Contact details:

ADC BioScientific Limited

Global House
Geddings Road
Hoddesdon
Hertfordshire
EN11 0NT
UK

Telephone: +44 (0)1992 464527

Fax: +44 (0)1992 444245
E-mail: sales@adc.co.uk
Website: http://www.adc.co.uk

For details of your nearest ADC approved agent refer to our website.

© ADC BioScientific, 2017

All rights reserved. No part of this printed document or enclosed pdf file (if applicable) may
be reproduced or transmitted in any form or by any means without prior written permission of
the copyright holder.

The product described in this manual is subject to continuous development and, while every
effort is taken to ensure that the information contained herein is correct, ADC BioScientific
Ltd cannot accept any liability for errors or omissions or their consequences.
Issue 4-104 LCi-SD SD user guide

Contents
1. Introduction ........................................................................................................................ 5
1.1 Equipment list ............................................................................................................. 5
1.2 Description .................................................................................................................. 6
1.3 The Internal Calculations ............................................................................................ 7
2. Getting Started ................................................................................................................... 8
2.1 Initial Preparation ........................................................................................................ 8
2.2 Electrical Connections............................................................................................... 10
2.3 Switching On ............................................................................................................. 11
2.4 Display ...................................................................................................................... 12
2.5 Operation ................................................................................................................... 12
2.6 Error, Warning & Status Messages ........................................................................... 12
2.7 Low Battery Voltage ................................................................................................. 13
2.8 Checking the Chemical Column ............................................................................... 13
2.9 Fitting/changing a chamber ....................................................................................... 14
3. The Leaf Chamber ........................................................................................................... 15
3.1 General Description................................................................................................... 15
3.2 Leaf Chamber Constants ........................................................................................... 16
3.3 Leaf thermistor .......................................................................................................... 17
3.4 Leaf Spider (Broad and Narrow style heads only) .................................................... 17
3.5 Hold Q reading .......................................................................................................... 18
3.6 Enter given Q value ................................................................................................... 18
4. Arabidopsis & Small Leaf Chambers .............................................................................. 19
4.1 General description ................................................................................................... 19
4.2 Configuring the Chamber for use with an LCi-SD ................................................... 19
4.3 Leaf size/position: ..................................................................................................... 20
4.4 Leaf Temperature reading ......................................................................................... 20
4.5 Flowrate and stability ................................................................................................ 20
4.6 Use of the flexible neck or “Snake” .......................................................................... 20
5. The Soil pot ...................................................................................................................... 21
5.1 General Description................................................................................................... 21
5.2 Operation ................................................................................................................... 21
5.3 Preparing the Soil pot for use .................................................................................... 22
5.4 Soil respiration measurements .................................................................................. 24
5.5 Other considerations .................................................................................................. 24
5.6 Soil pot constants ...................................................................................................... 25

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5.7 Soil pot Dimensions .................................................................................................. 25
6. Routine Maintenance ....................................................................................................... 26
6.1 Chemicals .................................................................................................................. 26
6.2 Dust Filters ................................................................................................................ 26
6.3 Battery description .................................................................................................... 27
6.4 Battery Charging ....................................................................................................... 27
6.5 Battery Replacement ................................................................................................. 28
6.6 Battery Fuse............................................................................................................... 28
7. Set-up and Calibration ..................................................................................................... 29
7.1 Serial Link Port Set-up .............................................................................................. 29
7.2 Analogue Output Port Set-up .................................................................................... 29
7.3 Time & Date Set-up .................................................................................................. 29
7.4 Calibration. ................................................................................................................ 30
7.4.1 Flow check ............................................................................................................. 30
7.4.2 CO2 Zero ................................................................................................................ 31
7.4.3 CO2 signal phase correction .................................................................................. 32
7.4.4 H2O Calibration .................................................................................................... 32
7.4.5 CO2 Span Calibration ............................................................................................ 41
8. Measurement Configuration ............................................................................................ 44
8.1 The ‘config’ Function Menu ..................................................................................... 44
9. Graphical Display ............................................................................................................ 47
9.1 Introduction ............................................................................................................... 47
9.2 Operation ................................................................................................................... 47
10. Recording a Log ............................................................................................................ 49
10.1 The nature of a record ............................................................................................ 49
10.2 Taking a record ...................................................................................................... 49
10.3 Deleting a record ................................................................................................... 50
10.4 Sending a serial record .......................................................................................... 51
10.5 Deleting a serial record .......................................................................................... 51
10.6 Receiving a serial record ....................................................................................... 52
11. Data Files & Using The SD Card ................................................................................. 53
11.1 Selecting a File ...................................................................................................... 53
11.2 Reviewing Log Files .............................................................................................. 53
11.3 SD Card Data Format ............................................................................................ 53
11.4 Delete (Erase) Existing Files ................................................................................. 54
11.5 Copying Files using the USB ................................................................................ 54
11.6 Storing Cards ......................................................................................................... 54
11.7 Using Alternative Card Types ............................................................................... 54
12. How The Analyser Works ............................................................................................ 55
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12.1 Infrared Gas Analysis ............................................................................................ 55

12.2 Gas Correction ....................................................................................................... 55
12.3 Other measurements .............................................................................................. 56
12.4 Electrical Block Diagram ...................................................................................... 57
12.5 LCi-SD Gas Circuit Block Diagram ...................................................................... 58
12.6 The gas circuit Description .................................................................................... 59
13. Maintenance .................................................................................................................. 60
13.1 Tools ...................................................................................................................... 60
13.2 Accessing the Inside of the Main Instrument ........................................................ 60
13.3 Air Flow (Mass Flowmeter) .................................................................................. 61
13.4 Filters ..................................................................................................................... 61
13.5 Display Contrast Setting ........................................................................................ 62
13.6 Pump ...................................................................................................................... 62
13.7 Chemical Column filters ........................................................................................ 62
13.8 Dismantling the Chamber ...................................................................................... 63
13.9 Removing the Handle Cover ................................................................................. 65
13.10 Checking the Source .............................................................................................. 66
13.11 Checking the Detector ........................................................................................... 67
13.12 Replacing the Source ............................................................................................. 68
13.13 Fault finding .......................................................................................................... 72
Appendix 1. Parameter Information ................................................................................... 73
Appendix 2. Analogue Output Scaling ............................................................................... 75
Appendix 3. Calculated Parameters and Constants ............................................................ 76
Appendix 4. Derivation And Measured Values For Hfactor .............................................. 84
Appendix 5. Saturated Vapour Pressure ............................................................................. 86
Appendix 6. Chamber Exploded diagram ........................................................................... 87
Appendix 7. Console exploded diagram ............................................................................. 88
Appendix 8. LCi-SD Menu Structure ................................................................................. 89
Appendix 9. Technical Specification .................................................................................. 90
Appendix 10. Small Buffer Volume Construction................................................................ 91
Appendix 11. Spares and Accessories .................................................................................. 95
USER NOTES: ........................................................................................................................ 96

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1. INTRODUCTION
This manual covers the operation and maintenance of the LCi-SD Leaf Chamber/Soil
Respiration Analysis System.

1.1 Equipment list

The LCi-SD Analyser is supplied in a convenient carrying case containing the following
items.
LCi-SD Analyser “Console”
LCi-SD Analyser “Handle” or “PLC”
Carrying strap
Battery charger and power lead
Air probe and ground spike
SD card
Leaf thermistor M.PLC-011 (where applicable *)
Spare leaf chamber gasket set (where applicable *)
Leaf chamber jaw spring (where applicable *)
Handy “Menu structure” card
LCi-SD “User guide” Manual (This manual)
Jaw screw adjustment tool
In addition to the above items there is a boxed “Spares kit” SKF-115 which contains some
of the spares listed in see Appendix 10

Air probe
spare soda-lime
bottle

Reusuable
Drying agent Ground spike
for air probe

Power cable &

Battery charger
LCi-SD Console
Other accessories

SD card

LCi-SD “handle”
(PLC)

* If the LCi-SD system is part of a SRS1000 soil respiration system it is not supplied with a leaf thermistor
or spare leaf chamber gasket set but does include the chamber jaw spring in case a leaf chamber is ordered
at a later date. The spring will also be included in any system whose default leaf chamber is either an
Arabidopsis leaf or Small leaf style.

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Please note – The supplied carry case is for ‘By Hand’ transportation only, if the instrument is being shipped
by courier (for instance back to ADC for servicing) then it is highly recommended that suitable packaging –
such as a cardboard box filled with polystyrene chip is used to protect both the case and instrument.

1.2 Description
The LCi-SD (with its leaf chamber / soil pot) is specifically designed for portability and
field use, and provides internal battery power suitable for up to 10 hours of continuous
operation. Its purpose is to measure the environment of a leaf contained in the jaws of the
chamber, and to calculate the photosynthetic activity of the leaf or, when used with a soil
pot, to measure the gas exchange associated with soil biomass respiration.

The instrument comprises a main console containing a large Liquid Crystal Display (LCD),
a 5-button keypad and a microprocessor controlled operating system with signal
conditioning, air supply unit and PC (Personal Computer) card data storage. A Leaf
Chamber (PLC) is connected to the Console by an umbilical cord.

The Leaf chamber contains the PCA-275A printed circuit board comprising conditioning
and pre-amplifier circuitry for Chamber temperature, leaf temperature and PAR
(Photosynthetically Active Radiation) sensors. Two laser-trimmed humidity sensors
provide the reference and analysis humidity signals and an Infrared Optical bench is used
for CO2 analysis.

The main console supplies air with a relatively stable CO2 concentration at a controlled
flow-rate to the leaf chamber (or soil pot). The CO2 and H2O concentrations are measured,
and the air is directed over both surfaces of the leaf * (or allowed to flow around the soil
pot). The discharged air leaving the chamber (or soil pot) is analysed, and its (generally
decreased) CO2 content and (increased) H2O content determined.
* Except for the Arabidopsis leaf chamber (see section 4)

From the known airflow rate and differences in gas concentration, the assimilation and
transpiration rates are calculated and updated every second with a complete analysis cycle
taking about 20 seconds depending on the flow-rate used.
A small fan in the chamber ensures thorough mixing of the air around the leaf.

The system also measures leaf (or soil) temperature, chamber air temperature, PAR
(Photosynthetically Active Radiation), and atmospheric pressure. The PAR at the leaf and
the radiant energy balance of the leaf are calculated, (see Appendix 4).

Measured and calculated data is displayed on the large Liquid Crystal Display (LCD) on
the front panel of the console. The display has three pages, which can be scrolled through
using the “page” key. The data, (listed in the Log? and screen columns in Appendix 1) can
either be logged on a SD card or sent directly to a “dumb” terminal via the RS232 serial
link connector.

The SD card, which is located in a socket at the front of the unit, can be removed by pressing
it in to release it. The stored log (file) can be viewed on the LCD display, dragged to a PC
over the USB, or loaded directly into a spreadsheet on a PC equipped with a SD card reader.

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The measurements are carried out in an ‘Open System’ configuration in which fresh gas
(air) is passed through the PLC (Plant Leaf Chamber) on a continuous basis. Measurements
are carried out on the state of the incoming gas (the ‘reference’ levels) and after passing the
leaf/soil specimen (the ‘analysis’ levels); the gas is then vented away. This arrangement
tolerates some outward gas leakage and ad/absorption by the materials used in the gas path.

By comparison, in a ‘Closed System’, a gas sample is continuously circulated and measured

over a period of time to establish rates of change in the parameters measured. This is
therefore less tolerant to leakage and material ad/absorption.

1.3 The Internal Calculations

A complete list of Units and Symbols used, either for display, or for the purpose of
calculations, are given in Appendix 1.

A number of internal calculations are performed repetitively using the measured parameters
and various correction factors. These produce intermediate results and values for various
photosynthetic parameters derived from established formulae. Derivations for these and the
soil respiration calculations are given in Appendix 3

The calculated values are displayed on the screen to serve their main purpose of providing
a check on the validity of the measured data. This is useful for reference just before a record
is taken, and as a means of checking that the leaf is photosynthetically stable or equilibrium
is reached in the soil pot.

For a typical leaf, CO2 flux will be between -10 to +100 mol/m2/s and H2O flux will be
between 0 to 15 mmol/m2/s.

The analyser performs some checks on magnitudes of readings, particularly of certain

settings, which have pre-set limits (for example minimum airflow rate). There is, however,
a wide tolerance on ‘allowable’ settings for which the user is responsible (for example leaf
area), and which can significantly affect the validity of the photosynthesis measurements.

Further information on photosynthesis and its measurement can be found in

“Photosynthesis” by Hall and Rao, Pub. Cambridge University Press

“Plant Physiological Ecology field methods and instrumentation” by Pearcy,
Ehleringer, Mooney and Rundel, Pub. Chapman and Hall
“Techniques in Bioproductivity and Photosynthesis” by Hall, Long and Scurlock, Pub.
Pergamon Press.

Further information on soil respiration and its measurement can be found in

“Quantitative Comparison of In Situ Soil CO2 Flux Measurement Methods” by Knoepp

and Vose. Research Paper.

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2. GETTING STARTED
WARNING: If fitting or changing a chamber please read section 2.9 for further
information and advice before proceeding.

Note that this section assumes that a Broad, Narrow or Conifer (conventional) leaf chamber
is being used. Please read in conjunction with section 4 if using an Arabidopsis or Small
leaf chamber or section 5 if using a soil pot.

2.1 Initial Preparation

The LCi-SD is delivered with the internal battery fully charged and connected and the Soda
Lime column filled with fresh self-indicating Soda Lime.
If not using the LCi-SD from new check to ensure the Soda Lime is in good condition (See
section 2.8 Checking the Chemical Column for details)

Connect the leaf chamber’s (PLC) umbilical cable 15-pin plug to the LCi-SD console
connector and the three colour-coded pipes to their respective colour–coded entries (red
pipe to red entry etc). (see photograph in section 2.2)

The LCi-SD system requires a fresh air supply and preferably one that will not be unduly
influenced by the operator or local crop conditions as far as CO2 &/or H2O levels are
concerned.

The air supply should be taken from a region where the CO2 levels are reasonably stable,
preferably some 3-4 meters above ground level. The metal-bodied filter supplied in the
spares kit should be fitted in the air supply pipe, at the instrument end or the far end, as
convenient. It should be fitted with the smallest part of its body nearest to the LCi-SD.

The ADC air probe (supplied) provides such an arrangement. In use the probe should be
extended to its full length. The probe can be fitted to a tripod or attached to the ground spike
(also supplied) which can then be inserted into the ground. Note that the air probe type LC4-
070 shipped up to the end of 2015 is glass fibre, but its replacement type, LC5-070 is carbon
fibre, which is conductive and should not be extended under overhead high voltage power
lines due to the danger of electrocution.

When using the LCi-SD in a laboratory, a length of tube to the outside of the building away
from traffic will normally suffice. Good buffering against ambient changes can be obtained
with a plastic 25 litre container by making two gas connections in the lid, and arranging for
the inlet pipe to reach to the bottom of the container. This ensures maximum buffering and
minimum chance of water reaching the LCi-SD. A smaller container, typically 4.5 litres
may be used indoors if the air is sucked in from outside. Appendix 8 illustrates such a
volume. In some rare cases this 4.5 litre volume may not be big enough.

If the chamber has been left with the jaws closed for a few hours or more, the gaskets will
need to reform. This is achieved by leaving the jaws open for at least half an hour before
use (longer for badly flattened gaskets). In severe cases, it might be necessary to replace
the gaskets, which are self-adhesive. (See Appendix 10 for part numbers and section 12).

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The jaws should be left open overnight (ideally somewhere warm) in cases where the gasket
has been severely compressed, it will often recover.
It is advisable to latch the chamber jaws open when not in use.

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2.2 Electrical Connections

Power Socket

This is provided for an external 12-volt supply or the battery charger connection, and is
current limited. Reverse current flow is not prevented, which allows you to power external
equipment from the LCi-SD battery provided that the power requirements are modest.

The power socket (CON1 on the electrical block diagram) mates with a standard 5 pin 240
DIN audio plug connector. This is provided in the spares kit, pre-wired with red (+) and
black (-) power leads terminated in shielded 4mm plugs.

This socket also provides two analogue output channels of 0-5V, being voltage sources
intended for connection to a high input impedance (1M) recorder channel. They are
protected against an accidental short circuit to ground.
The connections are: Channel one = pin 4 Channel two = pin 1 0V ground = pin 5

The parameter to be output is selected by the user with /output/port/select/↑/ or /↓/ (see
appendix 8). The / outp1/2 / key toggles between output 1 & 2 The parameters and their
respective scaling are detailed in Appendices 1 & 2

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RS232C serial port

The RS232C connector (CON3 on the electrical block diagram) mates with a standard 9
pin ‘D’ type serial link cable socket (female). A suitable cable is included in the spares kit.
It provides RS232C signals and handshake lines to suit standard printers, VDU’s, PC’s etc.
The user sets the baud rate and handshake protocols. The socket connectivity is PC
standard.

AUXILIARY port (No longer fitted from serial number 32025)

USB Connector (Not shown in picture)

The USB connector is located on the long flat side next to the SD card socket. When
connected to a PC the LCi-SD appears as a mass storage device and files can be copied or
moved from/to a PC.

