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PP Systems CIRAS-2 User Manual
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CIRAS-2
Portable Photosynthesis System
Operator‟s Manual
Version 2.04
For Remote Control Softw
are (RCS) Version 1.07 or greater.
©
2010
PP Sy
stems. A
ll Rights Reserved
12
th
May 2010
PP Sy
stems, Inc.
110 Haverhill
Road, Suite 30
1
Amesbury, MA 0191
3 U.S.A.
Tel: +1 978 834-
0505
Fax: +1 978 834-
0545
Email:
support@ppsy
stems
.com
W
eb Site:
http://ww
w.ppsy
stems
.com
2
Table of Contents
Table of Contents
3
Preface
12
Notice
12
Documentation Conventions
12
User Registration
12
Service & Warranty
13
Contact Information
13
Unpacking Your Equipment
13
CIRAS-2 Essentials
14
Before Powering on and Operating the System
14
Important Precautions
14
Getting Started
15
Installing CIRAS-2 Remote Control Software on Your Computer
16
Avoiding UI-To-PC Communication Errors
16
Click ? at any Time for On-Line Help
19
Preparations for Use
20
Step 1. Insert 12V Nimh Battery Packs into Main Console
20
Step 2. Connect CIRAS-2 Power Supply
20
Step 3. Make Leaf Cuvette Electrical and Gas Connections
21
CIRAS-2 Gas/Electrical Connection Panel - Detailed View
21
Step 4. Connect Leaf Cuvette Power Cable to External 12V DC Power Supply
22
Step 5. Inspect Absorber Columns and Water Vapor Equilibrator
22
CIRAS-2 Console - Front Layout
23
Step 6. Insert CO Cartridge
23
CO 2 Holder and Regulator Assembly
24
Step 7. Connect CIRAS-2/PC Interface Cable
24
Step 8. Power on CIRAS-2
25
Step 9. Close the Leaf Cuvette
26
Step 10. Start CIRAS-2 RCS Program on Your Computer
26
Familiarizing Yourself with the Measurement Display
27
LED Tuning
27
Gas Exchange Measurement Screen
28
Data Display and Control Values
28
Control Setpoints
28
Measured Parameters
29
Calculated Variables
29
Display Toggle
29
Graph Display Options
30
Plot Type Toggle
30
Current y Axis Variable
30
Status Bar
30
Errors and Warnings
30
CIRAS-2 Status
30
CIRAS-2 Mode
30
Power Status
30
CIRAS-2 Power
31
Power Source
31
Left and Right Battery Power Status
31
CIRAS RCS Menu Bar
32
File Menu
32
Recalculate Data
32
Export Data
32
View Diagnostics Report
32
Connections Menu
32
Login
32
Connect
33
Disconnect
33
Connect Add-On
33
Com Port
33
Setup Menu
33
Settings
33
View Setup Details
34
Graphing
34
Preferences
34
Reset
34
Utilities Menu
34
Zero
34
Diff Bal
35
Measure [Quit]
35
Initialise
35
Pulse Alarm
36
Simultaneous Measurements with CIRAS-2 and FMS2
36
Diagnostics
36
Stored Diff Bal
37
Calibration
37
Calibration Check
37
Calibration Reset
37
CO2 Midpoint
37
Max C Determination
38
LED Tuning
38
CIRAS Recording
38
Recording Menu
38
Begin
39
End
39
Start (Steady)
39
Pause
39
Single Record
39
Multiple Record
40
Comment/Treatment
40
Response Level
40
Plugin Record
40
View Menu
40
Quick Info
40
Update Parameters
41
Errors
41
Warnings
41
Time Plot
41
Data Plot
41
Battery Status
41
Help Menu
42
Help
42
About
42
Diagnostics
42
Calibration & Stored Diff Bal
42
Recording
42
Closed Systems
42
Add-On Modules
42
About CIRAS
42
System Setup and Operation
43
Set File Options
43
Set Entry Name
43
Edit Entry Name
43
Add Entry
44
Delete Entry
44
Recording Options
44
Graphing Options
44
PRM File Options
44
PRM Entry Name
44
Edit Entry Name
44
Delete Entry
45
Accessory
45
Add Custom Accessory
46
Light Type
47
Leaf Temperature
47
Leaf Temperature Determination: Explanations
47
Leaf )
47
Energy Balance
47
Thermistor
48
Direct Leaf Temperature Measurement - Common Problems
48
Infrared (IR)
48
Leaf Area
48
Boundary Layer Resistance
49
Percent of Stomata on Upper Leaf Surface
49
Zero/Diff Bal Mode
49
Manual with Warnings
49
Automatic
49
Auto Zero with Stored Diff Bal
49
Manual Without Warnings
49
Choice of Zero Mode - Recommendations
49
Changes in Zero Readings
50
Analysis Flow
51
