Decagon Devices SC-1 User manual

L e a f P o r o m e t e r
Operator’s Manual
Version 8

Decagon Devices, Inc.
2365 NE Hopkins Court
Pullman, WA 99163
Tel: [phone]
Fax: [phone]
www.decagon.com
Trademarks:
“Leaf Porometer” is a registered
trademark of Decagon Devices, Inc.
© 2 5-2 1 Decagon Devices, Inc.
All rights reserved.

Leaf Porometer Operator’s Manual
i
Table of Contents
1. Introduction . . . . . . . . . . . . . . . . . . 1
Customer Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Seller’s Liability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Repair Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Repair Costs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
. About the Leaf Porometer . . . . . . 4
Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Overview of the Leaf Porometer . . . . . . . . . . . . . . . . . . . 5
Components of the Leaf Porometer . . . . . . . . . . . . . . . . . 5
Keyboard Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
The Sensor Head . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Setting the Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Calibration Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Manual Mode vs. Auto Mode . . . . . . . . . . . . . . . . . . . . . . 9
Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
3. The Menus . . . . . . . . . . . . . . . . . . . 11
The Measurement Menu . . . . . . . . . . . . . . . . . . . . . . . . . 11
Measuring Small Leaves & Needles . . . . . . . . . . . . . . . . 13
Taking a Measurement in Auto Mode . . . . . . . . . . . . . . 13
Taking a Manual Mode Measurement . . . . . . . . . . . . . . . 15
Saving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Averaging Readings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Measurement Troubleshooting . . . . . . . . . . . . . . . . . . . . 18
Measurement Precautions . . . . . . . . . . . . . . . . . . . . . . . . 19
The Data Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
The Configuration Menu . . . . . . . . . . . . . . . . . . . . . . . . . 25

Leaf Porometer Operator’s Manual
ii
4. Sensor Head Calibration . . . . . . 31
5. Leaf Porometer Utility . . . . . . . . 45
Downloading Your Data . . . . . . . . . . . . . . . . . . . . . . . . . 46
How Saved Data Are Organized . . . . . . . . . . . . . . . . . . . 48
Erasing Your Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Setting the Date and Time . . . . . . . . . . . . . . . . . . . . . . . . 5
Calibration Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Retrieving Leaf Porometer Information . . . . . . . . . . . . . 51
The Menus and Their Functions . . . . . . . . . . . . . . . . . . . 52
6. Leaf Porometer Theory . . . . . . . 58
Stomatal Conductance . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
How the Leaf Porometer Works . . . . . . . . . . . . . . . . . . . 58
7. Care and Maintenance . . . . . . . . 68
Changing the Batteries . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Cleaning the Sensor Block . . . . . . . . . . . . . . . . . . . . . . . . 68
General Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Upgrading Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
8. Troubleshooting . . . . . . . . . . . . . 75
Further Reading . . . . . . . . . . . . . . . 83
CE Compliance. . . . . . . . . . . . . . . . . 85
Appendix A - Send Feedback . . . . 86

Leaf Porometer Operator’s Manual
1. Introduction
1
1. Introduction
Thank you for purchasing Decagon Devices’ Leaf Porometer.
The Leaf Porometer is a device used to measure stomatal
conductance in leaves. This manual is designed to help you
understand the functions of your Leaf Porometer, make
high-quality stomatal conductance measurements, and help
you get the most out of your Leaf Porometer.
Customer Support
When contacting us, via fax or e-mail, include your Leaf
Porometer’s serial number (this can be found on the inside
of the battery cover), the firmware version you are currently
using, your name, address, phone and fax number, and a
description of your problem.
Phone:
United States/Canada (toll free): 1-800-755-2751.
Outside of the U.S./Canada: 1-509-332-2756.
Fax: [phone]
E-Mail: s [e-mail].
Warranty
The Leaf Porometer is covered by a standard, one-year war-
ranty on parts and labor, and is activated upon the arrival of
the instrument at your location.