2.3 Switching On
Note: The /power off/ key is the only means of turning off the LCi-SD (apart from
disconnecting the battery). If the screen is too light or too dark the contrast may need
adjusting (see section 2.6 Error, Warning & Status Messages).

Switch ON by pressing the front panel “page” key l  at the top right-hand side of the
display. The screen will display the ADC trademark, operating system software version and
instrument serial number.

A few seconds after switch-on, the screen will display page 1 of three main pages showing
a set of parameters and values. The page (on) key will cycle between the three main pages.
Appendix 8 (Menu structure) shows all the pages and how they are related. The ‘function’
headings displayed at the top of each page correspond to the keys on the keypad above.

The parameters displayed on the screen include values for CO2 & H2O. With no leaf in the
chamber, CO2 anl should equal ambient CO2 ref, H2O anl should equal ambient H2O ref.
Tch (chamber temperature) and Q (PAR) should also reflect ambient conditions.

Note that after first switching on, the LCi-SD requires about five minutes for CO2
measurements to stabilise. It will display an ‘analyser is warming up’ message during this
time, and will beep when it is ready. Until then the CO2 readings will display n/a (not
available). Once the readings have settled down a check can be made to ensure that the
chamber gaskets are sealing. (Reference and Analysis readings will be similar)

Note: If you wish to bypass the warm up timer, press the left button just after it has been
switched on and is displaying the software version and serial number.

The LCi-SD comes with factory-installed default settings (see section 8.1), some of which
may need to be changed for immediate use (e.g. time & date, serial link).

Close the leaf chamber head (In the case of Conifer chambers ensure that the clip is latched)
and check that the chamber fan is rotating (usually it can be heard).

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2.4 Display
The Display unit is a LCD type with an adjustable contrast control. If the user prefers a
different contrast level, adjustment is available using potentiometer RV92 (Located in the
right hand corner of the PCA-288 ‘digital’ board.)

2.5 Operation
Prior to taking measurements on a leaf, the chamber sensors can be checked as follows.
With the chamber closed, after a few seconds the CO2ref & CO2anl readings on the LCi-
SD display should stabilise to give similar CO2 levels.
The H2O levels should also be checked for similarity and that PAR (Q) and chamber
temperatures (Tch) readings are in accordance with ambient conditions.
If these checks are satisfactory, leaf measurements can be made.

Once the leaf is enclosed in the chamber, it may take up to 2 minutes to re-adjust to its new
microclimate. During this period CO2 & H2O values will gradually stabilise. Generally a
good indication is when the value for Ci (substomatal CO2) has stabilised.

After readings are stable, a ‘record’ may be taken (see section 9.2).

2.6 Error, Warning & Status Messages

Depending on the state of the LCi-SD, or the way it is being operated; various messages
may be presented on the screen. These are of three types, ‘error’, ‘warning’ or ‘status’.

Error messages occur when a serious problem is experienced. If a software problem occurs
that results in the LCi-SD becoming inoperative, a message ‘fatal error! – cannot continue’
appears on the screen. Further lines giving an indication of the type of error that has
occurred accompany it.
In the first instance, operating the ‘page’ key can clear an error. If this action does not clear
the error, or the error re-occurs after a short time, switch off the LCi-SD and after a short
interval switch it back on.
If the instrument is switched on but does not respond to key presses, pressing
simultaneously the page key (top right) and the two leftmost keys will invoke a hardware
reset.

Warning messages indicate that it is not possible to comply with a user request. The text
of the message always describes why compliance is not possible, offering the user the
opportunity to correct the situation.
Warning messages usually appear with an OK function label, which, if operated, will allow
the user to continue anyway.

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Status messages are those that indicate the functional state of the LCi-SD, and are generally
associated with time-consuming tasks which are occupying the processor, and during which
time other normal functions are suspended. Since these messages usually relate to the
function or facility involved, these should not be disturbed in the meantime. For example,
do not disable the printer whilst the ‘printing record’ status message is on the screen.

2.7 Low Battery Voltage

The internal battery voltage is monitored to detect if the battery is close to being fully
discharged. When the battery voltages falls to 10.8 volts a ‘Warning: BATTERY LOW!’
message will appear on the status line.

At this point, there is typically about 5 minutes life left in the battery. This should allow
enough time for the user to either connect a charger or conclude his current record. If the
warning message is ignored, the LCi-SD will switch itself off once the battery voltage falls
to 10.5 volts! The message BATTERY EXHAUSTED – SWITCHING OFF will appear
just before the LCi-SD switches off.

The battery power is shown as a bar graph at the bottom of screen page 3, and also
numerically on the diagnostics page. The battery should be recharged (see section Error!
Reference source not found.) after any significant period of use, or if it is less than 12V.

2.8 Checking the Chemical Column

The removable column (furthest from the connectors see figure 2.2) holds soda lime, which
is used to strip carbon dioxide. The other column is used as a water trap and filter. On
delivery the soda lime column is filled with an indicating Soda Lime.

To maintain the performance on the LCi-SD, always replenish the soda lime when it
is exhausted. This is shown by a colour change of white to violet. (See also section 6.1)

Disconnect the column by pulling it outwards at the top and bottom then lift off the top cap.
Fill the column to just below the top with the chemical. Tap the column a few times against
a solid surface to compact the chemical and top up as required. Replace the top cap. Ensure
that all ‘O’ rings are lightly greased with the supplied silicone grease and that both ends are
located tightly to prevent gas leaks then refit the column to the console.

It is possible to use the LCi-SD on its side so that the columns are horizontal. Ordinarily in
the horizontal position, chemical in the column would not be effective, as it would settle so
as to leave a continuous horizontal air gap. To avoid this problem, the soft plastic cap (OP2-
134) in the spares kit may be fitted half way along the column. The hole in the cap forces
the air to pass through the main bulk of chemical. The cap also allows the economy of a
half-used chemical column to be easily half emptied.

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2.9 Fitting/changing a chamber
This information applies to all chamber types and to the Soil pot.
Note that only the “conventional” broad, narrow and conifer leaf chambers have separate
upper and lower jaws whilst the Arabidopsis and Small leaf chambers and the Soil pot
feature an “interface block”. All references to “jaw” in this section also apply to the
“interface block” where applicable.

Description

The jaw is fitted to the handle using three captive screws. The three screws carry the
analysis stirrer fan signal, the "Jaw closed" sensor switch signal.and the ground return.
The Arabidopsis and Small leaf chambers and the Soil pot do not contain a “Jaw closed”
sensor switch and so the screw is grounded.
Care should be taken as described below.

Fitting a chamber

Before fitting the chamber, check to see that the five “O” rings are all in place (two gas
stems and three sensor housings.
When fitting a chamber, press down on the jaw itself then turn the three captive screws
USING THE FINGERS ONLY. A jaw screw adjustment tool (LCI-220) is provided in the
flight case , this may be used to tighten the screws but only to the point where the tool starts
to bend.

DO NOT USE A SCREWDRIVER OR COIN as overtightening the screws may destroy

the electrical connections through to the circuit board inside.

DO NOT PUSH DOWN ON THE SCREWS as this may dislodge the mounting bushes
from the handle baseplate, causing loss of the electrical connections. To ensure that the jaw
forms a good gas-tight seal it is only necessary to push down on the jaw itself (a small gap
between the jaw and the handle baseplate is permissable as the "O" ring seals will ensure a
gas-tight seal)

Removing a chamber

When removing a chamber it is permissable to use a small coin to unscrew the three captive
screws but again it should be stressed that no downwards pressure should be applied to the
screwheads.

Check to ensure that the small "O" rings on the two gas stems in the handle baseplate remain
in place and are not carried away in the jaw.

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3. THE LEAF CHAMBER

3.1 General Description
The PLC consists of a handle and an interchangeable leaf chamber or soil pot (See section
5 for Soil pot description and Appendix 6 for an “exploded” view of the handle assembly).

There are five styles of leaf chamber available. These are Arabidopsis, Small, Broad,
Narrow and Conifer leaves. Refer to section Error! Reference source not found. for a
escription of Arabidopsis and Small leaf chambers, which are very different in design to the
other chambers.

The handle houses a jack socket for use with a detachable leaf temperature sensor, a ‘record’
switch, and an electronics board providing sensor amplifiers for signals to the LCi-SD
console.
An umbilical cable is attached to the handle linking the electrical signals and gas lines to the
LCi-SD console. Repeated bending can damage this cable. When storing the chamber, try
to avoid tight bends in the cable especially where it joins the handle and plug.

To minimise noise on the measurements, the chamber should be held as steady as possible
during the measurement. To assist the user in this regard, the underside of the chamber has
a thread for a ¼” Whitworth tripod screw.

The Broad, Narrow and Conifer leaf chambers consist of an upper and lower head section
and a radiation shield. The radiation shield can be easily removed without affecting the
functionality of the chamber. You may wish to do this where solar radiation is not a problem,
and the shield is too bulky.

The PAR sensor is mounted on the upper head section and is accessed by removing the heat
shield. The sensor housing is an “interference fit” in its mounting bracket.

The upper head section can be removed to give access to the gaskets, the stirrer, and the
three lower jaw fixing screws. Remove the jaw by pressing down to compress the spring,
then twisting the jaw to disengage the hinge pin on the slotted side then withdrawing the
other hinge pin. This

The three fixing screws and lower section can be removed to access the temperature and
humidity sensors.

To change a chamber (see Appendix 6), unscrew the two mounting screws in the radiation
shield by about 10 turns, it is not necessary to remove the screws completely as they are
“captive”.
Lift off the radiation shield and pull the PAR sensor off its mounting plate.

While holding the upper jaw fully open, twist it slightly so the hinge pin slides out on the
slot side. The upper jaw can now be lifted away from the handle, exposing the lower jaw
fixings.

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Unscrew the three knurled captive screws, which retain the bottom jaw, about 6 turns. It is
not necessary to completely remove them. The bottom jaw can now be removed, exposing
the two humidity sensors, Chamber temperature sensor and the two gas entry stems. Note
that the gas entries and the three sensor housing all have an “O” ring seal. It is important
that these seals are not lost. Spare “O” rings are supplied in the Spares kit (Also see
Appendix 10).

When replacing the jaws, note that the coin slots in the knurled screws are intended to assist
with removal rather than tightening, finger tight is generally sufficient.

If the chamber is changed for a different style, it is necessary to inform the analyser using
/config/ and /+/ or /-/ until the chamber displayed is the chamber type fitted.
Note: Selecting the correct configuration and performing a flow check is essential if
changing between “conventional” leaf chambers and the Arabidopsis/Small leaf
chambers or the Soil pot.

When the correct configuration is selected the appropriate factory default values of rb, Hfac,
and Trw (see below and section 3.2) are automatically chosen, and they may then be
individually adjusted if required.

The chosen configuration and any manual changes made to the values by the user are saved
at power off.

The broad chamber has a square (6.25cm2) aperture sealed around the edge, and can be used
for any flat leaf, whether the leaf fills the aperture or not.

The narrow chamber has a rectangular (5.8cm2) aperture sealed around the edge, and can be
used for long flat leaves, i.e. grasses etc.

The conifer chamber is cylindrical in design with sealed edges and can be used for non-flat
plant material i.e. conifer needles, small fruits etc.

3.2 Leaf Chamber Constants

The design of the leaf chamber affects various parameters, which are constants for a
particular design or type. These include ‘rb’ (boundary layer resistance), ‘Hfactor’ (the level
of radiation energy affecting the leaf (referred to as ‘Trans’ on LCA2 & 3)), and ‘Trw’ (the
transmission factor of the chamber windows {and radiation shield where applicable} to
PAR). These constants may be changed with /config/select/. When the appropriate
parameter is highlighted, it can be modified with the /+/ and /-/ keys.

‘rb’
The value for ‘rb’ is influenced by the efficiency of gas mixing within the
chamber, ab/ad-sorption of CO2/H2O of the materials used, and ‘dead’ volume.
[see section 8.1 for typical values].

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‘Hfactor’
Previously defined as ‘Trans’ in LCA2 & 3 references, Hfactor is affected by the
material used for the shield (if fitted) and the chamber window. This is due to
the different transmission factors at the wavelengths in the visible and infrared
regions, the position of the PAR sensor (inside or outside the cuvette), and the
type of light source. [see Appendix 4].

‘Trw’
On the chambers, the measurement of PAR is via a sensor mounted on the upper
jaw adjacent to the window. The value for PAR at the leaf (Qleaf) is therefore
less than that measured (Q) by factor ‘Trw’ – the transmission factor of PAR
introduced by the arrangement of the chamber shield &/or window.
(See Section 8.1 for typical values, with and without the shield.)

3.3 Leaf thermistor

The leaf temperature may be measured as an alternative method to calculating it. The
software switch between the two options is Tl mtd in the /config/ menu.

In general, if the broad chamber has a large broad leaf with a known area, or is so big that it
completely fills the chamber, so that its area is 6.25cm2, then calculated leaf temperature is
best.

If the area is uncertain, e.g. conifers, the temperature will need to be measured. This
measurement is made with a microchip thermistor attached to a jack plug with thin wires
(supplied). The plug connects to a socket on the chamber handle and the thermistor is rested
on the leaf with the wires trapped between the jaws together with the leaf. To hold the
thermistor in position it is sometimes easier to insert it in a small cut made in the leaf with
a scalpel, or by taping the wires to the edge of the chamber.

3.4 Leaf Spider (Broad and Narrow style heads only)

The integral thermistor is a similar microchip on a springy ‘spider’ mounting that is fitted in
the Broad and Narrow jaws and touches the underside of the leaf. It is held in place in the
lower jaw with two pins. To fit it, remove the top jaw, connect the horizontal pin of the spider
by pushing on the back of the connector socket. When it is fully connected, align the vertical
connector with its mating pin, and push it together by pressing on the back of the connector
socket. To remove the spider, use a pair of thin nose pliers with serrated jaws, or a strong
pair of tweezers with serrated jaws. Hold the end of the vertical socket and pull it off gently,
ensuring that there is no sudden snatch when it finally disengages. Then hold the horizontal
socket between the two plates and pull the connector off about 1mm. With a cocktail stick
or similar, hold the free side of the spider above the edge of the jaw, whilst pushing apart the
connector with another stick.

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3.5 Hold Q reading

The first main menu page has two buttons ( /Q hold/ & /Q rel./ ) that hold or release the
PAR (Qleaf) reading. This facility can be used with a light unit as follows: The PAR sensor
is removed from its usual position, and placed in the chamber. The resultant PAR reading
(Qleaf) is held by pressing the /Q hold/ button. The PAR sensor is removed from the chamber,
and replaced by the leaf. All subsequent calculations are based on the frozen value, which
can be used for many leaves. Normal operation is restored with the /Q rel./ button

3.6 Enter given Q value

This facility allows the use of an alternative light source with a known radiation output.

In addition to the two buttons referred to in paragraph 3.4 the first main menu page also has
a button ( /Q given/ ) that allows a given value of PAR (Q) to be used.

The “given” value is entered from the /config/ menu by selecting Q then using the +/-
buttons to enter the required value. The default value is 1500µmols m-2 s-1. Any value
between 0 and 3000 in increments of 5 may be entered in each of the eight leaf chamber
configuration set-ups. Once the /Q given/ button is pressed the given value will conform to
whatever configuration is being used at the time. Press the /Q rel/ button to return to
measured values.
If the /Q hold/ button is pressed whilst “given Q” is being used the current value for Q will
be held even when changing to an alternative configuration set-up. Note however that when
the /Q rel./ button is pressed the value for Q will return to measured not given.

Note: The given value entered in the configuration set-up is for PAR (Q) and not PAR
(Qleaf) which takes window and shield transmission factors into account. To obtain a specific
value for Qleaf the given value will need to be calculated. Given = Qleaf / Trw
E.g. Required Qleaf = 2000µmols m2 s-1 Q given = 2000 / 0.87 = 2299

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4. ARABIDOPSIS & SMALL LEAF CHAMBERS

4.1 General description
These chambers are designed specifically to access small leaves that grow close to the
ground. Due to their very small size they do not have light or temperature climate controls
available and do not have a radiation heat shield. The head consists of an “interface block”
that attaches to the handle using three captive screws and spacers (see following paragraph
and figure for LCpro+ configuration) and a leaf chamber that is carried at the end of a
flexible neck or “snake”. The flexible neck allows the leaf chamber to be positioned where
needed. The “snake” can then be locked into position by means of a lever on the interface
block.

The chamber jaw has an offset spring that holds the jaw closed. When the jaw is opened
manually the spring passes through the fulcrum point and holds the jaw open. When not in
use the jaw should be left in the open position to prevent the gaskets from becoming
compressed.

4.2 Configuring the Chamber for use with an LCi-SD

The three fixing screws that secure the interface block to the chamber handle are each fitted
with a spacer that is required for the longer sensor bodies on an LCpro analyser.. They
ensure correct spacing to suit the handle sensors and correct electrical connection or
insulation as appropriate. When using the chamber on an LCi-SD these spacers must be
fitted directly under the head of the captive screws as shown in the right–hand figure below.

The configuration is as described below.

The interface block has a spacer fitted onto

each of the fixing screws on the upper side of Metal Spacers
the interface.