Averaging Limit
51
System Setup
51
Probe Type
51
Air Supply on
51
Cuvette Flow
51
Light Type
51
Par
51
Energy Factor
51
Value
51
Cuvette Environment
52
Control Types
53
CO 2 (0-2000 Ppm)
53
Supply (Ref) Approximate Ppm
53
Supply (Ref) Set Ppm
53
Cuvette (An) Set Ppm
53
About CO Control Types
53
H2O (0-100% or 0 Mb-Dewpoint)
53
Supply (Ref) % Ambient
53
Supply (Ref) Set Mb
53
Cuvette (An) % RH (Vs. Leaf T)
53
Cuvette (An) Set Mb (0-Dewpoint)
54
Leaf to Cuvette VPD
54
About H 2 O Control Types
54
Determination of Actual Ambient RH
54
Par
54
Cuvette Flow
54
Temperature
55
Track Ambient
55
Entered Values
55
None
55
Which Control Type Should I Use
55
If Performing a Light Response
55
Customized Operation of CIRAS-2 with Ambient CO
55
If Performing a Basic CO Response
55
Customized Operation of CIRAS-2 at Humidity Levels above Ambient
56
CIRAS-2 Time
56
Analog Outputs
56
CO 2 Analog Outputs
57
H 2 O Analog Outputs
57
Examples of Analog Outputs
57
Automatically Update CIRAS
58
Graphing Preferences
59
Time Plot
59
Select Variables
59
Font Size
59
Time Plot Details
60
Select Variable to Edit
60
Time Span
60
Data Plot
60
Shown Variable on y Axis
60
Observing and Recording Leaf Gas Exchange
61
Checking the System with an Empty Cuvette
61
Select Recording Options
62
Treatment Editor
63
Treatment Groups
63
Treatment Items
63
Recording Mode
64
Placing the Leaf in the Cuvette
65
Keypress Recording
67
Timed Recording
68
Settle Time (Seconds)
69
Steady Pn Options
69
Use Steady Pn
69
Steady Pn Value
69
Recording at Pre-Set Intervals
69
Recording Block Options
69
Record Interval (Seconds)
69
Enable Recording Blocks
70
Recording Blocks of Data at Pre-Set Intervals
70
Suspending and Resuming Recording
70
Response Curve
70
Editing Response Variable Values
71
Editing All the Values in a Row
71
Editing Groups of Values
72
Editing Individual Values
72
Enabling Levels
73
Recording Options
74
Repeat
74
Interval
74
Zero Settle Time
74
Steady Pn Options
75
Automatic Response
75
Manual Response
75
PAR Type - Use Sensor
75
CO 2 Control Type
75
H 2 O Control Type
75
Light Type
75
Temperature Control
75
Batch Response Curves
78
Enable Batch Response Levels
78
Batch Level Options
78
Show Prompt
78
Force Zero and Automatic Settle
78
Repeat
79
CIRAS Internal Recording
79
Enable Internal Recording
80
Record Interval
80
Apply Internal Recording
80
Transfer Data
80
Clear CIRAS Memory
80
Stored Diff Bal
80
Recalculate Data
83
Processing Options
84
Recalculation Values
85
Information
85
Options
89
Load Output File in Spreadsheet
90
Load Output File in Named Program
90
Export Data
90
Options
90
Include File Information
91
Export Fields
91
Options
92
Transferring Data from CIRAS-2 to Your Computer
93
PCMCIA Card
93
RS232 (Null Modem) Connection
93
Establishing an Activesync Connection for Data Transfer from UI to PC
93
Activesync® Communications Software
94
For Customers that Are Using the Integral PC (Pencentra)
95
For Customers that Are Using Our User Interface (UI)
95
USB Connection
95
Installation of USB Drivers on Your PC
95
Establishing an Activesync Connection for Data Transfer from UI to PC
96
Shutting down the CIRAS-2 System
97
Measuring Chlorophyll Fluorescence with the CFM
98
Getting Started with the CFM
98
Firmware & Software Requirements
98
Software Installation
98
Power Requirements
99
Leaf Cuvette Window
99
Replacing Cuvette Window
99
Connecting the CFM to CIRAS-2
100
Operation from External PC
101
Stand-Alone Operation (User Interface)
102
CFM Operation
103
Default Adaptation
104
Dark Adaptation
104
Far Red Adaptation
104
No Adaptation
104
CFM Recording Options
104
Dark Period (Minutes)
105
Prompt When „Expired
105
After Dark Adaptation, Perform
105
CFM Setup
106
Recovery Period (Seconds)
106
If Batch Response, Dark Adapt for each Level
106