Leaf Porometer Operator’s Manual
1. Introduction
2
Seller’s Liability
Seller warrants new equipment of its own manufacture
against defective workmanship and materials for a period of
one year from the date of receipt of equipment (the results
of ordinary wear and tear, neglect, misuse, accident and
excessive deterioration due to corrosion from any cause are
not considered to be a defect); but Seller’s liability for defec-
tive parts shall, in no event, exceed the furnishing of
replacement parts f.o.b. the factory where originally manu-
factured. Material and equipment covered hereby which is
not manufactured by the Seller shall be covered only by the
warranty of its manufacturer. Seller shall not be liable to
Buyer for loss, damage, or injuries to persons (including
death), or to property or things of whatsoever kind (includ-
ing, but not without limitation, loss of anticipated profits),
occasioned by or arising out of the installation, operation,
use, misuse, nonuse, repair, or replacement of said material
and equipment, or out of the use of any method or process
for which the same may be employed. The use of this
equipment constitute’s Buyer’s acceptance of the terms set
forth in this warranty. There are no understandings, repre-
sentations, or warranties of any kind, express, implied, stat-
utory or otherwise, (including, but not without limitation,
the implied warranties of merchantibility and fitness for a
particular purpose), not expressly set forth herein.
Repair Instructions
If your Leaf Porometer should ever require a repair, call
Decagon at [phone] or 1-800-755-2751 (United
States and Canada). We will ask you for your address, phone
number, your Leaf Porometer’s serial number, and your cur-
rent firmware version. For non-warranty repairs, we will
also ask for a method of payment.

Leaf Porometer Operator’s Manual
1. Introduction
3
Before shipping yo r instr ment to Decagon, please
contact Decagon to obtain a Req est Maintenance
A thorization N mber (RMA). This will allow Decagon’s
repair staff to keep track of your porometer. Once you have
acquired an RMA, send your Leaf Porometer to Decagon.
Please include a document listing the complete shipping
address, name, and department of the person responsible
for the instrument, as well as a description of the problem.
This will better help our technicians and shipping depart-
ment to expedite repair on your Leaf Porometer, and ship it
back to you.
Please pack your Leaf Porometer carefully. Ship it back in
the carrying case, preferably inside a cardboard box. Ship to:
Decagon Devices Inc.
2365 NE Hopkins Co rt
P llman, WA 99163
Repair Costs
Manufacturer’s defects and instruments under warranty will
be repaired at no cost. For non-warranty repairs, costs for
parts, labor, and shipping will be billed to you.

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
4
. About the Leaf Porometer
The Leaf Porometer is a battery-operated, menu-driven
device used to measure stomatal conductance of leaves. Sto-
matal conductance is a function of the density, size, and
degree of opening, of stomata, which are pores in plants
that open to the outside air. The Leaf Porometer measures
stomatal conductance by putting the conductance of a leaf
in series with two known conductance elements, and com-
paring the humidity measurements between them. It can
display information in three selectable units:
• mmol/m
2
s (millimoles per meter squared
seconds)
• m
2
s/mol (meters squared seconds per mole)
• s/m (seconds per meter)
The first is a unit of conductance, while the other two are
units of resistance. To change between them, use the arrow
keys when taking a reading (see “Making a Measurement,”
pp. 16). They can also be altered by using the Units screen
under the Configuration Menu.
Specifications
Operating Environments: 5 - 4
o
C; - 9 % relative
humidity (non-condensing). NOTE: At temperatures less than
10° C, Automatic mode may experience errors, despite corrections
that have been made (See Chapter 3 more information about
Auto mode.)

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
5
Acc racy: 1 %
Sample Chamber Apert re: 6.35mm ( .25 in)
Meas rement Range: to 1 mmol/m
2
s
1
Microcontroller Dimensions: 15.8 x 9.5 x 3.3 cm (6.2 x
3.75 x 1.3 in)
Data Storage: 4 95 measurements
Data Retrieval: Direct via RS-232
Keypad: Six-key, menu-driven
Clock: 24-hour, +/- one minute per month
Interface Cable: RS-232 serial cable (included)
Power S pply: Four type “AA” batteries (included)
Overview of the Leaf Porometer
The Leaf Porometer features an easy-to-use, six-button,
menu-driven interface. There are three primary menus: the
Main Menu, Data Menu, and Configuration Menu (See
“Menus,” Chapter 3). You can navigate between each of
these by pressing the Menu button.
Components of the Leaf Porometer
The Leaf Porometer and its components come to you in a
foam-padded carrying case. You should find the following
items inside when your Leaf Porometer arrives:
• Leaf Porometer controller
• RS-232 cable
• Operator’s manual, including a CD-ROM with the
Leaf Porometer Utility
• Sensor head
• Teflon filter disks
• Replacement leaf pad/outer leaf pad (see p. 8)

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
6
• Calibration plate
• Bottle of distilled water
• Tweezers
• Calibration filter paper disks
Keyboard Functions
Here is a brief overview of each key’s function:

