PP Systems CIRAS-3 User Manual

CIRAS-3
Portable Photosynthesis System
Operation Manual
Version 1.09
2017 PP Systems. All Rights Reserved
7
th
August 2017
PP Systems
110 Haverhill Road, Suite 301
Amesbury, MA 01913 U.S.A.
Tel: +1 978-834-0505 Fax: +1 978-834-0545
Email: support@ppsystems.com URL: www.ppsystems.com

PP Systems CIRAS-3 Specifications

General

Brand	PP Systems
Model	CIRAS-3
Category	Measuring Instruments
Language	English

Summary

Welcome

User Registration

Service & Warranty

Returning equipment to PP Systems

Procedure for returning equipment for service or repair.

Contact Information

Unpacking and Storage of Your Equipment

CIRAS-3 Tutorial & Basic Operation

Let’s Get Started

Charge internal battery packs

Instructions for charging the system's internal battery packs.

Inspect desiccants

Check and ensure desiccants are fresh and properly seated.

Insert a fresh CO2 cartridge

Connect the PLC3 Universal Leaf Cuvette to the CIRAS-3 console

Connect light unit to PLC3 Universal Leaf Cuvette

Power up the CIRAS-3 System

System Warm up

Setting up the CIRAS-3 System

Setting up the graphical display for data plots

Let’s check out both the numerical and graphical display

Let’s have a look at the environmental controls

It’s about time we start taking some data on a real plant

Placing the leaf inside the cuvette

What should I be looking for at this point?

Reviewing and Transferring Data Files

Quick Start

Section 1. Technical Specification

CIRAS-3 Main Console

Technical specifications of the CIRAS-3 main console unit.

PLC3 Leaf Cuvettes

CFM-3 Chlorophyll Fluorescence Module

Section 2. What’s new with CIRAS-3?

General Changes to CIRAS-3 Hardware

Overview of hardware improvements in the CIRAS-3 compared to previous models.

PLC3 Series Leaf Cuvettes

LED Light Unit (RGBW)

Changes to CIRAS-3 Software

Section 3. Summary of System Design

Overview and Theory

Explanation of the CIRAS-3 system design and operating principles.

Section 4. System Components and Assembly

CIRAS-3 Main Console

Description of the CIRAS-3 console's front panel components and user interface.

System Power

Information about the AC power supply adapter and its function.

Battery Pack

Battery Pack Installation

Charging Batteries inside the CIRAS-3 Console

CIRAS-3 Rear Console

Battery Charging Socket (EXT PWR) and LED

Power

Mini-USB (PC)

PLC Connections

CO2 Cartridge Holder

CO2 Cartridges

How do I determine the state of the CO2 cartridge?

Gas Ports and Link Pipe

Auxiliary Connector

Zero Column

CO2/H2O Control Columns and H2O Equilibrator

PLC3 Series Leaf Cuvettes

PLC3 Universal Leaf Cuvette

Details on the universal cuvette for broad leaves.

PLC3 Narrow Leaf Cuvette

Description of the cuvette for grasses and narrow leaves.

PLC3 Conifer Leaf Cuvette

Description of the cuvette for conifers and short needles.

PLC3 Temperature Control

Temperature Measurement

Temperature Control Type

LCD on Leaf Cuvette

PAR Measurement

Light Control (Optional)

PLC3 Universal LED Light Unit (RGBW)

Features and specifications of the RGBW LED light unit.

PLC3 Narrow and Conifer LED Light Unit

CFM-3 Chlorophyll Fluorescence Module

Section 5. CIRAS-3 Console Software

Overview

General overview of the CIRAS-3 console software interface.

Basics of Navigating Console Screens and Menus

Numeric View of Data and Control Variables

Section 6. Startup Routine and System Stability Checks

Before You Power Up CIRAS-3

Pre-operational checklist before powering on the system.

Startup and Warm up

CO2 Cartridge Status

Changing a CO2 Cartridge

Checking Stability - Before You Place a Leaf in the Chamber

Survey Measurements – Some Tips

Additional Filtering in Dirty/Dusty Environments

Section 7. Basic Functions - Viewing and Controlling CIRAS-3

Settings (F2)

Defining operational environments and setting system parameters.

Settings Graph Set (F5)

Controls (F3)

Controls Graph Set (F5)

Toggle View (F4)

Reviewing and Transferring Data Files

Section 8. Operations

Operations (F1)

Accessing various system functions like recording and calibration.