Plastic Spacer

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4.3 Leaf size/position:
The Arabidopsis leaf chamber (active window
diameter 11mm) has an air supply in its base. A leaf
in this chamber should be arranged so that it does not
fully cover the chamber (see figure), otherwise there
would not be any airflow over the top surface.

There is however, no restriction on the position of the leaf in the Small leaf chamber (active
window diameter 16.5mm) because it has an air supply path in both the top and base.

4.4 Leaf Temperature reading

Note that since there is no integral leaf thermistor in either of these chambers, the measured
leaf thermistor reading (Tl (m)) will be invalid and read ↑o/r↑ (over range) unless the
thermistor probe (Part No. PLC-011) is plugged into the jack socket. The message “Tleaf
probe error” will appear on the Status line. Alternatively the calculated rather than measured
leaf temperature reading method (Tl (C)) can be selected.

4.5 Flowrate and stability

The exposed leaf area in both these chambers is small (being a maximum of 0.95cm2 for the
Arabidopsis chamber and 2.14cm2 for the Small leaf chamber). In order to obtain a
reasonable CO2 it is necessary to reduce the airflow (by selecting /config/Uset/) to a low
value e.g. the minimum value of 68. This will give a CO2 of about 10-ppm for the
Arabidopsis chamber with a large active leaf. With such low values of CO2, it is necessary
to ensure good stability of the CO2 concentration in the supply air. This can be obtained by
taking the air supply from a place away from human breath, by ensuring that the air probe
is used or drawing air via a large container e.g. a 25 litre container as used for carrying water.
It is advisable to perform a flow check calibration when changing from the Broad, Narrow,
and Conifer leaf chambers or Soil pot to an Arabidopsis leaf or Small leaf chamber.

4.6 Use of the flexible neck or “Snake”

The handle should be supported on a small tripod or laid on the ground next to the plant.
The “snake” can then be positioned with the leaf to be tested inserted in the chamber and
finally locked in place by moving the locking lever down into its slot.
When not in use the “snake” should be left in the relaxed position, (locking lever up) in
order to prevent stress of the tensioning wire.

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5. THE SOIL POT

5.1 General Description
The ADC LCi/LCpro soil pot is a chamber incorporating an enclosed volume used for the
measurement of gas exchange associated with soil biomass respiration. It is designed
specifically for use with the LCi-SD and LCpro-SD.

The Soil pot consists of an acrylic pot containing an air stirrer fan and pressure equalisation
vent. A separate temperature probe is supplied that may be inserted in the soil adjacent to
that under analysis. In addition a stainless steel “ground spike” to support the soil pot and a
“Collar insertion pad” is supplied for pushing the collar into firm soils.

5.2 Operation
To use the soil pot it should be selected as the chamber type in the configuration menu (see
section 3.1). Since the analysis flow has quite a different characteristic than the leaf
chambers it is important to carry out a flow check when the chamber is changed to and from
the soil pot. When making such a change the software reminds the user of this and asks
whether a flow check should be done. Note that it is important that the relevant chamber is
attached when the flow check takes place.

The soil pot accepts “reference” air and passes “analysis” air to the cell in the same manner
as conventional chambers. The flow of air into the soil pot is controlled by the “Uset”
function in the configuration menu of the LCi-SD. An excess of air is provided to the hood
over that extracted for measurement, and a pressure relief vent ensures that the hood is not
pressurised as this would interfere with the gas exchange at the soil/air interface.

The temperature and humidity of the air within the soil pot is monitored in the normal
fashion by the chamber sensors Tch, Ean, Eref.
The soil temperature is measured with the special soil temperature probe supplied, which
is plugged into the handle’s jack socket. This probe uses the same type of thermistor as the
leaf temperature probe and has a small non-linear response, which is compensated for by
the software in the analyser. The temperature range of both sensors is : -5°C to +50°C

A “Leaf Chamber Jaws OPEN” message will be present until the soil pot has been attached
correctly. A “Tleaf probe error ” will be seen on the instrument’s status line if the leaf
temperature method is set to “measured” until either the probe supplied or the standard Leaf
Thermistor probe (ADC Part No. M.PLC-011) is connected. It is advisable to always use a
temperature probe and configure the leaf temperature method to “measured” (Tlm).

Since the air above soil can be near dew point the warning “analyser condensation risk” is
more likely to occur than with leaf chambers. The risk of condensation can be removed if
the instrument is at ambient temperature or above so ensure that the instrument is left on
without making a measurement for an hour or so if it has been taken from a colder
environment.

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5.3 Preparing the Soil pot for use

5.3.1 Removing the existing leaf chamber

Remove the Shield from the current leaf chamber upper jaw, unplug the PAR sensor then
unhinge the upper jaw from the handle. Using a suitable coin (if required), unscrew the
three captive screws from the handle and detach the lower jaw from the handle, unplugging
the Peltier cable if necessary. Safely store the upper and lower
jaws, shield and spring.
Note: When swapping between leaf chambers and the soil pot,
be careful not to lose the ‘O’ rings, particularly the two small
ones. If these two remain in the chamber jaw, poke them out
and fit them to the ends of their pipes before fitting the Soil
pot.
Captive screws

5.3.2 Attaching the soil pot to the handle

The soil pot is attached to the LCi-SD handle in the same manner as a leaf chamber, using
the three captive screws. (See photo).

Important Note:
The LCpro-SD sensors are longer than the LCi-SD,
requiring longer screws and spacers to be fitted. In
order for the Soil pot to be used on both instruments
the same length screws and spacers are used but their
configuration is different. In the default
configuration (suitable for the LCpro-SD) the
spacers are fitted on the outside of the hood (see
figure) and the fan drive screw’s spacer (bottom
screw in photo) is plastic to avoid a short circuit to
the handle baseplate.

If the soil pot is to be used with an LCi-SD

analyser, the spacers on the three screws should Shown in LCpro
all be metal and fitted directly under the heads of configuration
the captive screws. (See figure right). An extra captive screw
spacer
metal spacer is provided in the spares kit for this
purpose.
Shown in LCi-
SD configuration
configuration
The spacers are not threaded all the way through
and should be fitted onto the screws threaded end
first to avoid the spacer binding. (see figure right)

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Issue 4-104 LCi-SD SD user guide

The PAR sensor

should be fitted in the
top of the vent spacer
as shown.

5.3.3 Inserting the “Collar”

The “collar” (if used) should be inserted into the soil as far as is necessary to eliminate
diffusion through the soil. If for example the
soil is loose, the collar should be inserted quite
deeply. This is in order to minimise gas
transference through the soil and also to
provide more support to the soil pot. Firmer soil
may be difficult to penetrate and the “Collar
insertion pad” should be used. (See Photo).
Using the Insertion pad minimises the
possibility of damage to the collar.

Note: Depending on the soil condition the user

may feel the collar is not required and may
insert the soil pot directly. This may disturb the soil to a lesser degree and allow
measurements to be taken sooner than would otherwise be the case.
See “5.5 other considerations”

5.3.4 Locating the hood on the collar

Once the “Collar” has been inserted the soil pot (coupled to the handle), can be installed.
The soil pot should be placed above the collar and pushed down until the hood forms a
good seal over the collar.

5.3.5 Attaching the “ground spike” and PAR sensor

A metal spike is provided to support the

handle, it provides best support when
angled towards the rear of the handle (see
photo). It does not need to be fitted at all
times, but will help take the strain off the
umbilical cable, or help support the
handle if the Soil pot is being used on a
gradient. A ‘foot’ is supplied that may be
fitted to the ground spike for use in soft
media – such as sand. It is not
recommended that this is used to insert
the spike with any great force.

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5.3.6 Flow check calibration (See also section 5.5 “Other considerations”)

A flow check calibration will now need to be performed. This is important as the fan in
the soil pot has different characteristics compared with the leaf chambers which can affect
the analysis gas settling time, especially at very low flow rates. If the settling time is too
short then inaccurate readings may be obtained.
The suggested flow rate is 200 µmols s-1. Ensure that the displayed NCER reading is stable
before doing this flow check. The flow check need only be done once even if the
instrument is switched off, unless the jaw type is changed and used in another
configuration. If the flow rate or jaw type is changed then redo the flow check calibration.

5.4 Soil respiration measurements

The soil pot is now ready to begin soil respiration measurement, but read “5.5 other
considerations” before continuing. After measurements have been recorded the log file may
be downloaded into a computer and calculations performed to determine the amount of soil
respiration taking place. See “Appendix 3 Calculated parameters and constants”.

Note: at a flow rate of 200 µmols s-1 it will take 15-20 minutes for the instrument to obtain
an accurate reading starting from either the end of stage six if just done, or from the
instrument having completed its warm up (indicated by a short bleep) having been switched
on.

Important Note:
After refitting the leaf chamber it is important to repeat the flow check calibration.

5.5 Other considerations

The “Collar insertion pad” should not be left on top of the collar before a measurement, as
the soil should be allowed to ‘breathe’ naturally.

It is recommended that the collar be left in place for at least a few hours for a minor soil
disturbance and at least a day for a major one before results are taken in earnest.

Additional collars may be purchased enabling several test sites to be defined and the collars
left in place. This also has the advantage that the collar is only inserted once, avoiding further
soil disturbance, which is known to upset soil respiration.

Flow check calibration is performed to allow the analyser a long enough time for gas
readings to become constant during the reference and analysis parts of the cycle and should
preferably be done at the same flow as the user intends to operate the soil pot.
The recommendations above are suitable for most applications but if the user wishes to keep
the cycle time as short as possible or the soil is very active, then the calibration should be
performed at higher flow rates such as 250 – 300 µmols s-1

When a soil pot is fitted, neither the temperature nor the light control should be activated
either in a sequence or in climate control. This is because the control circuit will consume
battery power to no good effect.

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5.6 Soil pot constants

The only soil pot constant relevant for respiration calculations is the area so other leaf
chamber associated constants are not displayed once the soil pot is selected. This has been
pre-set to 97.5 cm2 which assumes the collar is used (see section 3.3). This can be altered in
the usual way changed with configure set up select.

Screenshot:

5.7 Soil pot Dimensions

5.7.1 Using the soil pot without a collar

The surface area of the enclosed soil is nominally 132.5cm2

The volume of the soil pot (without soil intrusion) is nominally 839cm3 (839ml)

5.7.2 Using the soil pot with a collar:

The surface area of the enclosed soil is nominally 97.5cm2

The volume of the soil pot (without soil intrusion) is nominally 803cm3 (803ml)

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6. ROUTINE MAINTENANCE

6.1 Chemicals
The performance of the LCi-SD is dependent on the satisfactory condition of the soda lime,
which is in the column furthest from the connectors. The life expectancy of the soda lime
before it becomes exhausted depends on use and ambient conditions; but is approximately
200 hours at normal CO2 (air) levels. The soda lime supplied is an indicating type, which
turns from white when fresh, to violet when exhausted. Some water content is necessary
to assist the chemical reaction, which is to convert CO2 to calcium carbonate + H2O. Re-
conversion back to soda lime is not practicable, the colour may revert back when stored in
an airtight container, it will not work for long if used.

Alternative Chemicals

Soda lime is commonly available, but is unlikely to be an indicating type – this will lead to
erroneous CO2 measurements if the soda lime is used (unknowingly) in an exhausted state.
Occasional calibration of CO2 and/or H2O ‘span’ levels may be necessary. Unless a serious
problem (with a part) exists, the need for re-calibration is not usually obvious, and may only
become apparent if LCi-SD values are in disagreement with another similar instrument, or
known gas concentrations. In this case however, note also that if the ‘zero’ chemical is
exhausted, a false zero calibration will occur resulting in lower values!

6.2 Dust Filters

Although ‘clean’ chemicals are supplied, in practice fine dust particles can be given off,
which eventually may cause a malfunction of the mass flow sensors and/or the optical
bench. This will also be the case if dust or pollen is drawn in from the air supply.

The filters used are designed to prevent this, but will gradually restrict the airflow in the
process.

If difficulty is experienced in obtaining the maximum (PLC) flow of 340 mol sec-1,(ie.
indicated flow ‘u’ very much less than 340 µmol sec-1 and pump “racing”) this can be taken
as a sign that filters should be changed.

The most likely filter to become blocked is the external plastic bodied one, if fitted.
Otherwise, check the 3cm diameter disc filter with a Luer connector, located under the top
bezel. In dusty atmospheres, with continuous operation, and no other external filtering, this
can become blocked in less than a week. If in doubt, compare its colour with the one in the
spares kit. The other filters are not transparent so cannot be checked visually.

The next filter to check is the external metal bodied one, if fitted. It contains a 25m gauze
filter element that can be cleaned with a small brush. Replace it with the largest part of the
body on the inlet side as this will ensure that trapped dirt is on the outside of the mesh and
can be easily removed.

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6.3 Battery description

The LCi-SD has an internal sealed re-chargeable lead-acid battery, which, when fully
charged, operates the system for about 10 hours. Battery power is shown on a bar graph,
and also as a numerical voltage ‘Vbatt in the /config/diagnose/ page. The battery and the
supply fuse are located in the base of the console, and are accessed by rotating the two
spring fasteners on the bottom panel and opening it. The battery can then be lifted out, and
removed, after disconnecting the two spade terminals.

Spares are available through ADC, or as advised by local agents.

When the battery in the LCi-SD is near to a discharged state, a warning – low battery
voltage message is flashed on the display. In this event, terminate the work as soon as
possible, switch the LCi-SD off and, either recharge, or replace the battery. If a suitable
external DC power source is on hand, connect it to the LCi-SD as soon as the message
appears. In this case, work can continue undisturbed.

If you plan to store the instrument, fully charge the battery first. Giving it an 8-hour top up
charge at least once every 6 months will maximise its life. It is not necessary to remove the
battery, but if you do, and leave it out for a few weeks, you may find that the rechargeable
clock battery has become discharged and so you will need to reset the clock.

6.4 Battery Charging

The battery can be re-charged in situ via the five-pin power socket on the side, using the
charger lead supplied or it can be removed (See section 6.5 Battery Replacement) and
charged directly. The LCi-SD can also operate from an external 12-volt supply of at least
0.3A capability (using the charger lead), without the internal battery fitted. Be aware that
there is no diode to prevent power flow back out of the battery (although there is a fuse), so
disconnect the charger from the LCi-SD when the charger is disconnected from the mains.

The main battery will give several years service, providing the following precautions are
taken:

Never over-charge the battery as this can damage it. An indication that a battery is being
overcharged is a noticeable rise in temperature. When the instrument is being used in the
field on a daily basis, an overnight charge will be sufficient; do not leave the battery on
continuous charge for more than a day.

Never store the battery in a discharged condition – this will shorten its life.

Never charge the battery using a constant current supply, commonly used to charge Ni-
cad batteries – this can over-charge it. A constant voltage supply only should be used, i.e.
one in which the charge current (which must be monitored) is set by adjusting the supply
voltage, or an ADC battery charger.

In the field, the battery can be charged to some extent by connecting it with the power cable
supplied to a vehicle battery. It will be more fully charged if the vehicle engine is running.
For field operations, spare, fully charged batteries will extend operating time.

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6.5 Battery Replacement
Battery replacement can be done at any time but, before doing so, switch the LCi-SD OFF
via the /power off/ function. Data held at the time will then be preserved. Batteries cannot
be expected to last beyond 5 years. Symptoms of a faulty battery are a short running time
even after it has been left on charge for 8 hours, or a very small charging current, even if it
appears to be discharged.

With the instrument upside down, undo the two fasteners on the base plate of the LCi-SD
by rotating them a quarter turn; the base plate can then be removed to expose the battery.
Disconnect the battery by gripping the spade terminals and not the wires. Turn the
instrument the right way up to withdraw the battery. Reconnect a replacement, ensuring
that the LCi-SD RED lead terminal is connected to + and the black terminal to –. Fit the
battery into the LCi-SD, and replace the base plate by rotating the two fasteners a quarter
turn then pressing firmly until they are heard to click.

6.6 Battery Fuse

The battery fuse is a 20mm glass type located in a clip type holder alongside the battery
under the base plate. This 1Amp fuse is connected in series with the battery ‘positive’. The
battery will need to be removed to access and change the fuse.
Under normal conditions, the fuse should not fail. If it does, it could be due to an internal
fault, by a high voltage applied externally, by an external supply reversal or by the battery
over-charging which can cause its terminal voltage to increase. Providing the cause of fuse
failure/s is removed, and the fuse is replaced (a spare is provided), the LCi-SD will have
been protected from permanent damage.

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7. SET-UP AND CALIBRATION

While in use, all the current attributes and settings are retained indefinitely by a non-volatile
electrically alterable RAM. A small rechargeable battery supplies the clock. If the LCi-SD
supply is removed (e.g. its battery is discharged), this battery will become discharged,
typically after 7 weeks. It will be automatically re-charged when LCi-SD power is re-
applied, but it will be necessary for the user to set the date and time (See section 7.3).

7.1 Serial Link Port Set-up

/output/serial/ gives a menu to select baud rate and handshake protocol.
Set the required baud rate by highlighting it with the /select/ key then use the /+/ and /-/
keys to cycle through the options of 300, 1200, 2400, 4800, 9600, 19200, 38400, 75800,
115200 and 230400 baud.
Highlight the handshake to cycle through the options of “none”, “CTS”, “xon-xoff” and
“use CTS for record”. If you select “CTS for record”, you will not be able to send recorded
data over the serial port. If you try to do so you will get a message ‘Serial port set for record
trigger’.

