key points of using canopy sensors - aclimas · 05/03/2013 16 a) trial measurements 3. angle and...

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SWIM - Sustainable Water Integrated Management Demonstration Project

Key points of using Canopy Sensors

SPAD-502Plus (Konica Minolta)

Chlorophyll content

Visual Senescence Scoring

Stay-green

Infrared Thermometer INF151 (UEI)

Canopy temperature

Greenseeker® 505 Handheld

(NTech Industries, Inc.)

NDVI

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Chlorophyll Content

Fv/Fm

Canopy Temperature

NDVI

Senescence

(Zadoks scale)

1. When to measure?

2. Equipment

a) Mechanical Specifications

b) Components & Accessories

3. Measurements

a) Preparation

b) Trial Measurements

4. Data Download & Processing

5. Common Problems & Solutions

Greenseeker 505 HandHeld

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GreenSeeker - NDVI

• Any time of the day.

• Plant surfaces must be dry and not wet from dew.

• Avoid windy days. Wind can modify canopy structure.

• Early vigor: 5, 10 and 15 days after emergence.

• Biotic and abiotic stress detection: measurements

before, during and after stress.

• Biomass and crop growth rate: periodic measurements

from emergence to end of anthesis.

• Senescence: weekly or every 3 to 4 days measurements

from anthesis to maturity.

a) Mechanical Specifications

- Weight Unit – 6 kg.

- Weight of Unit, case and accessories – 17 kg.

- Case dimensions – 35.5 x 35.5 x 129.5 cm.

- Over long distances should be transported in its box


- GreenSeeker 100-240 V AC battery charger

Keeping the unit plugged when not in use will extend

the battery life.

- Control Box

Battery, circuit board to interface power and switches to the sensor and external

connectors.

Charged

Charging

Power connector

Power Switch/ Indicator

External Data port (RS232 Collection of data)

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Pocket PC – displays and stores the data from the sensor. Should always be charged if

not the collected data will be erased.

NTech Capture© – pre-loaded software to capture the readings from GreenSeeker

Handheld Sensor, display the current reading, and store for later data analysis or to

make fertilizer recommendations.

Pocket PC

Extension pole

Trigger Switch

(small buzzer)

Pocket PC

Cradle

DB9 (RS232) serial cable


- Sensor head

Takes the reflectance readings

Active - Internal illumination

Pocket PC

Control box

Sensor

Head

Shoulder

Strap

Extension

pole

Sensor

mount

12 – pin connector

Pask A, Pietragalla J, Mullan D, Reynolds M (2012) Physiological breeding II: A field guide to wheat phenotyping. CIMMYT, Mexico

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a) Preparation

1. Fully charge batteries of Pocket PC & Sensor Unit

- Usually > 6h (over-night).

2. Check connections

- Sensor head, control box, extension pole and Pocket PC.

3. Check sensor head position to the crop

- Horizontally positioned in relation to the ground

- Adjust the distance to the canopy (string with a weight helps), by adjusting the

sensor head angle and the extension pole.

4. Adjust shoulder straps

- Place the strap diagonally across the body.

b) Trial measurements

1. Turn on the Control Box and the Pocket PC. Allow 10 min to equilibrate with

ambient temperature. If “Unidentified USB Device” error message appears on the

Pocket PC display write: “ftdi_ser.dll” and press OK.

2. On the Pocket PC:

2.1. Go to Start > Programs and run NTechCapture software;

2.2. Select Sensor > Start GreenSeeker and select Logging Plots.

3. Position the Sensor at the start of the plot. Press and hold the trigger and traverse

the region (speed 1 m s-1). Release the trigger. Data is recorded to the file.

4. When completed the data collection, go to File > Save – assign file name.

Display

NDVI: last NDVI point recorded for the plot

AVG NDVI: average NDVI of all points measured for the plot

Sample: number of measured plots

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Problem: “Unidentified USB Device” error message appears on the Pocket PC display

after turning it on:

Solution: write “ftdi_ser.dll”:

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When data is saved three comma-delimited ASCII text files are created in the Pocket PC internal memory or removable memory card in My Device\My Documents\NtechCapture:

- ‘filename.txt’ — all data collected. NDVI, Vegetation Index (VI = Red/NIR) values for each plot (≈ 10 values/ sec);

- ‘filenameAvg.txt’ — average NDVI and VI for each plot; - ‘filenameDiag.txt’ — diagnostic information for the sensor.

