation........................................................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 CO2Efflux and Net Canopy CO2Flux............................................................................................140
Theory....................................................................................................................................................140
FCO2Units for measurement of Soil CO2Efflux................................................................................141
References.........................................................................................................................................142
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......................................................................................................147
Closed System Operation......................................................................................................................147
Measurement Sequence .......................................................................................................................150
Initial Test Measurement Sequence..................................................................................................151
Recording Measurements .....................................................................................................................151

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Section 12. Data Output...........................................................................................................................153
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 ................................................................................................................161
Stomatal Conductance.......................................................................................................................161
Net Photosynthesis............................................................................................................................161
Intercellular CO2Concentration.........................................................................................................162
Physical Constants Used in Equations..............................................................................................163
Definition of Symbols.........................................................................................................................163
Section 13. Troubleshooting & Diagnosis................................................................................................165
System Power .......................................................................................................................................165
CO2Measurement and Control.............................................................................................................166
H2O Measurement and Control.............................................................................................................168
Temperature Measurement and Control...............................................................................................169
PAR Measurement and Control ............................................................................................................170
Flow Control.......................................................................................................................................171
Data Management.................................................................................................................................172
Status Codes Displayed on the CIRAS-3 LCD..................................................................................173
Other Status Codes/Messages..........................................................................................................177
Section 14. Routine Maintenance............................................................................................................178
CIRAS-3 Main Console .........................................................................................................................178
Battery Pack (Li-ion Battery)..............................................................................................................178
Battery Removal ................................................................................................................................179
Battery Storage..................................................................................................................................179

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Battery Disposal.................................................................................................................................179
External Battery Pack (For extended operation in the field)..............................................................180
Air Sampling Pumps (Reference and Analysis).................................................................................180
Replacement of Reference and Analysis Pump................................................................................181
Servicing the Air Sampling Pump (Reference & Analysis)................................................................181
Air Supply Pump................................................................................................................................182
Air Filters............................................................................................................................................183
External 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 Repackaging ...........................................................................................................189
Foam Filters.......................................................................................................................................189
Absorber Filters..................................................................................................................................190
“O” Rings............................................................................................................................................190
CO2Regulator....................................................................................................................................190
CO2Calibration......................................................................................................................................192
H2O Calibration......................................................................................................................................193
PLC3 Leaf Cuvettes ..............................................................................................................................193
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

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Boundary Layer Determination (rb)........................................................................................................197
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 Control....................................................................................................................................203
Batteries & Power Supplies...................................................................................................................203
Cables/Data Storage.............................................................................................................................203
Leaf Cuvette Accessories......................................................................................................................203

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Welcome
Thank you very much for purchasing our CIRAS-3 Portable Photosynthesis System. We greatly
appreciate your business and we look forward to working with you and your research team for many
years to come.
This operation manual is based on our software Version 1.09 and above along with the following system
firmware and above:
•FW Version: V. 1.04 and above
•Air Version: V. 3.02 and above
•IRGA Version: V. 3.06 and above
•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. Our latest software and
documentation can be downloaded free of charge from our website if you are registered with us (See
User Registration on page 11). For users running older software and firmware versions, the CIRAS-3,
This product is manufactured in accordance with CE
requirements. For more information on system
conformity please get in contact with PP System.

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PLC3 and Light unit (if applicable) may need to be returned to PP Systems for a factory update which will
bring your system up to date and allow you to perform future updates locally without having to return the
instruments to our factory. Please contact PP Systems for more information.
Information contained in this operation manual is subject to change without notice. Registered users of
PP Systems products and instruments may obtain updated documentation and software by visiting the
Users Area of our website.
This manual and the information contained within are copyrighted to PP Systems. No part of the
manual may be copied, stored, transmitted or reproduced in any way or by any means including,
but not limited to, photocopying, photography, magnetic or other mechanical or electronic means,
without the prior written consent of PP Systems, Inc.
For applications where failure of this equipment to function correctly would lead to consequential damage,
the 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 does not cover injury to persons or property or other consequential damage.
This manual is provided to help you install and operate the equipment. Every effort has been made to
ensure that the information it contains is accurate and complete. PP Systems does not accept any
liability for losses or damages resulting from the use of this information.
It is the operator’s responsibility to review this information prior to installation and operation of the
equipment. 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.
Only REGISTERED users will be allowed access to the protected “Users” section of our web site. This
section will contain important product information including hardware/software updates, application notes,
newsletters, etc.
Thank you in advance for your cooperation.