7.2 Analogue Output Port Set-up

/output/ gives a display of a list of parameters, one of which can be selected for the chart
recorder output. The menu gives the usual cursor controls over a number of parameters,
which can be selected with the /+/ and /-/ keys. The selected parameter will not be output
until the page key is pressed.

7.2.1 Output Parameters & Scaling

The type of parameter which can be output is selected from those which are measured
directly or indirectly by the LCi-SD or its leaf chamber, and usually after any
compensation has been applied.

Appendix 1 lists the parameters available for analogue output, together with their
expected ‘offset’, if any, and full scale output range.
The port output is scaled at 0.0V = zero or offset and +5.0V = full scale readings (see
Appendix 2 for further details)

7.3 Time & Date Set-up

Pressing /configure / time/date/ displays the Time and Date menu. Press /select/ to step
through hours; minutes; seconds; day; month; year Pressing /change+/ or /change-/
increments or decrements the chosen parameter (except for seconds which resets to zero).
The clock is in a 24-hour format.

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LCi-SD user guide Issue 4-104
7.4 Calibration.
Press /calibrate/ to access the calibration menu. The various options can be chosen with
/select/ and the /+/ and /-/ keys used to set the value where applicable. Press /do cal/ to start
the calibration.

7.4.1 Flow check

Note: The displayed values for u and uset are related to the Air Supply Unit (ASU)
which provides flow to the leaf chamber. Although proportional to the ASU flow to
some extent, the values displayed during a Flow Check calibration are the estimated
flow through the analysis cell and the time allowed before the gas is stable and a
reading taken. Typical values for broad, narrow and conifer chambers are shown
below.
Analysis times for Soil chambers and Arabidopsis style chambers may be longer due
to the larger chamber volume and lower advised ASU flow respectively.

It is strongly recommended to perform a flow check calibration if you change between

chamber types or make a change to the chamber air supply flow larger than 30%. The flow
check calibration checks that the cycle times are long enough for the gas in the analysis cell
to become stable before the absorption is measured. The flow check adjusts the cycle times
for both reference and analysis, therefore the chamber jaws must be fully closed before the
check is started.

Changing the flow by greater than 30% without doing a flow check may result in insufficient
settling time which may cause measurement errors because the gas concentration in the cell
will not have had time to stabilise. It can cause an offset in the CO2 readings even with
nothing in the chamber.

Typical flow values and normal variation from typical values that can be expected

ASU set flow Settling time (seconds) Estimated flow (µmols s-1)
(µmols s-1) Reference Analysis Reference Analysis
200 4.45 3.86 83 97
300 4.32 3.36 85 110
Variation 10% 10% - 25% 5% 10% - 20%

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7.4.2 CO2 Zero

The CO2 zero setting is automatically maintained by a software adjustment during each
zero cycle. The adjustment effectively changes the gain in order that the signal level, when
zero gas is flowing, is constant. For this to be performed correctly, the ‘zero’ soda lime
column must be kept in a non-exhausted state. If this is not the case, there will be an
apparent reduction in measured (span) values and a warning message ‘cref low, check
absorber’ when the soda lime is completely exhausted. This effect may therefore appear to
indicate that a ‘span’ calibration is necessary, when in fact it will not be. Prior to reaching
this conclusion, ensure that the chemical has been checked.

The degree of software zero adjustment being applied can be checked with
/config/diagnose/. The C(z) reading should lie between 50,000 and 60,000 counts. If this is
not the case, the warning message “cref low, check absorber” will already be displayed and
a hardware adjustment can be made.

To perform a CO2 zero enter the calibrate menu, and select CO2 zero, do cal. Adjust the
relevant pot using the pot adjustment tool provided in the spares kit (see the following
photograph below) to reduce the displayed count to within 100 counts of zero, turning it
clockwise if the display shows a down arrow. A value within 10% of the range will be
functional, and will cause ‘OK’ to be displayed. If the adjustment is very wrong, or if there
is another fault, other messages will be displayed; “CO2 low energy”, or “CO2 signal over-
range”.
The chemical in the column MUST be in a good condition at all times for correct zero
operation. If the check indicates maladjustment, check the state of the chemical before
any potentiometer adjustment.

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7.4.3 CO2 signal phase correction
It is not normally necessary to set the CO2 signal phase correction unless a new infrared
source or detector has been fitted or a large adjustment has been made to the CO2 zero.

The set phase operation is fully automatic but can be escaped from without effecting a
change by pressing any button.

During the set phase operation, the instrument performs a series of checks in 1° steps
between 65 ° and 100 ° to find the phase correction that gives the best CO2 signal energy.

During the scan the current angle being checked and the best angle found so far are
displayed. When the best angle remains the same, the scan has probably already found the
ideal angle. It is worth keeping an eye on the best angle and noting its value. Typically, the
phase correction angle is between 70 and 80 °.

When the scan is completed, it will show the best angle found and ask whether you wish to
save the new setting.

7.4.4 H2O Calibration

Recalibration and Small ∆ e offsets.

RH recalibration should not normally be required, unless a sensor has become faulty and
been replaced. As long as a system is returned every 4-5 years for service by ADC (which
includes RH calibration and a linearity test), then recalibration should not be necessary.
A small ∆e error due to component drift does not have a significant effect on the final
calculated value of transpiration rate (E).
A small ∆e error may however be eliminated by first making sure the air supply is stable i.e.
via a volume; second, by making sure the jaws are correctly fitted with no gaps in the
gaskets, no loose screws, no missing ‘o’ rings, and finally if a delta e is still present, then a
H2O span may be done in the calibration menu using the measured value of e’ref as the span
level. This should only be done after both e’ref and e’an have been stable for 20 minutes or
more at a flowrate of 200 µmol s-1 or higher.

Special note on Replacement Sensors

If replacing an RH sensor before recalibration, please be aware there are two types.
The original sensors will only work on the LCi and LCi-SD up to
and including software version 2.12.
The new type sensors will work in the LCi-SD with at least 2.13
software. The software version may be easily upgraded by parties
other than ADC, but a hardware modification may also be
required.
Contact ADC Bioscientific for more information on software
upgrading if required. The software version is displayed on the startup screen.
In the above photo, the original sensor is shown on the right, it has a rectangular shaped
sensor face. The new type is on the left, it has a small circular hole for the sensor face.
The part numbers are for the LCi, old type – LCi-032 and new type LCi-037.

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Full H2O Calibration

This may be done outside of ADC Bioscientific, but the following equipment will be
necessary. (If a dew point generator is being used then not all the following may be needed
depending on the additional features of the dewpoint generator, e.g whether it has a variable
air pump/flowmeter).
1. A source of dry air or granular drying agent.
2. A float flowmeter (air) of, or close to, the range 0-500ml/min (1000 ml/min if using method
2 of the H2O zero calibration). The company, Cole Parmer, supply suitable flowmeters.
3. A low voltage DC air pump that can go up to 500 ml/min (1000 ml/min if using method 2 of
the H2O zero calibration) or more with a variable power supply. ADC Bioscientific can supply
a suitable pump if required, but inexpensive alternatives are easily found online.
4. Two water bubblers (see appendix 11 for construction details), one of which must have the
means of allowing the water temperature to be accurately measured. Water bubblers can be
made using glass jars with air entries mounted through the lids, one entry (air in) will need a
length of tube below the water line as shown in the photographs. The ends of these tubes
should be attached to “air stones” which are made for aquariums, to ensure small bubbles,
which are important. Ideally two types of air stone should be used and the one that makes
the smallest bubbles used on the second water bubbler which also contains a thermocouple
to measure the water temperature. If making water bubblers from glass jars they must be
airtight. ADC Bioscientific can supply plastic air entries to mount through the lid. The lids
should be sealed with PTFE tape around the glass threads. Alternatively, a dew point
generator can be used.
5. An empty water bubbler jar (see appendix 11) to act as a water trap between the
flowmeter/pump and the water bubblers – when the pump is powered down, a small
amount of water is sucked out of the first bubbler and may reach the flowmeter without this
water trap.
6. Some means of measuring the water temperature in the final water bubbler, e.g. a
submerged thermocouple/digital thermometer probe through a hole in the lid, then sealing
the lid hole with glue (hot or resin glue) works well. Digital thermometers must be calibrated
and regularly tested to a high standard.
7. Some short lengths of PVC tubing bore diameter 3 to 4mm, one length of 4mm x 60cm.
8. A room thermometer of good accuracy or a second thermocouple if using a digital
thermometer.
9. If a linearity test (optional) is to be done, a good quality RH meter will also be required.
Preferably one that has been tested using saturated salts as a calibration medium, an
internet search will explain this.
Two types of “air stones” commonly used in
aquariums. The larger more expensive one on
the right produced smaller bubbles. It is
preferred if the second water bubbler makes
smaller bubbles than the first one.

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Method:
The calibration menu shown below will need to be used for the H2O zero and Span
calibration.

H2O zero calibration

First make sure the console has the correct time and date. This can be seen and edited by
going to config>time/date.

Method 1

This method requires a granular drying agent such as Drierite, it is slightly less accurate
than method 2 but easier to do. The normally inert chemical column of the LCi (normally
contains four pieces of removable foam) should be removed (switch the console off first),
and the pieces of foam removed and replaced with the granular drying agent.
Refit the chemical column, turn on the instrument and run the machine at a flowrate of
341 µmol s-1 for 20 minutes, reduce the flowrate to 200 µmol s-1 for 20 minutes then
perform a H2O zero from the calibration menu. Afterwards monitor the e’ref and e’an
values, they should be within 0.1mb of 0.0 mb over a period of 5 minutes, if not then
repeat the zero calibration.

The photos below show the console chemical columns fitted as normal (left) and fitted for
a H2O zero calibration (right) with a drying agent, in this case blue Drierite.

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Method 2 (recommended)

With the instrument switched on and warmed up, supply dry air into the black ringed
handle tube at a rate of 800-1000ml/min, this normally connects to the console as one of
the three colour coded tubes. Pure nitrogen may be used for this purpose. The air must be
completely dry. The black ringed handle tube goes directly to the closed jaws which is
where the two RH sensors are located.
Allow 20 minutes at this flowrate of 800-1000ml/min, then reduce the flowrate to about
300 ml/min, allow this to run for 20 minutes, then enter the calibration menu and calibrate
by selecting the H2O zero option.
Afterwards, monitor the e’ref and e’an values, they should be within 0.1mb of 0.0 mb
over a period of 5 minutes, if not then repeat the zero calibration.

H2O Span Calibration

Warning One:
The temperature of the water in the second bubbler should be equal to or less than
ambient temperature, otherwise water will drop out of the air in the tubing en route
to the black ringed handle pipe. If water does get into the black ringed handle pipe
then disconnect the pipe from the water bubblers, remove the jaws and blow
compressed air down the small brass entry sticking out of the handle (make sure it is
the smaller one of the two), water will be expelled (out) at the console end of the
black ringed handle pipe.
This risk is eliminated if you perform the calibration in a room which is slowly
increasing in temperature during the day, provided the water has been exposed to a
lower temperature overnight in the same room. This way the water temperature will
slightly lag behind the temperature of the room.

Warning Two:
When using the water bubblers, the Tch value on the console screen should be ≥ 1
°C above ambient temperature before connecting the black ringed handle pipe to the
two water bubblers. If this is not the case then running the system for 20 minutes is
normally enough for Tch to become ≥1 °C above ambient temperature. Make sure
the black ringed handle pipe is connected to the console during the warm up period.

Dew Point Generators

If using a dew point generator instead of the water bubbler method described, set the dew
point temperature 5 °C below the ambient temperature in which the calibration is being
done. Refer to the table in appendix 5 to get a mb value for the H2O span air.
Setting a dew point temperature below that of ambient reduces the risk of condensation.

IMPORTANT NOTE:
Before connecting everything together it is a good idea to raise the temperature of
the first water bubbler slightly above the second or final water bubbler. This ensures
the air is over saturated when leaving the first bubbler but reduced to the calculated
saturation value, accurately determined by water temperature, when leaving the

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second bubbler. This increase in water temperature is easily realised by adding
approximately a tablespoon (25ml added to about 250ml of room temperature
water) of boiling hot water to the first bubbler and mixing it up before replacing the
lid. The water in the first bubbler should be 5-10 °C warmer than in the second
bubbler.

Connect the “air out” entry of the pump to the “air in” port of the flowmeter, leaving the
“air in” entry of the pump free to suck in room air.
Connect the “air out” port of the flowmeter (F) to the buffer jar (B0) “short” port (the one
without the internal tube fitted), connect the other port of the buffer jar to the first bubbler
(B1) “air in” port (the one with the tube that connects to the air stone), connect the “air
out” of the first bubbler to the “air in” port (the one with the tube that connects to the “air
stone”) of the second bubbler (B2), this second bubbler should have some means of
measuring its water temperature e.g a submerged thermocouple probe.
Finally connect the “air out” port of the second bubbler to the black ringed handle pipe
(P), use a piece of 4mm bore PVC tubing about 60cm long. Form a loop in the 4mm
section secured with a cable tie as shown in the second photograph below, this way if
water vapour condensates in this piece of connecting pipe it can be seen and quickly
disconnected.
The first photo below shows the buffer jar and the two water bubblers connected in series,
the arrows indicate the direction of air flow. The second photo below shows complete
setup including the loop in the section of pipe which connects to the black ringed handle
pipe.

T = Thermocouple probe for measuring water temperature.

B0 = Buffer jar.
B1 = Water bubbler 1.
B2 = Water bubbler 2.
F = Float flowmeter.

The photo below shows the complete setup for H2O span calibration. Note that the loop
formed in the connecting pipe is attached to the black ringed handle pipe with the
connection made above the lowest part of the loop. Watch this loop during calibration and

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disconnect the handle pipe quickly if water forms in the loop. If this occurs then blow out
the water with compressed air and try again having first reduced the temperature (by a
few °C) in the second water bubbler.

Before powering up the pump (shown above connected to a variable power supply),
check that the water temperature is slightly cooler than ambient conditions, power up the
pump at a flowrate of 500ml/min. Carefully watch the pipework coming out of the
bubbler system and make sure no condensation is visible. Stop at once if it is present! As
a precaution you can disconnect the black ringed handle pipe and start the pump
and see if condensation occurs before reconnecting the black ringed handle pipe.

The photo below shows the water temperature being measured using a submerged
thermocouple (indicated by the black arrow and not touching the glass!) in the second
bubbler.

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IMPORTANT NOTE:

The thermocouple shown above in the second bubbler should not be in contact with the
side of the jar.

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IMPORTANT NOTE!
Make sure the thermocouple lead is sealed
around the hole in the lid where it enters the
second water bubbler as shown opposite. Glue
from a hot glue gun is good for a few weeks or
months but may need to be replaced over time.
Two part slow setting resin based glues are best
for long term use e.g araldite 2011.
Make sure the thermocouple is not touching the
side of the jar.

Run the pump at a flowrate of 500ml/min for 10-15 minutes, reduce the flowrate to 250-
300ml/min and continue to run the pump for another 10-15 minutes.
With the pump still running you are now ready to perform a H2O span calibration from
the calibration menu. First you must calculate the H2O saturated vapour pressure (SVP) in
mb value which is determined by the water temperature and the fact that the water
bubblers give an output of 100% RH.
Using the same formula as the LCP/I which is based on the Arden Buck 1981 formula for
saturated vapour pressure, the table can be used to quickly give this value in mb.

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Read the table down first then across, for example 20.5 °C would be the row labelled 20
and the column labelled 0.5 which gives a SVP value of 24.2mb.
Enter the value obtained from the table as the span level in the calibration menu, perform
the span calibration. Afterwards, monitor the e’ref and e’an values. They should be
within 0.1mb of the span value over a period of 1-2 minutes. If not, leave the system
alone for 10 minutes with the pump still running at 250-300ml/min then repeat the span
calibration using a new SVP value from the table, if the water temperature has changed.

Switching off

When the pump is switched off the

glass jars will be lightly pressurised
which will normally result in water
flowing backwards up the pipes. To
prevent this, simply remove both
pipes from the first water bubbler as
soon as the pump is switched off, as
shown opposite.

Empty the water away and allow the jars to dry out before placing them into
storage.

Linearity Test (optional)

This can be done as a basic check but is not necessary. You will need a good RH sensor
and a thermometer next to the console and close to the “air in” entry on the console.
Connect the black ringed handle pipe to the black coloured air port on the console.
Position the LCi system in a quiet corner and leave it to run on full flowrate (341µmol
sec-1) for 30 min. Note the e’ref value, when it is stable over a period of 10 minutes then
the linearity check may be done.
Obtain a value of SVP using the table, based on the air temperature. Multiply this by the
RH value/100, this calculated value is the water vapour partial pressure (PVP) of the air
being sucked into the LCi.
Compare this to the e’ref/e’an values on display, typically they will be within 2 mb of
each other.
The test is limited by the accuracy of the thermometer and the RH sensor next to the
LCP/I console, commercial RH meters are very rarely accurate and fast responding.