Note: Once the software is closed you cannot open a created file. After saving a data file, a new file can be created by tapping File > New. This will clear the data cells and allow the collection of new readings.

Download files to the computer:

Connect PDF to the USB-port and copy files from My Computer/ Mobile device to the

computer (ActiveSync must be installed in the computer).

Open files in MS Excel:

1. Launch Excel and select Open from the File menu.

2. Change File Types to All Files and select the .txt data file.

3. Select Delimited Text, delimited by commas and spaces. This will import data into

separate columns in the spreadsheet file.

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Problem Solution

“Unidentified USB Device” error message appears on the Pocket PC display after turning it on.

Write: “ftdi_ser.dll” and press OK.

Large variance in data. GreenSeeker sensor not held centrally over plot and/ or small plots – large border effect.

Variable reflectance values and/or with high error variance.

Low battery causing decreasing light source intensity affecting reflectance value. Charge unit.

Unintentional value recorded. Take note of plot number and delete value during processing.

GreenSeeker does not log data. Check connections and cable between Pocket PC and Control Box. If connections and cable are fine, reset Pocket PC (press & hold power button select reset).

Pocket PC errors or ‘hangs’. (e.g. ‘gate not available’). Reset Pocket PC.

Not all counts are recorded. General file without all counts. Usually a problem with the cable.

Battery does not charge. Battery charger light does not come on. Unit battery not charging. Probably broken fuse. Open Control Box and replace fuse.

1. When to measure?

2. Equipment

3. Measurements

a) Preparation


4. Common Problems & Solutions

5. Maintenance (Reading Checker)

SPAD-502Plus

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SPAD – Chlorophyll Content

• No restrictions on time of the day and environmental

conditions.

• Leaf surface should be dry.



• Peak chlorophyll: measurements should be done early

in the season, heading and mid-grain filling.



Measuring Head

Power Switch

All Data Clear Button

Battery Chamber

Cover (2 AA batteries)

1 Data Delete Button

Data Recall Button

Average Button

Display

Finger rest

Measurement

Centre Line

Receptor

Window

Sliding Depth Stop

SPAD-502Plus (Konica Minolta) Chlorophyll meter

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a) Preparation

1. Measuring chamber should be clean and the

rubber seal intact.

2. Turn SPAD on and allow 10 min to equilibrate with

the ambient temperature.


1. Calibration (always after turning on)

- With no sample close measuring head until beep.

- SPAD is calibrated.

Battery indicator


2. Calibration Errors

- Series of beeps – measuring head was not completed closed during calibration

or was opened before calibration was finished. Repeat calibration keeping

measuring head completely closed until calibration is finished.

- Series of beeps – measuring head emitting and/ or receiving windows may be

dirty. Clean and repeat calibration.

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3. Measurement 3.1. Adjust siding Depth Stop.

3.2. Place the leaf in the sensor:

- Measuring area 2 mm x 3 mm up to 1.2 mm thick;

- 1/3 to 1/2 of the way to the leaf base;

- Adaxial surface facing upwards;

- Avoid midrib, major veins & thick parts of the leaf.

3.3. Close measuring head until beep.

3.4. Reading displays in the screen.


3. Measurement

3.5. Repeat 3.1. to 3.4 up to N=5

(SPAD can store up to 4096 values or 1488 with GPS).

3.6. Review readings (and graphic trend):

- Press Data Recall button;

- Remove outliers and retake measurements if needed.

3.7. Press Average button and record average value.

3.8. Press All Data Clear button twice

(go to next plot start from 1.).

3. Measurement Errors

Series of beeps and ‘ERROR’ message while measuring:

- Measured head was not closed completely or was

opened before the measurement was completed.

- Sample is too thick or thin.

- Repeat measurement with head completely closed.

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Problem Solution

SPAD not giving readings but emitting beeps when closed.

Chamber and/ or chamber seal is dirty or leaf not positioned correctly. Retake reading.

Large variation in SPAD values within a plot.

Maintain consistent point of measurement along the leaf. Lower values might be associated with the leaf being: damaged, diseased or leaf tip has been inserted. Healthy and clean leaves should be used.