When a CIRAS Record Is Taken, Perform
107
If Response Curve, at End of Level, Perform
107
Complete CFM Recording with
107
Save Trace Data
107
Include „Pre" and „Post" Data
107
Calculation Options
107
Modulation Beam
107
Enable Modulating Beam
108
Mod. Level
108
Gain
108
Perform CFM Tuning
108
CFM Graphing Options
109
CFM Time Plot
109
CFM Data Plot
109
CIRAS-CFM Display
110
Recd
110
CFM Display Buttons
111
CFM Tuning
111
Recording Chlorophyll Fluorescence
113
Keypress Recording with CFM
113
Response Curve Recording with CFM
117
CFM Output
119
Calculation Error Codes
120
Brief Introduction to Chlorophyll Fluorescence
121
What Is Chlorophyll Fluorescence
121
Techniques for Measuring Chlorophyll Fluorescence
122
Common Fluorescence Measurements
124
Fluorescence Induction Analysis (Kautsky Curve)
124
Quantum Efficiency of Photosystem II
126
Glossary of Fluorescence Terms
127
Measuring Soil Respiration with CIRAS-2
129
Soil Respiration Measurement Display
129
Prompt
129
Parameters
129
Settings
130
Soil Respiration Operational Settings
130
Chamber Properties
131
Volume (CM 3 )
131
Area (CM 2 )
131
System Type
131
Recording Parameters
131
CO 2 Change
131
Maximum Time
131
System Temperature
131
Results
132
Data File
132
Select File Mode
132
Treatment
132
New Measurement
132
Graphing Options
132
Recording in Soil Respiration Mode
133
Diagnostics
135
Analyser A/D Reads
135
Analyser Temperature ( O C)
136
Atmospheric Pressure (Mb)
136
Pressure Difference (Mb)
136
Stored Zeros
136
Reset Stored Zeros
136
CO 2 Reference
136
CO 2 Analysis
136
H 2 O Reference
136
H 2 O Analysis
136
Valve Settings
136
Apply Valves to Measure
137
Apply Valves to Diff/Bal
137
Flows
137
Reference
137
Analysis
137
Log An/Ref
137
Temperature & PLC State
137
Temperature ( C)
137
Ambient
137
Blender
137
Cuvette Air
138
Leaf/Sensor Base
138
Radiation Sensor
138
Cuvette State
138
Probe
138
Apply
139
Flows
139
Control [D/A]
139
Analyser Flows
139
Apply Analyser Flow Control
140
Cuvette Air Supply
140
Forwarding Flow [A/D] / Cuvette Flow [A/D]
140
Flow (Mls/Min)
140
Flow Requested
140
Flow Measured
140
Control Setting
140
Auto Cuvette
140
Light Control
140
Temperature Control
141
Apply Lamp 1 Leds
141
Batteries & Voltages
141
Board Voltage
141
Cuvette Voltage
141
Left Battery Voltage
141
Right Battery Voltage
142
Current Battery/Power Source
142
Report
142
Quick Report
142
Extended Report
142
Calibration
145
External Connections for CO Calibrations
145
CO 2 Calibrations Using the Internal Standard
145
CO 2 Calibrations Using a Gas Cylinder
145
H 2 O Calibration Sources and Connections
146
PP Systems" Water Vapor Calibrator
146
Performing Calibrations
147
Calibration Check
147
Calibration Reset
149
CO2 Midpoint
149
Gas Connections for CO Midpoint
149
Max C Determination
151
Appendix 1. Cuvettes and Probes
153
Identification of Leaf Cuvette Types
153
Leaf Cuvettes Fitted with a FLAT GLASS WINDOW
153
Leaf Cuvettes Fitted with a PLASTIC HEMI-CYLINDER
153
CIRAS-2 Settings for Leaf Cuvettes and Probes
154
Appendix 2. CIRAS-2 Consumables and Spares
155
Appendix 3. Photosynthesis Equations Used in CIRAS-2
157
Calculations
157
Step 1.0
157
Step 2.0
157
Step 3.0
158
Step 4.0
159
Step 5.0
160
Step 6.0
160
Symbol Definitions
161
Measured Parameters
161
Calculated Parameters
161
Physical Constants Used in Equations
162
Saturated Vapor Pressure of Water from Air Temperature
162
References
163
Addendum
164
Corrections to Stomatal Resistance Measurements for Differing Transpiration Rates from Upper and Lower Leaf Surfaces
164
Magnitude of Errors in RS
166
User Notes
167
4
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PP Systems CIRAS-2 Specifications
General
Brand
PP Systems
Model
CIRAS-2
Category
Measuring Instruments
Language
English
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