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7.4.5 CO2 Span Calibration

The CO2 span calibration setting may be recalibrated by one of two methods, the first method
is somewhat crude and not recommended unless an instrument has lost its stored calibration
setting, the second method is to be preferred.

Note before using either method

Using a stable air supply either from a small volume or from the extended air probe (or the
bottled gas if using method 2)
Set the flowrate to 341µmol/sec, perform a phasecheck config>diagnose>sysinfo>auto
phase, followed by a CO2 zero calibration (in the calibration menu – you will need a
potentiometer adjustment tool to insert into the handle jack socket and rotate until the screen
displays “ok” when in CO2 zero calibration mode).
Lastly perform a CO2 flowcheck, from the calibration menu (the jaws must be correctly fitted
with all 5 o rings making a good seal from the jaws to the handle. Make sure the jaw gaskets
have no gap around them, a small gap can be fixed with an elastic band around the jaws).

Method 1. The ambient method.

This can only be done in an open area, several Km away from and ideally not downwind of
any major sources of CO2 such as cars, buildings etc. It should be done in an open area not
for example in a forest environment. A good location would be on a coast with light wind or
an onshore breeze. Connect the console air in port to a buffer volume or the air probe
(extended and held upright by use of the groundspike) using 3 or 4mm bore PVC tubing.
Next enter the calibration menu and perform a CO2 span calibration, having first adjusted the
span gas ppm level in the calibration menu to 400 ppm (in 2017) this being a typical global
average. After calibration exit the calibration menu and monitor Cref for a couple of minutes,
redo the calibration if Cref deviates more than 10ppm away from the span gas value.

Method 2. The bottled gas method.

To do this you will need a pressurized bottle/cylinder of gas made from a mixture of CO2 and
Nitrogen. The PPM value of the CO2 must be known to a good level of certainty e.g 1%
accuracy. The span gas should be 40-99% of the maximum range of the instrument.

Equipment:
You will also need a two stage pressure regulator fitted to the gas bottle/cylinder to reduce
the pressure to approximately ¼ bar or 3.6 PSI, a ball or needle valve, some 3 or 4mm bore
PVC tubing, a T piece and a float flowmeter with a range of or close to 100ml to 1000 ml or
more per minute. The flowmeter must allow enough reverse flow for the console to run at
maximum flow rate – most float flowmeters do but some ball type flowmeters do not, this
should be tested as follows:
Set the console flowrate to 341µmol/sec, use a piece of PVC tubing, 3 or 4 mm bore to
connect the inlet of the flowmeter to the air in port of the console. If the console pump
becomes very noisy then disconnect the flowmeter quickly – it will not be suitable. A small
increase in pump noise is acceptable.

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Setting up the Equipment:

Connect the output of the two stage regulator to the ball/needle valve, then connect the
remaining entry of the valve to one air entry of the T piece. Connect one of the remaining air
entries of the T piece to the air in port of the console. Connect the last air entry of the T piece
to the flowmeter air in entry. The diagram and photograph below show this setup:

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Method:

Turn on the LCP/LCi and set the flow to 341µmol/sec. Turn off the variable valve (ball or
needle).
Next use the two stage pressure regulator to set the pressure to or slightly under 0.25BAR or
3.6 PSI. Very slowly open the variable valve until the flow meter reads about 200 ml/min –
this reading will fluctuate over the instruments CO2 cycle.
Adjust the control valve so that the flowmeter never drops below 100 ml/min, watch this for a
minute to make sure and continue to monitor this while performing the calibration. The
excess flow ensures that the system always has a surplus of span gas and never dilutes this by
sucking in non span gas.
After the system has finished its warm up cycle – this will clear from the status line of the
display and the console will make a beep noise to indicate this, perform the steps laid out in
“notes before using either method”.
After 5 minutes enter the calibration menu and adjust the CO2 Span value to the value of the
gas being used, then perform the CO2 span.
After calibration exit the calibration menu and watch the Cref reading for a couple of
minutes, repeat the span calibration if Cref deviates more than 0.5%+4ppm away from the
span gas value.

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8. MEASUREMENT CONFIGURATION
8.1 The ‘config’ Function Menu
Refer to Appendix 8 for the menu tree
Use /config/ to get to menu /select/+/-/diagnose/.
The various options can be chosen with /select/.
Use /+/ &/-/ to alter the parameter selected. The type of chamber (cfg) you are using can be
selected from: broad, narrow, conifer, soil pot, arab., small, user1, user2, user3. The
chamber parameters, uset, area, Tl method, rb, Hfac, and Trw are stored separately for each
type, and the LCi-SD is factory set with suitable default values that match the chamber
supplied. You can change the parameters to suit your chamber and experiment conditions.

When the LCi-SD is switched on it will select whatever configuration was last in use.
User 1, 2 & 3 parameters mirror the Broad, Narrow & Conifer defaults respectively except
for flow (Broad & Narrow) and Trw (Conifer).

See the table on page 36 for default values.

/log/ goes to the menu accessed from /output/logging/. See Section 9 for details.

/cfg/ is the leaf chamber type which may be /broad/, /narrow/, /conifer/ /Soil pot/
/arab./ /small/ or three user defined types /user1,2 & 3/.

/Uset/ is used to set flow rates through the Leaf Chamber:

/area/ is used to input the effective leaf area exposed to PAR.

The area exposed depends upon the type of Leaf Chamber in use, and how much
of the leaf is within the window area. . It is not permissible to cover the whole
area when using the Arabidopsis chamber and so the user should set the area to
match that of the leaf area exposed in the chamber.
When using Conifer Chambers, the ‘area’ may have to be established by
experiment.
With Broad, Narrow and Small leaf chambers it is permissible for the leaf to
cover the whole chamber so the FULL default area may be used
For the FULL leaf areas for each chamber see the table below.

Note; within some experiments, some ‘constants’ may vary from one specimen
to another (e.g. area), and must be re-entered.

Tl mtd/ is used to determine the method with which the leaf temperature is obtained
and toggles between /calc / and /meas/.
Note: the toggle function is disabled in the soil pot configuration, which defaults to
measured

/calc/ selects the value as calculated by the LCi-SD from the energy balance
equation.

/meas/ uses the temperature measured by the leaf temperature thermistor.

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/rb/ is used to input the value of ‘boundary layer resistance to water vapour’, which
is a function of the leaf chamber type.

For Conifer type chambers, rb will be about 0.35, but is dependent on plant
morphology and should be determined.
For Arabidopsis and Small type chambers rb has not yet been determined by
experimentation but is expected to be in the order of 0.25 m2 s mol-1

/Hfac/ is used to enter the transmission factor of the total radiant energy into the leaf
chamber at the exposed leaf surface. This factor is dependant upon the materials
used in the construction of the shield and/or window of the Leaf Chamber. (For
LCA2 & 3 types of analysers, this factor is referred to as ‘Trans’). Appendix 4
gives the derivation of Hfac.

/Trw/ is the transmission factor of PAR into the leaf chamber at the exposed leaf
surface ie it is the factor which Q is multiplied by to obtain Qleaf. It is dependent
upon the materials used in the construction of the shield and window of the Leaf
Chamber.
Arabidopsis & Small leaf chambers do not possess a radiation heat shield and
so their transmission factor is 0.92

U set Area Tl mtd rb Hfac Trw

Units µmols s-1 cm2 n/a m2 s mol-1 n/a n/a
0.1 to
Range 68 to 341 0 to 100 * n/a 0.1 to 1.00
1.000
0.25 to 1.000
Steps *1 1 0.01 * n/a 0.01 0.001 0.01
with without
Chamber shield shield
Broad 200 6.25 Calc. 0.17 0.168 0.870 0.920
Narrow 200 5.80 Calc. 0.30 0.168 0.870 0.920
Conifer 200 100.00 Calc. 0.35 0.177 0.860 0.910
Soil pot 200 97.5 *2 Meas. *3 n/a n/a n/a n/a
Small 68 2.16 Calc. 0.25 0.168 n/a 0.920
Arab. 68 0.95 Calc. 0.25 0.168 n/a 0.920
User 1 68 6.25 Meas. 0.17 0.168 0.870
User 2 341 5.80 Meas. 0.30 0.168 0.870
User 3 200 100.00 Meas. 0.35 0.177 1.000

*1 The steps are greater when the /+/ or /-/ keys are held down.
*2 The soil-hood range is 0 to 400cm2 in 0.5cm2 steps – given value is for a version 2
soilhood with a soil collar.
*3The Tl method cannot be changed from measured.

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9. GRAPHICAL DISPLAY

9.1 Introduction
The LCi-SD has the facility to display parameters in graph form.
The graphing function is particularly useful to see if an experiment has settled and/or
proceeding as expected.

Two types of graph are available that plot either single parameter (bar chart) or dual
parameter (X-Y plot). Dual parameter graphs have each data set shown as a cross, the most
recent of which is shown “flashing”.

For all modes, the graphs are scaled automatically to make best use of the display resolution.
The parameter(s) to be plotted are selected from the analogue output settings (See section
7.2)

Either type of graph is capable of displaying up to 200 data sets. After this, the earliest sets
will be replaced by the most recent set. In the case of the single parameter Bar chart type,
this has the effect of appearing to scroll the graph from right to left as each new data set is
added.

The graph options are:

Single parameter bar chart.
O/P 1 parameter against time
O/P 1 parameter against record number
Dual parameter X,Y plot chart.
O/P 1 parameter against O/P 2 parameter (triggered by time)
O/P 1 parameter against O/P 2 parameter (triggered by record number)
Time may be set to 15 or 30 Seconds.

9.2 Operation
Before entering the graphs menu it is advisable to set up the analogue outputs to the
parameters required. This is detailed in section 7.2. Although the analogue outputs page can
be accessed from the graph set up, once exited the LCi-SD returns to the top level menu
necessitating re-entering the graph set up menu once again to complete the setting-up
procedure.

Graphs are set up by pressing /graph/setup in the / output /, / calibrate / , / graph /, / record
/ screen./.

Screenshot:

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The /X axis/ button toggles the X axis setting between ‘(as o/p2)’ and ‘time’ or ‘log record’
the latter being determined by the plot setting.

The /plot/ button determines when a plot is taken. It cycles the plot every value between ‘15
seconds’, ‘30 seconds’ and ‘log record’.

The / set o/p / button accesses the analogue output page where the graph parameters may be
set.

The / start/view / button starts the plotting. It opens up the graphical display screen as a
fourth top level screen.

To set O/P 1 against time for example first use /X axis/ and select either 15 or 30 seconds.
Use /X axis/ to toggle to ‘time’ and press / start/view / when ready.

To stop the graph press / graph / in the / output /, / calibrate / , / graph /, / record / screen.

Screenshot:

The /stop/ button stops the graph being updated but does not erase it in case it is required
for later reference.

The /clear/ button erases the graph data but allows it to be restarted with the current
parameters.

The /disable/ button erases the graph and removes it from the top level screens.

Finally the /set up/ button may be used to start a graph with new parameters as previously
explained.

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10. RECORDING A LOG

10.1 The nature of a record

The data record is associated with a log file, in which a single record is stored for every
‘record’ action. A single SD card can store a number of log files. The maximum number of
log files that can be accessed is 60. Additional records will be saved to the card, but the
oldest will not be available to the filing system.
The ‘record’ is a single recording of all the parameters listed in the Log? column of
Appendix 1. Parameter Information. The number of records that can be accumulated
depends on the size of the SD card and the amount of data already on it. A warning message
is displayed when the SD card is full.

10.2 Taking a record

Taking a record can be initiated by any one of four methods:
1/ via the keypad, by pressing the “record” key when displayed.
2/ via the ‘record’ pushbutton switch on the handle of the PLC
3/ by closing a remote switch connected between pins 7 (12V) and 8 (CTS) on the 9 pin
RS232 connector (it is necessary to set up the serial port to “use CTS for record” (see
Section 7.1).
4/ by sending “r” or “R” over the serial port from a “dumb terminal” such as WINDOWS
hyperterminal..

After a record is successfully taken, the LCi-SD beeps. If a log file has not been set, a
message appears “log file not set, set now?”. If you do not wish to take a record, the message
is cleared by a second ‘record’ action or by pressing the /no/ button. When a record is
‘taken’, it is appended sequentially to previous records on the SD card. It is stored in the
current log ‘filename’, as chosen by the user. The ‘record number’, which starts at ‘1’, is
automatically incremented. Parameter values are stored as signed integers, or in exponential
form; the associated units of measurement are NOT stored.

If records are to be taken at regular intervals, the timed log function can be used. It allows
log intervals of 1 minute to 100 minutes in minute increments to be chosen or the intervals
can be synchronised with the gas cycle in which case the increment will vary dependant on
the ASU flow. The time can be scrolled from 1 minute to 100 minutes using /change-/
allowing longer times to be selected quickly.
Select /logging/timed log/ change+ or change-. The analyser will default to 1 minute
increments and automatically take a record and store the results after the selected number
of minutes has passed. In order to select intervals synchronised with the gas cycle press
/timing/ which toggles the mode.

Screenshot:

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Selection of intervals synchronised to the gas cycles allows the maximum meaningful
update rate and optimises noise performance.
The timed log will continue until it is switched off by selecting /logging/timed log/manual/
or the SD card becomes full. This function can be used simultaneously with the sequence
function to give more records for each step of the sequence.

10.3 Deleting a record

If you have taken an unwanted record, it can be marked as ‘deleted’ on the log file, but it
still has a unique record number attached to it. To do this, hold the “record” key or the
record pushbutton on the chamber handle down continuously until the message “hold record
key to delete last record” appears. Continue to hold the key or pushbutton pressed until “last
record deleted” appears. If you release the key or pushbutton before the second message,
no action is taken, and the message “record not stored” appears.

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10.4 Sending a serial record

Rather than taking a record, it can be sent to the serial port. In this case, the record is not
appended to the log file. Sending a record requires the serial link to have been set-up
beforehand. (see Section 7.1). If this is attempted when the serial port has its CTS line
enabled to initiate a record (see above), an error message will be displayed..

The record can also be requested via the serial port: a “P” or “p” sent to the port will cause
the LCi-SD to transmit a single record. The serial data is sent in csv format, without labels
or headers, in the following sequence:

record number, date, time, e ref, delta e, c ref, delta c, PAR leaf, t chamber, t leaf, flow mol,
p mbar, ci, E, gs, A, area cm, rb.

Or if the soil pot is used:

record number, date, time, e ref, delta e, c ref, delta c, PAR leaf, t chamber, t leaf, flow mol,
p mbar, ce, Wflux, *, NCER, area cm, rb.

Where * = no data

10.5 Deleting a serial record

A serial record can also be marked as deleted. If you are recording to the serial port, and
follow the method for deleting in above, the ‘record number’ for the deleted record is
transmitted a second time, with the message, ‘record deleted’. As in recording to a file, the
’record number’ will continue to be incremented as if you had not deleted the record.

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10.6 Receiving a serial record
This applies to Windows 95, 98, NT and XP. For non-Windows systems, you will need to
use a terminal emulator.

Note: The /xmodem/ option on the LCi-SD will not work with Hyperterminal on
Windows systems.

1. Select Hyperterminal from the start menu: “START”, “PROGRAMS”,

“ACCESSORIES”, In WIN95 select “HYPERTERMINAL”, in later versions select
“COMMUNICATIONS”

2. Select (double click on) the Hypertm.exe icon.

3. Name your new connection e.g. LCi-SD, and choose an icon if desired. Click on
“OK”. This will save all your settings so that it is easy to repeat the transfer.

4. The system will ask you to type in a phone number as it assumes you will be
connecting via a modem. Ignore this and click on the “connect using” option window.
Select the COM port number that you intend using on your PC. The other options on
this window will then be automatically deselected. Click on “OK”. A window will
then appear asking you to set the COM port settings.
Select : bits per second 9600 (default) or as set on the LCi-SD
data bits 8
parity none
stop bits 1
flow control xon-xoff

5. Click on “OK”
Ensure the settings match those on your LCi-SD before transmitting data
(see section 6.1)

6. As a check, each time you press a “p” on the PC you will receive one data record.

7. Click on the “transfer” button and select “capture text”.

8. Enter a filename and click on “start”

9. The PC should then be ready to receive data from the LCi-SD, which can be sent by
pressing /send/ASCII/ on the LCi-SD.

10. To stop data transfer click on “call”, “disconnect”.

Tip: if you give your file a csv extension you will be able to import it directly into most
spreadsheet programs.

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11. DATA FILES & USING THE SD CARD

Never remove a card while you are recording or transferring files.

The SD card supplied has a minimum capacity of 1GB. All files are allocated in 512B blocks.
Log files vary in length depending on the recorded data. An empty 1GB card will hold a single
log file of around 8000 to 16000 records.

11.1 Selecting a File

When you first switch on, no file is selected. To set a file, install the SD card, press
/logging/file menu/ then either use the arrow buttons to select an existing file or leave the
arrow cursor pointing to *new file*. Press the /set log/ button. If you select an existing file,
records will be added to it otherwise if *new file* is chosen the LCi-SD will choose a default
file name with a value one higher that that currently on the card. You can change the name
if you wish by using the />/ /+/ /-/ and /del/ buttons.