Recording Options

Selecting recording modes: Manual, Timed, or Response curves.

Manual Recording

Timed Recording

Response Curves

Response Curve Scripts Editor

CFM-3 Script Settings Editor

Z-Diff Bal (F7)

Set Clock

View Saved (F4)

Calibration

Recalibrate

Initiating recalibration of gas analyzers and sensors.

Calibration Setup

CO2 Calibration

Procedure for calibrating the CO2 gas analyzers with a mixture.

H2O Calibration

Find Max C

Store Diff Bal

LED Calibrate

PAR Calibrate

Steps to Recalibrate PLC3 PAR Sensors

Steps for recalibrating external and internal PAR sensors.

Diagnostics

IRGA (F2)

Viewing diagnostic readings for IRGA sensors.

PLC (F3)

Temperature (F2)

Flow (F4)

Power (F5)

APA (F6)

Report (F7)

Firmware Upgrade

Section 9. CIRAS-3 Console and PC Utility Software

CIRAS-3 Console Software

Instructions for installing the console software.

Uninstall Instructions

Procedures for uninstalling the console software.

PC Utility Software

Installation Instructions for PC Utility

Instructions for installing the PC Utility software.

Uninstall Instructions

Procedures for uninstalling the PC Utility software.

PC Utility Operation

Create/Edit Response Scripts

Gas Exchange Script Settings

Configuring settings for gas exchange response scripts.

CFM-3 Script Settings

Configuring CFM-3 for chlorophyll fluorescence measurements.

Create/Edit Settings Files

Remote Display

Section 10. Measuring Chlorophyll Fluorescence with CFM-3

Overview of Chlorophyll Fluorescence

Basic principles of chlorophyll fluorescence measurement.

The Basics

Fundamental concepts of chlorophyll fluorescence in PSII.

Calculations Used for Chlorophyll Fluorescence Parameters

Chlorophyll Fluorescence Measurements – Setup and Operation

CFM-3 Set Up

CFM-3 Settings

CFM-3 Controls

Measurement of Fm’ with CIRAS-3

Measurement Principle

Principle behind measuring Fm' using the Multi-Pulse sequence.

Operations

CIRAS-3

Software and firmware requirements for using Multi-Pulse.

PLC3

Firmware requirements for using Multi-Pulse with PLC3.

Section 11. Closed System Measurements

Soil CO2 Efflux and Net Canopy CO2 Flux

Using CIRAS-3 for soil CO2 efflux and canopy CO2 flux measurements.

Theory

Theory behind respiration/assimilation measurements in closed chambers.

Simulated Soil Respiration Measurements

FCO2 Units for measurement of Soil CO2 Efflux

Electrical and Pneumatic Connection between the CIRAS-3 and SRC-1 / CPY-4

Electrical and Pneumatic Connection between the CIRAS-3 and SRC-2 / CPY-5

Configuring the CIRAS-3 console for measurement of Soil Respiration or Canopy Assimilation

SRC-2 Soil Respiration System Settings

CPY-5 Canopy Assimilation Chamber Settings

Do I Use Linear versus Quadratic

Closed System Operation

Numerical Data Display (SRC-1 and SRC-2)

Understanding the numerical data display for SRC-1/SRC-2.

Numerical Data Display (CPY-4 and CPY-5)

CPY-4 Control Settings

Measurement Sequence

Initial Test Measurement Sequence

Recording Measurements

Section 12. Data Output

Photosynthesis Data

Format of stored data for photosynthesis measurements.

Temperature Sensor Measurement

Temperature Control Type

Light Control Type

PLC3 Used

Photosynthesis and Chlorophyll Fluorescence Data

Record Types (RecType)

Closed System Operation Data

Summary of the Gas Exchange Equations Used in CIRAS-3

Mass Flow Equation

Equation for calculating the mass flow of air into the cuvette.

Transpiration

Equations for calculating transpiration rate from water vapor partial pressures.

Leaf Temperature

Saturation Vapor Pressure

Stomatal Conductance

Net Photosynthesis

Intercellular CO2 Concentration

Physical Constants Used in Equations

Definition of Symbols

Measured Parameters

Definitions of measured parameters in gas exchange calculations.

Calculated Parameters

Definitions of calculated parameters in gas exchange calculations.