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Service & Warranty
PP Systems' equipment warranty is limited to replacement of defective components, and does not cover
injury to persons or property or other consequential damage.
The equipment is covered under warranty for one complete year, parts and labor included. This, of
course, is provided that the equipment is properly installed, operated and maintained in accordance with
written instructions (i.e. Operator's Guide).
The warranty excludes all defects in equipment caused by incorrect installation, operation or
maintenance, misuse, alteration, and/or accident.
If for some reason, a fault is covered under warranty, it is the responsibility of the customer to return the
goods to 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 ([e-mail]) 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 you pay close attention to the following
procedure:
1. Contact PP Systems directly by email ([e-mail]) or by telephone [phone]-
0505) to obtain a Case Number for tracking and reference purposes. You will receive a “Service
Return Form” that must be completed and included with the return of your equipment.
2. If you have any stored data on your instrument that is important to you please retrieve it prior to
packing up your equipment. PP Systems is not responsible for any loss of data.
3. Safely pack your equipment in a rugged carton/case with suitable packing materials (bubble pack,
etc.). Remember to include the “Service Return Form”. PP Systems is not responsible for any
shipping related charges for equipment being returned to PP Systems (Amesbury, MA)
regardless of whether or not it is covered under warranty.
4. Notify the PP Systems’ Service Department when the equipment is packed and ready to be
shipped.

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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.
•Remove all batteries contained in the equipment. We don’t need them and this will eliminate any
problems associated with shipments containing Li-ion batteries. There is also no need to return
the power supply adapter or any cables.
•Remove the CO2cartridge from the CO2cartridge holder.
•To save on weight and shipping costs you can remove the desiccants from all absorber columns.
•Make sure that the PLC3 cuvette head is open so that the gaskets are not compressed or
damaged when received.
•Prior to performing any service on your equipment we must have an acceptable purchase order
or credit card information on file (Visa or MasterCard).
Contact Information
PP Systems, Inc.
110 Haverhill Rd, Suite 301
Amesbury, MA 01913 USA
Tel: [phone] Fax: [phone]
Sales: [e-mail]
Support: [e-mail]
Service: [e-mail]
URL: www.ppsystems.com

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Unpacking and Storage of Your Equipment
Unpacking
It is extremely important that you check the contents of your equipment immediately upon receipt to
ensure that your order is complete and that it has arrived safely. Please refer to the checklist supplied (if
applicable) for a detailed list of spares and accessories that are included with your order. DO NOT
DISCARD ANY OF THE PACKAGING MATERIAL UNTIL ALL OF THE ITEMS LISTED ARE
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. If you store your system in the
black transport case supplied with your system, please refer to the very important tip below.
Tip
If the CO2cartridge is pressurized we
STRONGLY suggest removing the entire
CO2cartridge holder and regulator from the
console and store it separately. See CO2
Regulator on page 190. Otherwise CO2will
slowly accumulate overnight inside the case
resulting in absorption into the PLC tubing as
well as the internal case foam material
affecting CO2measurements the following
day. The system should only be stored in the
case when a CO2cartridge is empty and fully
exhausted.

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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. In less than 2 hours you will have learned how to:
•Prepare the system for leaf gas exchange measurements
•Set up and modify all environmental controls (CO2, H2O, temperature and light)
•Navigate 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 you can use it much like the PLC3 Universal Light Unit:
CIRAS-3 Main Console
Part Number CRS300
PLC3 Universal Leaf Cuvette
Part Number CRS301
PLC3 Universal Light Unit (LED)
Part Number CRS304
In addition, we recommend that you have the following items available for this tutorial:
•CIRAS-3 power supply adapter
•One CO2cartridge
•USB flash drive
•Small tabletop tripod to hold PLC3 Universal Leaf Cuvette
•PC or laptop computer
•A well-watered, healthy plant for actual measurements. We recommend a plant that likes high
light (i.e. tomato, sunflower, etc.) and is typically found growing outdoors for best results.