Screenshot:

11.2 Reviewing Log Files

Press the /logging/file menu/ buttons then select a file as described above. Press
/options/review/. The data may be reviewed sequentially using /next/ and /previous/ or
switched between first and last record using / 1st/last / . Holding down /next/ or /previous/
for one second will increase the steps to ten at a time (or return to single steps if pressed
again for one second).

11.3 SD Card Data Format

SD cards are preformatted in a DOS format and the LCi-SD stores data on the SD card using
this format so files may be read with a PC which has a suitable card reader. Most current
PC’s and laptops have a card reader and if not external card readers are readily available at
a modest cost. Since SD cards are suitably preformatted a format function is not required on
the LCi-SD. In the unlikely event that the format of a card has been corrupted then it can be
formatted on a PC.

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11.4 Delete (Erase) Existing Files

Press /file menu/ , select a file as described above then press /options/delete. You will then
be asked to confirm /Yes/ or /No/ . If you wish to abort the deletion press /No/ otherwise
press /Yes/. ‘File erased’ will then be displayed. Press /Yes/ to acknowledge the
confirmation message.
If you currently have the selected file in use as a logging destination, you will not be allowed
to delete it. If you still wish to delete the file deselect it by pressing page then /no log/ then
starting the process again.

11.5 Copying Files using the USB

Files may be moved or copied using the USB connection. When a PC is connected over the
USB the SD card in the LCi-SD will looks like a mass storage device and will appear as
another drive on the PC.

Note: When the LCi-SD is connected using the USB no file operations can be carried
out from the LCi-SD front panel. To do so may corrupt the file system.

11.6 Storing Cards

In common with all computer storage media, they must not be exposed to extremes of
temperature, dampness or dirty environments.

The construction of the cards protects them from normal environments and handling but are
best kept in their plastic case or a suitable anti-static container when not in use.

11.7 Using Alternative Card Types

SD Cards are available from different manufacturers and with various capacities and all
those compatible with the SD card format should work in the LCi-SD. However only those
supplied by ADC BioScientific have been tested and guaranteed to work. If using SD cards
supplied from elsewhere it is suggested that cards from recognised manufacturers such as
Sandisk, Kingston or Transend, are used.

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12. HOW THE ANALYSER WORKS

12.1 Infrared Gas Analysis

The LCi-SD uses the principal of Non Dispersive Infrared (NDIR) for the CO2
measurement. This relies on the fact that CO2 absorbs energy in the infrared region in a
proportion related to the concentration of the gas. The gas sample to be measured is passed
through a tube (or cell). A source of infrared is directed down the cell which is gold plated
to maximise the intensity of the source. A solid state detector at the receiving end of the
cell measures the amplitude of the infrared signal, which will be reduced if CO 2 is present
in the gas sample. A thin film filter (TFF), with a pass band of 4.24m, is fitted in front of
the detector to narrow the bandwidth being measured to one which includes a strong
absorption band for CO2.

The reference (TO the chamber) and analysis (FROM the chamber) gases are alternated
with ‘zero’ gas during a measurement cycle which typically lasts 16-20 seconds. The ‘zero’
gas is generated by passing the air through soda lime, which removes all of the CO2. The
cycle time allows for the cell to re-fill, and is automatically adjusted to suit the current flow
rate, if requested by the user. This arrangement provides measurement of the CO2 content
in both the reference and the analysis gases, while eliminating much of the drift due to
temperature change etc.

The infrared source is pulsed at 8Hz to give an alternating waveform. The waveform varies
in amplitude with the energy absorbed by the gas, being a minimum when full-scale
concentration is present and a maximum when ‘zero’ or non-absorbing gas is present. The
waveform is rectified, with the resultant DC voltage at the zero condition providing a
reference for the subsequent measurement cycle. Any change in the zero reference
condition is applied ratiometrically to the measurement. This system provides very stable
gain settings, which are independent of the IR source condition (unless this has deteriorated
appreciably) and, are only slightly affected by deterioration of the optical elements.

12.2 Gas Correction

Measurement of a gas concentration using its IR absorption properties provides a
comparative measurement against a standard gas of known concentration. However, once
the system is calibrated, secondary effects relating to the state of that gas being measured
can subsequently affect the accuracy of measurement. This is also true of the stability of
the optical system.

The absorption properties are affected by changes in temperature and atmospheric pressure.
Variations due to changes in temperature are minimised with a thermal jacket around the
cell assembly. Ambient pressure is monitored by a sensor in the main unit and used to
compute a correction to the measured values.

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The presence of water vapour in the CO2 measurement introduces ‘interferent’, ‘density’,
and ‘pressure broadening’ effects which are dealt with as follows.

As an interferent, H2O partly shares the CO2 IR absorption band. Its presence, therefore,
appears as a proportionate level of CO2. The effect, however, is relatively small and is
eliminated by computing a reduction of the signal as a function of H2O. H2O in the gas
displaces CO2 and therefore reduces the density of CO2. At known temperature and pressure
the effect is predictable from physical laws, and is computed out.

H2O also has the more significant effect of broadening the CO2 IR response band and
therefore of increasing the signal for a given concentration of CO2. As part of the design,
in which the optical filters can also influence the results, the appropriate compensation has
been established experimentally, and a computed correction is applied based on this.

All the values used or displayed for CO2 and H2O are after full correction i.e. there are no
‘raw’ values used.

12.3 Other measurements

PAR (Q) is measured with a silicon-based sensor.

Chamber temperature (Tch) is measured with an accurate thermistor sensor mounted in the
leaf chamber.

Leaf temperature (Tl) is measured by a miniature thermistor sensor. The thermistor can be
positioned against the surface of the leaf. You can select an internally calculated value
derived from the energy balance equation or the value measured with the thermistor.

Gas flow rate (U) to the chamber is measured by an accurate air mass flow sensor and
controlled to either a default or user-selected level (Uset).

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12.4 Electrical Block Diagram

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12.5 LCi-SD Gas Circuit Block Diagram

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12.6 The gas circuit Description

Fresh air is drawn in via the trap and hydrophobic filter by the internal pump. The trap and
filter remove dust particles and help prevent water being sucked in. The filter contains a
porous PTFE membrane, which prevents the flow of water using the effect of surface
tension. If the water contains impurities, which substantially reduce the surface tension, e.g.
detergent, the water may be sucked in. Following the pump is the internal volume, the
purpose of which is to average out fluctuations of CO2 and H2O concentrations that occur
naturally in the background. This greatly reduces noise on differential measurements. The
air probe, if connected, will also help in this regard, having a volume of 460cc.

The air then splits 3 ways:

1/ Through the soda lime column to remove CO2 and then through a dust filter to remove
any soda lime dust. Soda lime contains water and in addition, generates more as a by-product
of the conversion process. This causes the air leaving the column to be very damp and, if the
analyser has been taken from a hot place to a cold place, condensation will form inside the
‘zero’ tube to the chamber. To minimise this effect, the air passes through an equilibriator pipe
that matches the water vapour concentration inside the tube to that of the outside.

2/ Directly to the analysis cell as ‘reference’ air when SV1 and SV2 are open.

3/ Through the mass flowmeter as air supply to the leaf in the chamber. The mass
flowmeter acts with the pump in a closed loop feedback system to keep the air supply constant
despite changes in pump loading due to the various states of SV1 and SV2.

The air supply to the chamber first passes through a temperature equilibration loop that
brings it to the chamber temperature. The air is stirred around the chamber with a fan, which
also blows air through the analysis cell when SV2 is open. The analysis cell being in the
handle gives a faster response than would be the case with a long length of pipe leading to
a cell in the main instrument. Excess air is allowed to escape via a waste valve in the top
half of the chamber. This air would otherwise pressurise the leaf if the jaws were tightly
shut.

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13. MAINTENANCE
Note: When the LCi-SD is first switched on, the display shows the ‘Instrument Serial
Number’ and ‘Software version’. Always quote these in correspondence about
the instrument

13.1 Tools
There are no special tools needed to dismantle the LCi-SD and replace parts, except for a
PLCC extractor, which is needed to replace the microprocessor. The use of a small sized
thermostatically controlled soldering iron is recommended to replace electronic
components, as is an anti-static wrist strap, especially when working on the digital board.
All screws are metric except the hexagonal pillars on the ‘D’ type connectors. All screw
heads are ‘Pozidrive’ (crosshead) types. A sphygmomanometer without the cuff is useful
for testing for leaks or, alternatively, a water manometer connected with pipe and a tee to a
100ml disposable syringe can be used. A small paintbrush is good for general cleaning, and
cotton wool buds and acetone or alcohol are good for cleaning the cell.

All pipes are push-on although some have been fitted using ‘Hellerman’ oil, which allows
pipes to push on easily, but sticks them in place when dry. If a pipe will not pull off easily,
do not continue to tug as the pipe tends to become thinner and grip even tighter, instead use
a pair of thin nosed pliers with one jaw either side of the connector to push on the end of
the pipe. This particularly applies to barbed plastic fitting, which might otherwise be
damaged. Note that if you remove a pipe from a barbed plastic fitting by cutting along the
length of the pipe with a sharp knife, you will probably damage the barb and introduce a
small leak.

13.2 Accessing the Inside of the Main Instrument

With the LCi-SD switched off, unscrew the 4 screws securing the strap clips, then the 5
securing screws around the top bezel of the LCi-SD after which the display panel can be
lifted up and to one side. (Care should be taken to protect the clear membrane over the
display as it can be easily damaged). The digital board (PCA-288) is attached to the display
panel and, unless you are taking static precautions, you should avoid touching the
electronics. Do not pull on the electrical cables.

To gain further access to the analogue board (PCA-271) and the piping, remove the three
M3 screws either side of the curved plate, the two near to the middle, and the two M2 screws
in the lower bezel. With care the curved plate can be lifted up and out. There is usually no
advantage in dismantling the LCi-SD further.

When replacing a set of screws it is best to have all of them inserted a few turns before
tightening any of them fully.

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13.3 Air Flow (Mass Flowmeter)

The mass flowmeter is in a closed feedback loop with the pump, and will drive it faster or
slower until the set flow is achieved. If the pump has stopped or is going as fast as possible,
the mass flowmeter may be faulty.

The air mass flowmeter is very stable. If its calibration changes, the cause is almost certainly
contamination inside it. If this happens, a subsequent re-calibration cannot be considered
reliable and a replacement of the flowmeter and its interface board (PCA-272) is
recommended. It might be possible to blow out the contamination. The board is supplied
pre-calibrated and, as such, replacement is a simple matter of removing the pipes [See
Section 12.1 if you experience difficulty], and pulling the flowmeter and its board off the
mounting pillars. Fitting the new board is a reversal of the removal procedure, but ensure
that the 5-way electrical connector is properly engaged before pushing the board onto its
pillars. Support the flowmeter with one hand while pushing the pipes back on with the
other.

13.4 Filters
Filters must be replaced if there is evidence that the pump is being over-loaded, as indicated
by an inability to achieve maximum airflow for example. Otherwise replacement should
be based on an assessment of previous use in dust-laden conditions, or visual inspection.

There is a hydrophobic filter and a particulate filter inside the main analyser and filters at
each end of the columns. The filters in the main unit can be accessed by removal of the top
(and side for maximum convenience) described in section 12.2 above. Individual filters can
be disconnected from their piping in each part of the gas circuit, and a new one inserted. If
during these operations piping is damaged, or a good seal cannot be achieved with existing
piping, then the section of pipe should be replaced with a new piece. If a section of pipe is
seen to contain any debris, it is easier and safer to replace the pipe.
Appendix 11. Spares and Accessories gives details of the necessary piping, excluding
the pipe in the umbilical cord connecting the chamber, repair of which is beyond normal
maintenance.

In the chamber, there is a permanent mesh filter under the stirrer, which is best cleaned of
large debris with a small paintbrush. The fan cannot be removed to assist cleaning and so
the paintbrush must be small enough to pass between the blades of the fan. If there is fine
dust on this filter, there is a risk that it will be pushed through the filter with the brush. It is
best to remove the handle cover, remove the pipe connecting the SV2 to the back of the
stirrer, and use a piece of pipe from the spares kit to blow backwards through the mesh filter
while you disturb the dust with the brush.

There is another permanently fitted mesh filter in the corner of the stirrer cavity in the upper
jaw, leading to the waste valve. The same general comment applies with regard to dust, but
you will not be able to blow backwards through the filter because the waste valve is one
way and is delicate.

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13.5 Display Contrast Setting
The normal contrast setting for the display changes little with variations in ambient
temperature. Manual re-adjustment to suit operator preferences is via the ‘contrast’
potentiometer on circuit board PCA-288 indicated in section 2.4. This can be accessed by
removal of the top display section of the LCi-SD as previously described. See Appendix 7
LCi-SD Console exploded diagram.

13.6 Pump
The pump is fixed to the analogue board by screws under the board, which are accessed by
removing the curved panel. Do not lose the two spacers that are in the grommets. The most
common pump problem is insufficient flow and is caused by contamination under the flap
valves. The valves can be accessed by removing the four self-tapping screws that retain the
head. Note the orientation of the parts. Some pumps have parts that will fit two ways round
but only one way is correct! Wipe the flaps, even if they look clean, with a smooth cloth.
Reassemble, but only tighten the screws enough to make the pump leak tight. After much
use (a few years), the motor bearings will become slack and noisy, and the pump will need
replacing.

13.7 Chemical Column filters

Maintenance on the chemical column is limited to checking the general condition of the ‘O’
rings. Air seals should be maintained around all of the ‘O’ rings. The use of silicon grease
provided will greatly assist this and help to keep the ‘O’ rings in good condition.
Occasionally the columns themselves should be cleaned in soapy water and left to dry
before replacement.

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13.8 Dismantling the Chamber

The radiation shield is removed by loosening (but not fully removing), the two knurled
captive screws. The shield can then be slid out from the retaining slots on the jaw-opening
lever. From serial number 31392 on onwards, the shield is hard faced both sides to minimise
scratching.

The par sensor is permanently connected electrically and must be detached by pulling it out
of its mounting plate if you wish to remove or exchange the jaws.

The top jaw can be removed by pressing against the spring so that one hinge pin is no longer
hooked in place. The jaw can then be twisted to disengage the pin then pulled away from
the other hinge. The top jaw contains the chamber window, a magnet, (which operates the
jaw-open detector reed switch when the chamber is closed), and the waste valve, (which is
only likely to cause problems if dirt gets on the seat).

The waste valve is a thin transparent diaphragm held against the valve seat by a spring, but
dismantling the jaw to access this is not recommended.

The window is made from Polycarbonate, and, with the exception of the Conifer window,
which is curved, is hard faced both sides.

The bottom jaw can be removed by unscrewing the three knurled captive screws. If they
are too stiff to loosen by hand, you can use a coin, but the slot should not be used for
tightening. It is not necessary to unscrew the screws so far that they become detached, they
just need to be loose.
With the bottom jaw removed, check that the fine mesh filter under the fan does not have
dirt in it. If it does, use a small paintbrush between the blades of the fan, or blow clean air
into the pipe.
The bottom jaw is constructed of two pieces of aluminium, screwed together with air tight
gasket compound. There are wires between the plates connecting from the fixing screws to
the fan and jaw-open reed switch sensor. It is not practical to dismantle it to this extent. If
you have problems with the fan or sensor, return the jaw to ADC Bioscientific or your local
Service Centre.

Removal of the bottom jaw exposes the analysis and reference humidity sensors and the
chamber temperature sensor (which looks like a black bead). Take care not to lose any of
the five ‘O’ rings. The humidity sensors can be withdrawn by unplugging them after the
M1.6 slotted countersink screws have been removed.

Note that the software stores separate span and zero constants for each of the sensors, so be
sure to put them back in their original locations if you wish to avoid re-calibration. If it is
possible that the sensors have become swapped when you reassemble it, and you have no
calibration facility, choose the locations that make the sensors most closely agree when
there is no leaf in the chamber. The sensors are interchangeable to within 5%RH without
re-calibration.

The temperature sensor has wires and a socket on the back and it can only be removed by
taking off the handle lid and disconnecting it. (see below and Appendix 6. Chamber
Exploded diagram). The socket will pass through the sensor hole with care The plug is not
polarised and so a note should be taken of its orientation (the white wire should be nearest

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the end of the board). If you are unsure, no damage will result from an incorrect orientation,
but the temperature reading will be obviously in error. The sensors are interchangeable to
better than 0.1C without re-calibration.

Before refitting a chamber lightly grease the five ‘O’ rings with the silicone grease supplied
before re-assembly, and be sure that the rings around the two humidity sensors and the
temperature sensor are pushed completely down to the flange before re-assembly.

The position and function of the connectors and the potentiometers on the printed circuit
board are shown on a label inside the cover.

Before proceeding further, note that the metal plate is at ground potential. A Mylar film
insulator is fitted between the circuit board and the metal back plate. However, if the circuit
board is allowed to come into contact with the back plate while the instrument is switched
on and connected to the chamber, it is possible the fuse will be blown or damage caused to
components on the circuit board.

The status of the solenoid valves is indicated by the light emitting diodes LED10 and
LED90 (see the gas circuit on page 48). The solenoid valves are both replaceable items and
cannot be dismantled.