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
7
Power: This key activates and deactivates the
Leaf Porometer. (NOTE: The device will auto-
matically turn off if not used for more than 10 min-
utes or 60 minutes if running in manual mode )
Menu: This key cycles between the three
menus at the top of the screen. NOTE:
Pressing Menu while changing a setting will cancel
any operations
Arrow Keys: These keys navigate within
menus and sub-menus, and modify
numerical values in sub-menus, as well as
select different units. Holding down an
arrow key allows you to scroll between dif-
ferent options quickly.
Escape: This key backs out of sub-menus
and can be used to cancel certain actions.
Enter: This key is used to make selections
within menus and sub-menus, and also
begins taking measurements.
The Sensor Head
The Leaf Porometer cannot take measurements without the
aid of the sensor head. This sensor head is responsible for
gathering the information (vapor pressure, humidity, etc.)
that the Leaf Porometer uses to calculate stomatal conduc-
tance in a leaf. The following illustration shows the external
components of the sensor head.

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
8
Setting the Time
You should make sure that the system time on the porometer
is correctly set. This will make sure the timestamps on down-
loaded readings are accurate (see “How Saved Data is Orga-
nized,” Chapter 4). You can do this manually in the porometer
(see “Time” in Chapter 3), or by using the Leaf Porometer
Utility (see “Setting The Date & Time” in Chapter 5).
Calibration Number
Each sensor head comes with a default five digit calibration
number that can be found on the tag on the sensor head cable
and on the calibration certificate. This default calibration
number has been entered into the leaf porometer readout unit
and will be applied to each measurement until a user initiated
calibration is performed. When a user initiated calibration is
performed, a new calibration number is generated and stored.
This new calibration number will be applied to all subsequent
measurements instead of the default calibration until a new
user initiated calibration is performed or the user requests a
reset to the default calibration.

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
9
Manual Mode vs. Auto Mode
When the porometer is in Manual Mode (see pg 15 for
instructions on how to configure the porometer to Manual
Mode), the stomatal conductance is measured directly from
the theory presented in Chapter 6 and displayed continu-
ously. The real time conductance measurement can be saved
at any time during a Manual Mode measurement. Manual
mode should only be used at low conductances (i.e. < 2
mmol m
-2
s
-1
). At higher conductances, the readings
become inaccurate and can take an exceptionally long time
to complete. For the theory in Chapter 6 to accurately pre-
dict the stomatal conductance using the steady state diffu-
sion technique, true steady state conditions must exist in the
diffusion path. The amount of time necessary to reach
steady state conditions is proportional to the conductance.
At conductances less than 2 mmol m
-2
s
-1
, steady state con-
ditions are generally reached in less than 5 minutes. At
higher conductances, steady state conditions can take up to
3 minutes. Please note that leaving the sensor head on the
leaf surface for more than a few minutes can cause the sto-
matal conductance to change in response to the presence of
the sensor head clip. Some common uses for manual mode
are measuring dark conductance in plants and measuring
conductance of static conductance materials (e.g. fruit peels,
waterproof fabric).
Auto Mode makes an accurate stomatal conductance mea-
surement in 3 seconds. To do this, the porometer takes the
first 3 seconds of stomatal conductance data and applies a
“look ahead” algorithm to predict the final stomatal con-
ductance reading that would be achieved if unlimited time
were allowed for true steady state conditions to occur. Auto

Leaf Porometer Operator’s Manual
2. About the Leaf Porometer
1
Mode has several advantages over Manual Mode and other
porometers. First, the 3 second Auto Mode measurement
duration ensures that stomatal conductance doesn’t change
due to the presence of the sensor head. Second, Auto Mode
takes only 3 seconds per measurement, ensuring that your
measurements are completed in a timely manner. Finally,
Auto Mode sets a definite endpoint for the measurement,
meaning that the user doesn’t have to pick an arbitrary end-
point, as is common with other diffusion porometers and
with Manual Mode measurements.
For the porometer to “detect” the presence of a transpiring
leaf and begin the Auto Mode measurement, the measured
stomatal conductance must reach 5 mmol m
-2
s
-1
So, if you
are making measurements on leaves with extremely low
conductances, it may be necessary to make the measure-
ments in Manual Mode.
Precautions
Before using or calibrating the porometer, remember:
• Avoid leaves that are wet or heavy with dew; never
take readings in the rain.
• Do not touch the Teflon disk, or get your fingers near
it, during a reading. This will cause inaccurate readings.
• If you blow into the sensor, it will take a few minutes
for the stomatal conductance reading to return to nor-
mal.
• Clean the sensor periodically to keep it free of dirt and
pollen that can build up during use and affect readings.
(See “Cleaning the Sensor Block,” in Chapter 7.)
• Avoid chemical fumes. Fumes can be extremely harm-
ful to the sensor (i.e. alcohol, gasoline, foam).