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Please Note
The measured and calculated data that is shown in this tutorial should be similar but not 100% identical to
what you will witness. Actual results will be based on the biological state and type of plant that you use
and its response to the environmental conditions presented. However, what is most important is that you
should observe stable and comparable results.
Let’s Get Started
Charge internal battery packs
Before taking your system to the field for measurements it is critical that the internal batteries are fully
charged. 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.
Inspect desiccants
Make sure that all desiccants are fresh before beginning measurements and that all columns are properly
seated in their respective manifolds. The soda lime can be either self-indicating or non-indicating. If
using non-indicating soda lime we recommend changing out more regularly to play it safe. The Drierite
will be blue in color when fresh. It turns from blue to pink as it becomes exhausted. The Molecular Sieve
is white and non-indicating. The Molecular Sieve should always be discarded when changing out the
Drierite. For this tutorial we recommend that you change out all desiccants to ensure that they are fresh.

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Insert a fresh CO2cartridge
CO2cartridges allow for accurate and precise control of CO2and we highly recommend using them for
best results. Unscrew the CO2cartridge holder and insert a new CO2cartridge as shown below. Next,
screw the holder into the CO2regulator turning clockwise until snug. If you hear a small hiss (indicating
the cartridge is being pierced) continue to turn the holder until snug to ensure that the cartridge is both
pierced and sealed properly into the regulator assembly. Each CO2cartridge will last at least 24 hours
from the time it is installed.
We use 8g CO2cartridges 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 CO2cartridges please contact PP Systems.
Is it possible to perform measurements under ambient conditions without using a
CO2cartridge?
Yes and it is very easy. To do so make sure that the CO2cartridge holder is empty and that the soda lime
is removed from the CO2/H2O 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. Go to Settings (F2) and select “Ambient (remove chemicals)” for CO2 Reference. We just
wanted to bring this to your attention for future use but for this tutorial we will be using a CO2cartridge for
controlling CO2.

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Is it possible to perform measurements under ambient H2O conditions in addition
to ambient CO2?
Yes and again this is quite easy. To do so make sure that the CO2cartridge holder is empty and that
both the soda lime and Drierite is removed from the CO2/H2O control column on the CIRAS-3 console.
The empty columns will ensure that ambient air is used for your reference air and the columns will act as
smoothing volumes. Go to Settings (F2) and select “Ambient (remove chemicals)” for CO2 Reference
and “Ambient (remove chemicals)” for H2O Reference. We just wanted to bring this to your attention for
future use but for this tutorial 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 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. Next connect the white pneumatic connector to the “Gas” port on the CIRAS-3. It will snap into
place. Close the cuvette head. The black link pipe should already be in place connecting the “REF IN”
and “AIR OUT” gas ports below the CO2source.
Connect light unit to PLC3 Universal Leaf Cuvette
Mount the light unit by aligning it to the front of the cuvette upper jaw (Step 1). Slide the light unit towards
the heat sink and fan on the top of the leaf cuvette. It should secure in place by two lock-in set screws as
shown below (Step 2). Connect electrically (Step 3).

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Step 1 Step 2 Step 3
Never stare directly at LEDs
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. It normally takes the system
approximately 10 minutes for the IRGAs to reach the required operating temperature of 55 oC and also
during this period the system will perform several Zero and Diff Bal cycles to ensure that everything is
working perfectly. The system performs more frequent Zero and Diff Bal cycles during the first 30
F1
F3
F2
F4
F6
F5
F7
F8

CIRAS-3 Operation Manual V. 1.09 20 [e-mail]
minutes and then after that they will be performed much less frequently (depending on Settings) or when
there is a large change in CO2(100 µmol mol-1) and/or H2O (5 mb) concentration.
During warm up note the dashes for Measured Data and Photosynthesis Data. This occurs during
system warm up, Zero and Diff Bal cycles. The numbers don’t mean anything during this period so don’t
be alarmed. Also note the IRGA warm up message in the lower left hand corner and the battery status 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 Cuvette, 18x25mm window) and all associated settings, options and environmental
controls for that accessory. Pressing the Tab key allows you to navigate through the fields. At this time,
press Tab to navigate from field to field and create a Settings file exactly as you see below. When in any
field you can press the Expand List (F4) to see all available options for that field. For Boundary Layer
Resistance enter the value for your PLC3. You can locate this value on the green “Tested” label on your
PLC3 handle.
F1
F3
F2
F4
F6
F5
F7
F8