Section 13. Troubleshooting & Diagnosis

System Power

Troubleshooting issues related to system power and battery operation.

CO2 Measurement and Control

CO2r levels are reading higher than expected

Diagnosing high CO2r readings due to leaks or calibration issues.

CO2r levels are reading lower than expected

Diagnosing low CO2r readings due to exhausted chemicals or cartridge.

My CO2r is more than 30 µmol mol-1 from my set point

Troubleshooting CO2r readings deviating from the set point.

CO2 exhausts from the cartridge quicker than usual and doesn’t last a full day

CO2 exhausts from the cartridge rapidly as soon as I attempt to install a fresh cartridge

My CO2 readings are drifting

My CO2d readings are fluctuating

H2O Measurement and Control

My H2Or levels are reading higher than expected

Diagnosing high H2Or readings due to leaks or scrubber issues.

My H2Or levels are reading lower than expected

Diagnosing low H2Or readings due to exhausted H2O scrubber.

My H2Or or H2Oa values are fluctuating

Troubleshooting fluctuating H2Or/H2Oa readings due to desiccants or pumps.

Temperature Measurement and Control

My leaf temperature readings appear to be incorrect

Diagnosing incorrect leaf temperature readings.

My Tamb value is reading much different than actual ambient

Troubleshooting Tamb sensor readings deviating from ambient.

PAR Measurement and Control

Why does my PARi reads lower than PARe

Explaining why PARi readings are typically lower than PARe.

I am using the light unit but I am unable to control light intensity

Troubleshooting light intensity control issues.

My PARe readings do not seem accurate

Diagnosing inaccurate PARe readings, suggesting recalibration.

Flow Control

I am unable to achieve the set cuvette flow rate

Troubleshooting issues with achieving the set cuvette flow rate.

My pumps seem to be running harder and louder than normal

Diagnosing pumps running louder due to gas circuit restrictions.

My reference pump is not running

Troubleshooting the reference pump not running.

Data Management

I am unable to record any measurements from either both the console and the PLC3

Resolving issues with starting or recording measurements.

I can’t find my data on the USB flash drive (memory stick)

Troubleshooting lost data on USB flash drives.

I can’t find my data stored in internal memory

Troubleshooting lost data stored in internal memory.

Status Codes Displayed on the CIRAS-3 LCD

Other Status Codes/Messages

Section 14. Routine Maintenance

CIRAS-3 Main Console

Accessing internal components of the main console for maintenance.

Battery Pack (Li-ion Battery)

Information on Li-ion battery packs and their capacity.

Battery Removal

Battery Storage

Battery Disposal

External Battery Pack (For extended operation in the field)

Air Sampling Pumps (Reference and Analysis)

Replacement of Reference and Analysis Pump

Servicing the Air Sampling Pump (Reference & Analysis)

Air Supply Pump

Air Filters

Air Supply Unit Hydrophobic Filter

Maintenance schedule for the air supply unit hydrophobic filter.

Blue Reference and Analysis Air Filters (5 micron)

Replacement schedule for blue reference and analysis air filters.

Gas Blender Air Filters (25 micron)

Information on gas blender air filters.

External Air Inlet Filter Assembly (Part Number STD558)

Desiccants and Absorber Columns

Zero Column Assembly

CO2 & H2O Control Column

Soda Lime

Drierite

Molecular Sieve

Molecular Sieve Repackaging

Foam Filters

Absorber Filters

“O” Rings

CO2 Regulator

CO2 Calibration

H2O Calibration

PLC3 Leaf Cuvettes

Cuvette Gaskets

Inspection and replacement of leaf cuvette gaskets for leak prevention.

Checking For Leaks Associated With the PLC3

PLC3 Leaf Cuvette Head Adjustment

PLC3 Pneumatic Connector

Environmental Sensors

Temperature

Troubleshooting temperature sensor measurements.

PAR

Frequent checks and recalibration of PAR sensors.

Boundary Layer Determination (rb)

Changing PLC3 Universal Head Plates

Replacement of PLC3 Glass Window (For Use with CFM-3)

Section 15. Consumables/Spares

Desiccants and Absorber Columns

List of common desiccants and absorber column parts.

Pumps & Air Filters

List of common pumps and air filter consumables.

CO2/H2O Control

Batteries & Power Supplies

Cables/Data Storage

Leaf Cuvette Accessories