Damage to the surface of the crop (e.g. frost, disease, etc.).

Do not use SPAD in dead material and avoid damaged areas of the crop.

1. Turn ON while pressing

1 DATA DELETE and DATA RECAL. 2. Calibrate

3. Remove

Depth Stop

4. Insert

Reading Checker &

Measure up to N=5

5. Check Average

Average value should be within the range of the Reading Checker. If not clean emitting and receiving windows and repeat. If it is still not within the range, there is a possible malfunctioning contact service centre. Turn Off and On to resume normal operation.

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1. When to measure?

2. Equipment

3. Measurements

a) Preparation


4. Common Problems & Solutions Infrared Thermometer INF151

(UEI)

IRT – Canopy Temperature

• Clear sky with little or no wind - measurements should be taken between 11:00am to 2:00pm.

• Days with high temperatures (> 25°C) and VPD work preferably.

• Leaf surface should be dry.





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Trigger

(ON/ Measurement Button)

Handle

Battery (9V) compartment


Canopy temperature

IR Sensor

Laser Pointer Bean

LCD Display Emissivity Button

(0.95, 0.90, 0.85)

Units Button

(°F and °C)

Back Light Button

(ON/ OFF)

Laser Button

(ON/ OFF)


Canopy temperature

Distance to scanned area ratio – 8:1

Wrong Right

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Pen Type Hygrometer DTH10 (UEI)

Temperature and Humidity meter

ON/ OFF Button

Hold Button

MIN/ MAX Button

Temp (F/C)

(Change unit from °F to °C)

Reset Button

Sensor

(CR2032 battery)

a) Preparation

1. Turn on the temperature/ humidity meter. Allow the instrument to equilibrate with

the ambient temperature (± 3 min), not exposing directly to sun. Record air

temperature and relative humidity (RH).

2. Turn on infrared thermometer by pressing the trigger and check if emissivity is set to

0.95. If not press Emissivity Button while pressing the trigger until 0.95 emissivity is

chosen. Allow IRT to equilibrate with the ambient temperature for 10 min.


1. Point the IRT to the plot and press the trigger - record reading (releasing the trigger

activates the 7 second auto-hold). A minimum of 3 measurements per 6 m2 plots is

advised, for 1 m2 plots one measurement is sufficient. Record the ambient

temperature and RH at the start of each plot measurement.

2. Advises:

- Take measurements of the part of the plot most exposed to the Sun;

- Avoid the shadow of the operator;

- The thermometer distance and angle should be constant;

- If readings of the same plot differ > 1 °C, repeat measurements.

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a) Trial Measurements

3. Angle and position of the thermometer determines the Spot.

Pask A, Pietragalla J, Mullan D, Reynolds M (2012) Physiological breeding II: A field guide to wheat phenotyping. CIMMYT, Mexico

Problem Solution

Initial canopy temperature values higher/ lower than on the rest of the trial.

IRT did not sufficient equilibrate with ambient temperature. Let IRT to equilibrate for at least 10 min with the ambient temperature.

Readings in the same plot differ by > 1 °C.

Check that IRT is being held correctly and consistently throughout measurements. Avoid borders, damaged/ senesced leaves, soil, etc..

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1. Methods/ Equipment

2. Calculations

Visual Senescence Scoring

Methods/ Equipment:

To be performed on flag-leaves and

repeated weekly or 3 to 4 days from

anthesis to physiological maturity.

1. Make a general observation by

standing at 45° angle to plot.

2. Randomly select and mark 5 (or

more) shoots and attribute scores to

each individual flag-leaf.

Visual Senescence Scoring Stay-green

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http://cran.r-project.org/ http://www.graphpad.com/

score = p0 + p1 x (1 – exp(( -p2 x STA/ p1)) + (10 – p1 – p0/ (1 + exp(-4 x p3 (STA – p4)/ (10 – p1 – p0)))

Fitting the senescence data

Score: visual senescence score

STA: thermal time after anthesis (°C days)

p0: score at anthesis

p1: score at the end of the slow phase

p2: maximum rate of the slow phase

p3: maximum rate at rapid phase (SenRate)

p4: date at which p3 is reached

SenOnset: onset of senescing phase date.

Stay-green associated with SenOnset and SenRate.