Leaf Porometer Operator’s Manual
3. The Menus
11
3. The Menus
The Leaf Porometer features three main menus, designed
for easy navigability and use.
The Measurement Menu
The Leaf Porometer displays the Measurement Menu when
first powered on.
At the top of the screen is the stomatal conductance num-
ber at left, and the currently selected unit of measurement at
right. Below are two columns of numbers. The left is the
sensor closest to the leaf, and the right is the sensor farthest
from the leaf. Each column has the temperature of that sen-
sor, and its percent humidity. The Leaf Porometer uses
these to calculate the stomatal conductance value (see
“How the Leaf Porometer Works” in Chapter 5).
Making a Measurement
The following sections discuss making a measurement in
both automatic and manual modes.

Leaf Porometer Operator’s Manual
3. The Menus
12
Before beginning a reading, make sure that the Leaf Porom-
eter is turned on, and that the sensor head is clean and
properly connected.
NOTE: Make sure you are holding the sensor in the correct manner
Holding the sensor head correctly is extremely important If you do not,
you can expose the Teflon disk to extra humidity and cause inaccurate
readings The pictures below illustrate the correct way to hold the exter-
nal sensor:
Correct Incorrect
Once you are holding the sensor head properly, place it on
the leaf as shown below.
NOTE: It is important to consider if you will be measuring adaxial
conductance (on the top of the leaf) or abaxial (the bottom) Since the
stomates of most leaves are on the bottom of the leaf, most measure-
ments will be abaxial:

Leaf Porometer Operator’s Manual
3. The Menus
13
Abaxial (Bottom) Adaxial (Top)
Measuring Small Leaves & Needles
When measuring small needles or leaves, they should be
inserted into the sensor as shown below. This is because sin-
gle needles or small leaves (including blades of grass) may
not adequately cover the apature of the sensor.
Taking a Measurement in Auto Mode
There are two modes in which to make measurements,
Automatic and Manual. The following illustrates how to
make a measurement in Auto mode:
Ca tion: Before sing, allow the sensor to eq ilibrate
to the ambient temperat re.

Leaf Porometer Operator’s Manual
3. The Menus
14
1. Select Auto mode. (Please see the “Manual Mode” sec-
tion later in this Chapter for instructions on how to
select an Auto mode from the Configuration Menu.)
2. Return to the Measurement Menu. You will be prompted
to press Enter to begin a reading.
3. After pressing Enter, the following screen will be
displayed:
4. The reading will begin once the sensor head is placed on
a leaf, and a conductance value greater than ambient is
detected. A progress bar will also indicate the reading is
underway.
If the following screen appears when you press Enter, open
the sensor and gently wave it in the air. You should not blow
into the sensor, as this will throw off readings for a few
minutes.

Leaf Porometer Operator’s Manual
3. The Menus
15
5. The measurement screen will resemble the following.
NOTE: In Auto mode, a timer will appear in the upper right
hand corner of the screen that indicates how many seconds remain
6. Once the time limit has expired, the porometer will dis-
play the final conductance. You may save or discard your
data. See “Saving Data” on the next page for instruc-
tions.
Taking a Manual Mode Measurement
Ca tion: Before sing, allow the sensor head to eq ili-
brate to the ambient temperat re.
1. Select Manual mode from the Configuration Menu.
Please note that manual mode is only for special situa-

Leaf Porometer Operator’s Manual
3. The Menus
16
tions with conductances below 2 mmol m
-2
s
-1
. See the
section “Manual Mode vs.Auto Mode” in Chapter 2 for
details.
2. Return to the Main menu and press Enter.
3. Place the sensor on a leaf. Unlike Automatic mode, there
is no time limit for taking readings, and the elapsed time
is displayed directly below the system time.
4. You may save your data at any point during the reading
by pressing Enter. See below for instructions on how to
save your data.
Saving Data
In Automatic mode, you can save data as soon as the timer
has expired; in Manual mode, you save your data without
interrupting your reading. To save your data in either mode,
1. The following screen will appear (you have to press
Enter in Manual mode to access it):