Solenoid valve SV1 is used to select Zero or Reference gas and is activated when LED 10
is lit. It can be tested as follows. Connect a Sphygmomanometer to the Red and White
sleeved pipes in turn and applying a very low pressure. When LED10 is lit the pressure will
be lost from the red pipe and when both LED10 and LED90 are not lit pressure will be lost
from the white pipe. If pressure is not lost from either pipe then it is likely that solenoid
valve SV2 is not operating and is stuck at the Zero/Reference end. If pressure gradually
drops then the valve is leaking and should be replaced.

Solenoid valve SV2 of a latching type; that is, it stays in its last position without power.
When LED90 is lit the valve is opened at the Analysis gas end. To leak test it, it is necessary
to remove the chamber to gain access to the Analysis gas stem. Connect the
sphygmomanometer to the gas stem and apply a very low pressure. The pressure should be
maintained whilst LED90 is out and lost rapidly when LED90 is lit. If the pressure falls
gradually there is either a leak or a blockage in the pipe between the valve and the cell.

If SV2 leaks, it is probably dirt on the seal, which might be possible to dislodge as follows.
Ensure that the valve is switched so that the leaky direction is open. Strip back 4mm of the
insulation from some 7/0.1 tinned copper wire and, while turning it, push it into the valve
entry that leaks. The wires will spread sideways and dislodge the dirt from under the seat.
Remove the wire, and blow clean air into the leaky port, to blow the dirt out. When replacing
the valves, refer to the piping diagram.

If the detector signal falls so far that CO2 zero cannot be manually corrected with the
potentiometer or it is known that dirty water has entered the analyser, it is possible that the
analysis cell will need cleaning, or that the source or detector is faulty. The procedure for
checking and replacing the source and detector is shown below.

To clean the cell, first remove the handle cover as shown below. It is best to first remove
the cell by unplugging the infrared source and detector leads from the circuit board,
removing the single M3 screw under the lower jaw and the M3 screws that retain the jaw-
open clip then pull the cell off the pipe that connects it to SV2.

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Remove the large insulation around the detector. Pull back the insulation around the cell
sufficiently to remove the two M2 screws that retain the detector housing. Remove the
infrared source and its two M2 screws, and the flow sensor housing and its two screws. You
can now look through the cell, which should appear uniformly shiny. If it appears dull or
patchy, it may be possible to clean it.

The cell is gold plated internally and can be cleaned with care with cotton wool wrapped
around a thin stick. For persistent dirt, alcohol or acetone can be used. If the cell has had
liquid in it for a few days, it is possible that there is corrosion under the plating, in which
case, it will need to be re-plated or replaced by ADC.

13.9 Removing the Handle Cover

Unscrew the two retaining screws from the tripod
boss.
Note the orientation of the boss – On some
instruments the fixing screws are not in the middle.

There are two screws holding the cable gland

in place. Remove them both

If you wish to completely remove the handle

cover, take a note of the orientation of the
connectors (there is a diagram inside the
handle cover) and unplug the two sockets of
the Tleaf thermistor and the CO2 zero
potentiometer wires from the PCB.

On early models that have not been upgraded

there is only a single twisted pair of wires
from the leaf thermistor jack socket to PL20
on the board.

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Later models have the CO2 zero potentiometer

mounted in the handle cover instead of on the
board so that an additional twisted pair of wires
runs from the jack-socket assembly to RV9 on
the board

On the diagram/label in the handle:

R indicates red
B indicates black
W indicates white
X indicates no connection (polarising pin)

13.10 Checking the Source

First remove the jaws and then the handle cover,

(see previously). It is not necessary to completely
remove the cover.
The source is indicated by the black arrow in the
above picture. It is a small light bulb, which has
been pre-aged to minimise drift. It has a thin
envelope to minimise infrared loss, and a low-
mass, fast response filament.

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Issue 4-104 LCi-SD SD user guide

Look for flashing coming from the small window

(A). This is best done in a dark area.
If the source has a white body then light can be
seen through the body.
If there is no sign of flashing then unplug the
source connector (B) and check resistance to see
if the source bulb is open circuit.
If there is no flashing and the source is open
circuit then the source (C) will need to be
replaced. It will also need to be replaced if it is
blackened or in any way dark.

The resistance of a good source is about 125 ohms. If there is flashing then carry out the next
test.

13.11 Checking the Detector

Before checking the detector, check the source is
OK. Remove the jaws and handle cover, without
disconnecting it electrically.
Check that the wires are not broken and that the
connector is securely fitted to the PCB pins.

Place the earth clip of an oscilloscope probe on the

metal body of the regulator as shown.

With a narrow oscilloscope probe measure the

signal on the red wire of the connector. This can be
done through the small hole in the side of the
connector.

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LCi-SD user guide Issue 4-104

The detector signal should be an approximate sine

wave between 3.5 and 2 volts peak to peak,
depending on (amongst other things), the setting of
the CO2 zero pot. If you do not have an oscilloscope
measure the voltage with an AC Voltmeter. If there
is no detector signal, then the detector is probably
faulty and will need to be replaced.

The detector can be removed with the cell in place. It is a static sensitive device and so static
precautions should be observed as for changing the EPROM. Unplug its connector, and remove
the large piece of insulation around the detector housing. Unscrew the knurled nut by turning
it counter-clockwise, but do not turn the circuit board. The circuit board, the socket, and the
detector may now be withdrawn. Do not touch the window on the detector. Any fingerprints
need to be removed with alcohol and cotton wool. If the detector is unplugged, note its
orientation with respect to the circuit board. Also note that there is a thin film filter (TFF)
assembly remaining in the end of the tubeset. It is a loose fit, and may fall out. Replacement is
a reversal of the removal procedure. Tighten the knurled nut with your fingers only, do not use
pliers, and do not turn the circuit board.
If you do have a detector signal then reassemble the handle cover, replace the cable clamp
securing screws and fit the camera tripod boss and its securing screws.
Leave the instrument to warm up for 10 minutes and reset the CO2 zero as indicated in the
manual.

13.12 Replacing the Source

Unscrew and remove the two screws from the lever

catch body.

Note that the retaining screws are off-set and not

central. Remember this when reassembling the
handle.

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Unscrew the analyzer retaining screw TWO

TURNS. Do not remove this screw completely
because it locates the analyser cell at the
detector end and prevents its pipe connection
and detector wires being strained.

This will give you just enough slack to lift

the source end of the analysis cell, giving
you access to the lower source retaining
screw. If there is not enough movement
to get a screwdriver on to the sources
lower screw then go back to the previous
instruction and unscrew the analyzer
retaining screw another half a turn and try
again.

Using a small flat bladed screwdriver,

unscrew and remove the upper and lower
source retaining screws. These screws are
stainless steel – Do not replace them with mild
steel types.

Using tweezers or long nose pliers gently pull

out the old source from the analyzer cell. Take
care not to allow any debris to get inside the
analysis cell.

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LCi-SD user guide Issue 4-104

Disconnect the sources electrical connection

from the circuit board.

Then remove the old source.

A thermal isolation gasket should have come

off with the old source.

Remove the thermal isolation gasket from the

old source and fit it onto the new
replacement source.

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Issue 4-104 LCi-SD SD user guide

Fit the new source in to the analyzer cell

and replace the two retaining screws.
Connect the electrical connections to the
circuit board on connector PL5. The
source is not polarized.

Refit the lever catch body, ensuring the

correct orientation so that the body sits
centrally on the handle.

Tighten the analyzer retaining screws but

DO NOT OVERTIGHTEN, the threads are
into plastic spacers.
Replace the Handle cover and Jaws.

Because the new source will have a different

output than the old one the CO2 Zero will need
to be set. Follow the instructions in this manual
or in the maintenance guide “Setting the CO2
zero on the LCi-SD”. If you attempt a zero
before the analyzer has warmed up, it will
prevent the zero taking place. Either wait for
the warming up period or turn off, turn back on
and press the left hand button while the serial
number and software version are still on the
screen. This will bypass the warm-up and allow
the CO2 zero to be set faster.

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13.13 Fault finding

Fault (warnings in quotes) Possible cause Remedy
Battery discharged Recharge battery
Analyser will not switch on
Fuse blown Replace fuse
Invoke hardware reset by pressing,
Analyser will not respond to
Software bug causing it to ignore keypad simultaneously, the left 2 keys and the right
key presses
key
Any pipe (red, white or black) is
Reconnect
disconnected.
Pump running fast but not The air inlet (top connector) is partially
Remove blockage or use bigger supply pipe
enough flow blocked or supply pipe is too thin or long
The black pipe is squashed flat inside the
Reposition the pipe.
chamber handle.
Pump supplies enough air
Pump bearings worn Replace pump
but is noisy
Difficulty removing or
Apply a thin wipe of silicone grease to the
dismantling chemical ‘O’ ring seals are dry
seals
column
The detector signal is out of range of the A-D
converter. Due to: Source failure Look for source flashing- light escapes
through the base. Measure resistance (125)
“CO2 signal failure”
Detector failure Using oscilloscope look for about 15mVpk-
pk triangle wave on pin 1 (blue) of PL1, on
PCA-275
Soda lime exhausted Check soda lime
Gain set too high Check settings as above
“CO2 low energy”
Dirt in the cell Remove and clean cell
I/R Source nearing end of useful life Inspect source, change if blackened
“Cref low, check absorber” Soda lime exhausted or red (zero) pipe
Check soda lime, if OK check pipe, if OK
Can and Cref readings very blocked, or valve SV1 stuck in NO position
check SV1
low or zero
Low, or negative CO2
Soda lime exhausted Check soda lime
values
Fan stopped (this happens if jaws are open) Check fan, shut jaws.
SV2 stuck Touch SV2. Check it clicks audibly and
Can low or zero tactually when LED90 on PCA-275 changes
state.
Fan outlet blocked Check outlet filter
In calibrate CO2 Zero mode, set approx.
Signal at A-D converter is out of range. Gain 3.3V pk-pk detector signal on PL2 pin 2
“CO2 signal overrange”
is set too high (red) on PCA-275 using RV4. Set 4.5V DC
on TP20 on PCA-271 using RV9
The analyser cannot reduce its span Check that the span gas is not being diluted.
“span gas reading is too
coefficient low enough for the value you Check that the value you have entered
low”
have set. matches the cylinder
Check that the analyser is not being
The analyser cannot increase its span
“span gas reading is too pressurised
coefficient high enough for the value you
high” Check that the value you have entered
have set.
matches the cylinder
“Current log file cannot be You cannot delete a file if it is enabled to
Switch logging off before deleting.
deleted (or renamed)” receive records
Pipe not connected or kinked in the handle Check
“Chamber flow not as set”
Air supply to analyser partially blocked Check
The Tleaf reading is outside the A-D Check probe is connected, and is not broken
“Tleaf probe error”
converter range. (should be 2k at 25C)

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APPENDIX 1. PARAMETER INFORMATION

Symbol Description Log? Analog Screen Units Type Range

o/p?
Uset Desired molar air flowrate 2 3 cfg µmols s-1 G 68-341
Us Flow per unit leaf area µmols m-2 s-1 Ca -
P atmospheric pressure 12 y 1 hid mBar M 600-1100
Log: Name of log file 3 cfg log G -
Power Bargraph showing battery state 2 M 10.5-14.3
Rb Boundary resistance to H2O 18 3 m2 s mol-1 G 0.1-9
rb set Boundary resistance at full flow cfg m2 s mol-1 G 0.1-9
C'an CO2 analysis (corrected for dilution) y 1* vpm M,Co 0-2000
^C Delta CO2 (Cref - C'an) 7 y 1* vpm Ca +/-2000
Cref CO2 reference 6 y 1* vpm M,Co 0-2000
Ci Sub-stomatal CO2 13 2 vpm Ca 0-2000
Dt Date (text) 2 diag
Hfac H factor - energy conversion factor 3 cfg F,G 0.1-1
e'ad H2Oanalysis, dilution corrected y 1 mBar Ca,Co 0-75
w'ad H2O analysis, dilution corrected y diag %RH Ca,Co 0-100
^e Delta H2O (w'an-Wref), partial p. 5 y 1 mBar Ca +/-75
^w Delta H2O (w'an-Wref), as %RH y %RH Ca +/-100
Eref H2O reference, as partial pressure 4 y 1 mBar Ca,Co 0-75
Wref H2O reference, as %RH y diag %RH M,Co 0-100
Area projected leaf surface area 17 3 cfg cm2 G 0.1-100
Tch leaf chamber temperature 9 y 1 °C M -5 to +50
u ASU mass flow (measured) 11 y 2 µmol s-1 M 68-341
Trw Chamber window transmission factor 3 cfg F,G 0.25-1
tleaf Leaf surface temperature 10 y 2 °C M,G -5 to +50
Q P.A.R. at window hid µmol m-2 s-1 M 0-3000
Qleaf P.A.R. incident on leaf surface 8 y 1 µmol m-2 s-1 Ca 0-3000
A Photosynthetic rate 16 2 µmol m-2 s-1 Ca 0-100
Cfg: Chamber type / configuration set 3 cfg
Mem. Free space on memory card log k bytes
Record Current record number 1 2 log

The parameter list is continued overleaf.

The “type” column indicates the method of derivation, according to the following code:
Ca = calculated (generally by a formula given in the appendices)
Co = corrected (by terms defined in the appendices)
F = Factors (established by experiment or other means)
G = Given (i.e. entered by the user)
K = constants (physical or scientific)
M = measured raw values (by transducers in the LCi-SD)
(Hfac was Trans on LCA-3)
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 LCi-SD user guide Issue 4-104
APPENDIX 1 PARAMETER INFORMATION (CONTINUED)
Analog
Symbol Description Log?
o/p?
Screen Units Type Range
gs Stomatal conductance of H2O 15 2 mol m-2 s-1 Ca 0.00-1.00
rs Stomatal resistance to H2O m2 s mol-1 Ca 0-100
Tl mtd Leaf temperature determination method 3 cfg
E Transpiration rate 14 2 mmol m-2 s-1 Ca 0-1
tm Time of day 3 diag
Vaux Aux input, scaled as volts Volts
[cab]a Infra-red absorption due to analysis CO2 diag hid % 0-40
[w]a Raw H2O analysis reading hid adc counts
Vbatt Battery voltage diag Volts 10.5 -14.3
Va(20%) Measured analyser flow µmol s-1
phase CO2 rectifier phase shift hid °
[cab]r Infra-red absorption due to reference CO2 diag hid % 0-40
[w]r Raw H2O reference reading hid adc counts
[c]z Raw CO2 zero reading y #REF! adc counts
Wflux Net H2O Exchange Rate 14 2 Mmol m-2 s-1 Ca
Ce Soil Respiration 13 2 mol s-1 Ca
NCER Net CO2 Exchange Rate 16 2 mol m-2 s-1 Ca 0-100

 Indicates position in log when soil pot is selected

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APPENDIX 2. ANALOGUE OUTPUT SCALING

Parameter & Symbol Units Reading @ 0V Reading @ 5V Units/V

Atmospheric pressure (p) mBar 600 1100 100
Analysis CO2 (c’an) vpm 0 2000 400
Delta CO2 (∆c) vpm -200 +200 80
Reference CO2 (cref) vpm 0 2000 400
Analysis H2O (e’an) mBar 0 100 20
Delta H2O (∆e) mBar -5 +5 2
Reference H2O (eref) mbar 0 100 20
Analysis humidity (w’an) %RH 0 100 20
Delta humidity (∆w) %RH -5 +5 2
Reference humidity (wref) %RH 0 100 20
Leaf chamber temperature (Tch) C -5 +50 11
Flow (u) mol s-1 0 342 68.4
Leaf temperature (meas/calc’d) (Tl) C -5 +50 11
Qleaf (PAR @ leaf surface) (qleaf) mol m-2 s-1 0 3000 600
*1
Raw CO2 zero at TP20 ([c]z) Volts 4.05 5 0.19
*2
Raw CO2 zero Diagnostic ([c]z) A-D count 53000 60000 1400

*1
Volts measured at TP20 during zero parts of gas cycle or CO2 zero calibration.
*2
A-D count optimally 56500 for “perfect” CO2 zero calibration.
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APPENDIX 3. CALCULATED PARAMETERS AND CONSTANTS

CO2 Concentration

The IRGA measures the absorption of infra-red due to the presence of CO2. This value must be scaled
and linearised to get the actual concentration. The processing is done in several steps as shown below
for the analysis channel, the reference channel is treated the same, substituting subscript ‘r’.
z a  ra
[cab ]a  za

Where [cab]a absorption due (mainly) to CO 2

za detector signal at zero
ra detector signal at current reading

the calibration set during span adjustment:

can  Lc ([cab ]a s)

Where Lc linearisation function for CO2

[cab]a absorption of infra-red due to CO2
s span factor; determined during calibration (span adjustment)

The reading is now compensated for changes in atmospheric pressure. The LCi-SD leaf chamber and IRGA cell
are very close to ambient pressure.

( pref  p) a
c an ' = c an (1 + )
pref
Where can' pressure corrected CO2 value
pref ambient pressure at last span adjustment, mbar
p ambient pressure, mbar
a pressure compensation factor (1.4)

The IRGA CO2 reading is slightly influenced by the presence of water vapour (pressure broadening).
The water vapour readings are used to compensate the measured readings:

Can ' '  Can '(Can ' wman )

Where can’’ reading compensated for the presence of H2O
wman H2O concentration, as a molar fraction

Finally, leaf transpiration causes the net volume of air leaving the leaf chamber to be higher than that
entering. This volume increase tends to dilute the CO2 concentration, causing can and wan to be lower.
Dilution compensation removes this effect, so that the c e value reflects the differences due to
absorption by the leaf, not transpiration. This compensation is only applied to the analysis reading.

1 wm
cand  can ' ' ( 1 wmrefan )
Where cand Final, compensated reading, as displayed
wmref Reference water vapour concentration, as molar fraction
wman Analysis water vapour concentration, as molar fraction

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APPENDIX 3 (Continued)

Molar flow of air per m2 of leaf surface

symbol: us (mol m-2 s-1)

u
us =
area

Where u molar air flow in mol s-1

area projected leaf area in m2

Difference in CO2 concentration

symbol: C, vpm(mol mol-1)

c = cref - c’ an

where Cref CO2 flowing into leaf chamber, mol mol-1

C'an CO2 flowing out from leaf chamber, mol mol-1 , dilution corrected

Photosynthetic Rate (Rate of CO2 exchange in the leaf chamber)

symbol: A (mol m-2 s-1)

A = u s c

where us mass flow of air per m2 of leaf area, mol m-2 s-1
c difference in CO2 concentration through chamber, dilution corrected, mol
mol -1.

Water vapour pressure in and out of leaf chamber

The calculation for reference is show for illustration. Substitute e'an and rhan for the analysis
calculation.

symbol eref into leaf chamber (mbar)

ean out of leaf chamber
rhref
eref = 100
es

where rhref water vapour concentration as %rh (as measured)

es saturated vapour pressure, mbar (see later)

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LCi-SD user guide Issue 4-104
APPENDIX 3 (Continued)

Calculation of molar concentration of water vapour in and out of leaf chamber

The calculation for reference water vapour is shown for illustration.

symbol wmref into leaf chamber (ratio)

wman out of leaf chamber

e ref
wmref =
pamb

where eref water vapour pressure into chamber, mbar

pamb ambient pressure, mbar

Difference in water vapour pressure

Note that w and RH are calculated in exactly the same way. The dilution corrected analysis
value is used.

symbol e (mbar)
e = e’ an - eref

where eref water vapour pressure into leaf chamber, mbar

e'an water vapour pressure out of leaf chamber, mbar, dilution corrected

Transpiration rate

symbol: E (mol m-2 s-1)

e u s
E =
p

where e differential water vapour concentration, mbar, dilution corrected

us mass flow of air into leaf chamber per square metre of leaf area,
mol s-1 m-2
p atmospheric pressure, mBar

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APPENDIX 3 (Continued)

Leaf surface temperature

Where calculated. This value may also be measured or given.

symbol: Tleaf (C)

 
 
 Q x H factor - E  1
T leaf = T ch +  
 
0.93 M a C p 
  + 4 T ch + 273.16  
3 

 rb  

where Tch leaf chamber temperature, C

Q photon flux density incident on leaf chamber window, mol m-2 s -1
Hfactor energy conversion factor (was TRANS on LCA-3) J/mol
 latent heat of vaporisation of water, J mol-1
E Transpiration rate, mol m-2 s-1
Ma molecular weight of air
Cp specific heat at constant pressure, J g-1 K
rb boundary layer resistance to vapour transfer, m2 s-1 mol-1
(0.93 is conversion factor for above to give boundary layer resistance to
heat)
 is Boltzmann's constant, Wm-2K-4

Stomatal resistance to water vapour

symbol: rs (m2 s mol-1)

( wleaf - wman )
rs = - rb
 eu s 
 
 p 

where wleaf saturated water vapour concentration at leaf temperature, mol mol-1, thus:-

es
wleaf =
p

es saturated vapour pressure at leaf surface temp, mBar

p atmospheric pressure, mBar
e differential water vapour concentration, mbar, dilution corrected
wman water vapour concentration out of leaf chamber, mol mol-1
rb boundary layer resistance to water vapour, m2 s mol-1
us mass flow of air per m2 of leaf area, mol m-2 s-1

1
Energy balance equation for calculating Leaf temperature PARKINSON, K.J. (1983) Porometry in S.E.B. Symposium of
Instrumentation for Environmental Physiology, Cambridge University Press

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APPENDIX 3 (Continued)

Sub-stomatal cavity CO2 concentration

symbol: ci (mol mol-1)

E
(( g c - ) c’ an ) - A
2 2
Ci =
E
gc +
2

where
1
gc =
1.6 r s + 1.37 r b

c'an CO2 flowing out from leaf chamber, mol mol-1, dilution corrected.
E Transpiration rate, mol m-2 s-1
A photosynthetic rate of CO2 exchange in the leaf chamber, mol m-2
s-1
rb boundary layer resistance to water vapour, m2 s-1 mol-1
rs stomatal resistance to water vapour, m2 s-1 mol-1

2
Calculation for Ci, Substomatal CO2 von CAEMMERER, S. and FARQUHAR, G.H. (1981)
Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves. Planta 153:376-387

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APPENDIX 3 (Continued)

Saturated vapour pressure of water at leaf surface temperature

symbol: es (bar)
For Tleaf>= 0
  T 
 T leaf  18.564- leaf  
  
 254.4
-3  
es = 6.13753 10 e  T leaf +255.57 
 
 

For Tleaf < 0, above water

 17.966T leaf 
-3  
es = 6.13753x 10 e T leaf +247.15

(Arden L Buck, Journal Appl. Meterology vol 20 1981 pp1527-1532)

where Tleaf leaf surface temperature, C

Stomatal conductance of water vapour

symbol: gs units: mol m-2 s-1

1
gs =
rs

where rs stomatal resistance to water vapour, m2 s-1 mol-1

P.A.R. incident on leaf surface

symbol: Qleaf units: mol s-1 m-2

Qleaf = Q x Tr w

where Q Photon flux density incident on leaf chamber window, mol m-2 s-1
Trw Leaf chamber window transmission factor to P.A.R. (given)

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LCi-SD user guide Issue 4-104
APPENDIX 3 (Continued)

Soil Respiration (Net Molar Flow of CO2 in/out of the Soil)

symbol: Ce (μ mol s-1)

Ce = u (c)

where u molar air flow in mol s-1

c difference in CO2 concentration through soil pot, dilution corrected, mol
mol -1.

Net CO2 Exchange Rate (Ce per unit area)

symbol: NCER (mol s-1 m-2)

NCER = u s (c)

where us molar flow of air per square meter of soil, mol m-2 s-1
c difference in CO2 concentration through soil pot, dilution corrected,
mol mol -1.
Note: This is equivalent to -A

Net H2O Exchange Rate (Soil Flux)

symbol: Wflux (m mol s-1 m-2)

e u s
W flux =
p

where us molar flow of air per square meter of soil, mol m-2 s-1
e differential water vapour concentration, mbar, dilution corrected
p atmospheric pressure, mBar
Note: This is equivalent to E

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APPENDIX 3 (Continued)

Constants

Volume of 1 micro-mole of air at 20C and 1 Bar (Vm20C)

Value used is 2.4387x10-2 m3.

Latent heat of vaporisation of water ()

Value used is 45064.3 - (tch x 42.9) Joule mol-1

Boltzmann's constant ()

Value used is 5.7 x 10-8 W m-2 K-4.

Molecular weight of air (Ma)

Value used is 28.97

Specific heat at constant pressure (Cp)

Value used is 1.012 J g-1 K-1

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APPENDIX 4. DERIVATION AND MEASURED VALUES FOR

HFACTOR
The leaf temperature can be calculated from the energy balance, as shown in Appendix 3. This requires
knowledge of the total incident radiation H absorbed by the leaf, which in sunlight lies between 0.4 and
3.0 microns. This therefore includes the PAR radiation (0.4 – 0.7) and near infrared radiation (0.7 –
3.0).

The Hfactor is used to convert the measured PAR value into a figure for the total energy absorbed,
which will depend upon the visible/infrared ratio of the incident radiation. This in turn is determined
by the nature of the energy source and conditions, and also by the absorption properties of the leaf and
the leaf chamber windows.

H = Q x Hfactor

A value for Hfactor is given by the following equation:

Hfactor = a.e.f. + a1.c.d.

Where;

H = energy absorbed by the leaf in W/m

Q = PAR in mol m-2 s-1
a = conversion from incident photon flux density between 0.4 & 0.7 to radiant energy
a1 = conversion from incident photon flux density between 0.7 & 3.0 to radiant energy
[a & a1 vary with light source and type of light sensor – a silicon type is used with the LCi-SD]
c = the fraction of infrared transmitted by the chamber windows and shield if fitted
d = the fraction of infrared absorbed by the leaf
e = the fraction of visible transmitted by the chamber windows and shield if fitted
f = the fraction of visible absorbed by the leaf

Typical values for the above factors are;

a = 0.2188 for sunlight(K.J.McCree,1972,Agricultural Meteorology,10, p443-453 etc.)

a1 = 0.1205 (based on 361.5wm-2/3000mol m-2 s-1 at  ave = 0.992)
c = 0.6
d = 0.2 (for typical leaves)
e = 0.88 (Broad & Narrow chambers), 0.93 (Conifer chamber)
f = 0.8 (for typical leaves)

These values give Hfactor = 0.168 (Broad & Narrow chambers) – for sunlight
= 0.177 (Conifer chamber)
= 0.168 (Arab. & Small chambers)

Other values have been obtained for sunlight and various light sources, based on the Broad
and Narrow chambers and using a silicon PAR sensor. These are given in the following
table, and generally are to be recommended.

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APPENDIX 4 (Continued)

Measured Hfactor values and conditions.

PLC with Perspex Shield

and Windows
LIGHT SOURCES PAR sensor outside chamber PAR sensor inside chamber

Sun & Sky 0.168 0.214

Tungsten 3000C 0.340 0.429

Warm white fluorescent 0.109 0.139

Cold white fluorescent 0.113 0.144

Grolux fluorescent 0.118 0.150

Tungsten 3000C with IR filter 0.160*

*Configuration used with the ADC Light Unit

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APPENDIX 5. SATURATED VAPOUR PRESSURE

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APPENDIX 6. CHAMBER EXPLODED DIAGRAM

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LCi-SD user guide Issue 4-104

APPENDIX 7. CONSOLE EXPLODED DIAGRAM

PCA-288 DIGITAL

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APPENDIX 8. LCI-SD MENU STRUCTURE

Pressing the “Page” key in “sub-level” menus returns to previous level except where shown. Pressing the
“Page” key in the “top-level” menu steps through the three main pages.

logging record
if no file set
to file timed no
serial menu log log yes no

change change
  set log options timing manual
+ -
if no file selected

> + - del rename delete review

> + - del

1st / previou
yes no last s next more

output calibrate graph record

if no file set see logging menu
Outp. do Start/ Toggles between“start/view”
½   serial select + - calib. set up stop clear
view and “disabled”
These keys appear only
when graph is set up.
change change Start/
Select x axis plot set o/p view
+ -

Q options power off configure record

if no file set see logging menu
Hold release given climate time / SD
Q Q Q Q yes no date
set up diagnose
Card

sys.
info
info

auto
OK phase

change change change change

select select
+ - + -

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APPENDIX 9. TECHNICAL SPECIFICATION

Measurement range and technique: CO2: 0-2000 ppm, 1ppm resolution
Infra red gas analysis, differential open system,
auto zero, automatic atmospheric pressure and
temperature compensation.

H2O: 0-75mbar, 0.1 mbar resolution

Two laser trimmed, fast response RH sensors.

PAR: 0-3000 mol m-2 sec-1 Silicon photocell

Chamber temperature: -5C to +50C Precision thermistor. 0.2C accuracy

Leaf temperature: -5°C to +50°C Energy balance or microchip thermistor

Gas Exchange Repeatability: CO2: 0.1% of reading @ 370ppm

H2O: 0.5% R.H.

Linearity: CO2: 0.5% of reading

H2O: 0.5% RH

Temperature effect on span CO2: <0.05% of f.s.d. per C

Flow rate in PLC: 100ml to 500ml min-1

Flow rate accuracy:  2% of f.s.d.

Display: 240 x 64 dot matrix super twist LCD

Warm up time: 5 minutes at 20C

Recorded data: SD Card

Battery: 2.6 AH lead acid 12V to give 10 hours

Battery charger: 90 to 260V, 50/60 Hz

Analogue output: 0 to 5V on user selected parameter

RS232 output: User selected rates up to 19200 baud

USB Slave Peripheral

Electrical connections Power: 5 pin DIN
Analogue out: 5 pin DIN
RS232: 9 pin D type. “AT” pin configuration.
Chamber: 15 pin high density D type
USB: USB Mini B
Gas connections: 3mm barbed

Power requirements: 0.3A @ 12V DC

Operating temperature: 5C to 45C

Dimensions (H x W x D overall) Console: 240 x 125 x 140 mm

Chamber: 300 x 80 x 75 mm

Weight (typical) Console: 2.4 kgs

Chamber: 0.6 kgs

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APPENDIX 10. SMALL BUFFER VOLUME CONSTRUCTION

A useful accessory for the LCi is a small buffer volume made from a clean glass jar. Clean
glass has very little gas “hangup” and when water is added to the jar it can be used as a water
bubbler for making 100% RH air if two are connected in series, useful if a H2O recalibration
needs to be done.
The main purpose however is to average out or stabilize the CO2 level going into a console.

The small buffer consists of a glass jar with two air entries (also known as 1/8” bulkhead
connectors) mounted through the lid. The assembly must be air tight, this being achieved with
the use of two part glue and PTFE tape.

The small buffer volume is shown above left, the parts required to make one are shown above
right.

Parts used (above right): A glass jar at least 500 ml in volume, some PTFE tape, two plastic
M6 washers, two 1/8” barbed bulkhead connectors (ADC part number 614-802). Some slow
setting araldite 2011 glue, (quick setting glues may be used but they are not suitable for use
as a water bubbler) and a short length of 3mm bore PVC tubing to go inside the jar.

One of the air entries of the buffer volume has an internal tube attached which drops to the
bottom of the jar. When connecting to a console, be sure to connect the other entry without
the internal tube attached. This means that any water that finds its way into the jar is left on
the bottom of the jar while the air is drawn out from the top. It also allows the air to be
volumised by being drawn through the length of the jaw from the bottom to the top which
helps to average the CO2 readings. If the buffer is used to wet the air by adding water, then
this tube, located well below the waterline, means that air will exit the tube in the form of
bubbles moving through the water then into the air pocket above, which results in the air
being wetted. Two such water bubblers in series are sufficient to produce 100% RH or fully
saturated air. Provided the end of the internal tube is capped with a suitable diffuser.

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First, drill or punch two 6.3mm holes in the lid approximately 22mm apart as shown below
left. Next mount the bulkhead connectors as shown below centre and below right.

Next apply some two part glue using a cocktail stick to make a seal around the bulkhead
connectors on both sides of the lid as shown below.

Next apply a few turns of PTFE tape to the glass thread on the jar, be sure to apply in the
direction as shown (clockwise) so that the lid screws on with the same direction as the tape
(see below left). Before screwing on the lid, cut a 3 mm bore length of tubing to length of the
jar minus 20mm (see below right).

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Connect this length of tubing to one of the

bulkhead connectors on the inside of the lid (see
left). If this buffer is connected to a console then
the console “air in” entry connects to the buffer
entry without the long tube on it, the “short” air
entry.

Screw the lid onto the jar quite tightly, if the PTFE tape is unravelled by doing this then it has
probably been put on in the wrong direction. If you have a manometer then you can leak test
the volume by connecting to one entry and blocking the other.

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Note on Water Bubblers.

In order to use the buffer volume as a 100% RH generator or “water bubbler” it will be
necessary to make and connect two in series and fit an “air stone” to the internal tube before
adding water to the jar to half fill it. Two such “air stones” are shown below and can be
obtained from suppliers of aquarium equipment.

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APPENDIX 11. SPARES AND ACCESSORIES

Part No. Description

022-204 800mA fuse glass time delay

197-710 SD card 2G
299-494 13.8V lead acid charger for 12 V battery
631-100 Aluminium dismantleable filter
630-963 Hydrophobic filter
630-980 Filter plastic disposable
650-952 ‘O’ ring 6.07 bore x 1.78
651-551 ‘O’ ring 28.3 bore x 1.78
653-085 ‘O’ ring 2.54 bore x1.02
650-240 ‘O’ ring 2 bore x 1
706-555 tube PVC 2 bore
708-656 tube PVC 3 bore
708-454 tube butyl 3 bore
809-151 silicone grease
867-056 trimming tool
994-151 cable 9-way female to female (3 metre)
994-283 Cable USB A to mini B
LCB-129 gasket broad front
LCi-SD-023A Source assembly
LCi-SD-053 V probe lead assy.
LCi-SD-059 lead assy. power/chart
LCi-SD-131 gasket broad back
LCi-SD-168 belt/neck strap
LCM-068 soda lime – white to violet indicating
OP2-134 Column gas mixer
PLC-011 leaf temperature thermistor assembly

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