Photon Systems Instruments PlantPen PRI Series Guide

PlantPen
NDVI & PRI
Manual and User Guide
Please read this manual before operating this product
PSI, spol. s r. o., Drásov 470, 664 24 Drásov, Czech Republic
FAX: [phone], TEL: [phone], www.psi.cz

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© PSI (Photon Systems Instruments), spol. s r. o. (hereinafter PSI), 2018
This document and its parts can be copied or provided to a third party only with the express permission of PSI.
The contents of this manual have been verified to correspond to the specifications of the device. However, deviations cannot
be ruled out. Therefore, a complete correspondence between the manual and the real device cannot be guaranteed. The
information in this manual is regularly checked, and corrections may be made in subsequent versions.
The visualizations shown in this manual are only illustrative.
This manual is an integral part of the purchase and delivery of equipment and its accessories and both Parties must abide
by it.

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TABLE OF CONTENTS
1Information Before Using PlantPen Device..................................................................................................................... 6
2Technical Specification.................................................................................................................................................... 7
3General Information ....................................................................................................................................................... 8
3.1 Device Description................................................................................................................................................. 9
4List of Equipment and Customer Information .............................................................................................................. 10
5Care and Maintenance.................................................................................................................................................. 11
6Principle of Measurement ............................................................................................................................................ 12
7How to Get Started ....................................................................................................................................................... 13
7.1 PRI Measurement................................................................................................................................................ 13
7.1.1 Calibration....................................................................................................................................................... 13
7.1.2 Measurement.................................................................................................................................................. 13
7.2 NDVI Measurement............................................................................................................................................. 14
7.2.1 Calibration....................................................................................................................................................... 14
7.2.2 Measurement.................................................................................................................................................. 14
8Control Menu Tree........................................................................................................................................................ 15
9USB Connection ............................................................................................................................................................ 20
10 Bluetooth Connection.............................................................................................................................................. 21
10.1 Bluetooth Pairing................................................................................................................................................. 21
11 FluorPen Software ................................................................................................................................................... 25
11.1 Software Installation ........................................................................................................................................... 25
11.2 Menu and Icon Explanation................................................................................................................................. 26
11.2.1 Main Menu ................................................................................................................................................. 26
11.2.2 Menu Settings............................................................................................................................................. 27
11.2.3 Menu Online Control .................................................................................................................................. 28
11.3 Data Transfer and Visualization........................................................................................................................... 29
11.4 Firmware Update................................................................................................................................................. 31
12 GPS Module ............................................................................................................................................................. 33
12.1 GPS / PlantPen Operation ................................................................................................................................... 33
12.2 Data Download.................................................................................................................................................... 34

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13 Warranty Terms and Conditions.............................................................................................................................. 35
14 Troubleshooting and Customer Support ................................................................................................................. 36

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1INFORMATION BEFORE USING PLANTPEN DEVICE
Read this manual carefully before operating the device. If you are not sure about anything in the manual, contact the
manufacturer for clarification.
By accepting the device, the customer agrees to follow the instructions in this guide.
Always follow corresponding manuals while working with the PlantPen device or doing the maintenance.
It is forbidden to interfere with the hardware or software of the PlantPen device in any way without previous agreement
with the manufacturer.
The following table presents basic highlight symbols used in this manual:
Symbol
Description
Important information, read carefully.
Complementary and additional information.
Tab. 1 Used symbols.

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2TECHNICAL SPECIFICATION
Measured Parameters:
PRI (Photochemical Reflectance Index) = (R531 –R570) / (R531 + R570) Reference: Sellers et al. (1985)
NDVI (Normalized Difference Vegetative Index) = (R740 –R660) / (R740 + R660) Reference: Rouse et al. (1974)
Measuring Light:
Internal dual wavelength light source R531 = 531 nm, R570 = 570 nm for PRI 210
Internal dual wavelength light source VIS = 635nm, NIR = 760nm for NDVI 310
Detector Wavelength Range:
PIN photodiode with 500 to 600 nm bandpass filters for PRI 210
PIN photodiode with 620 to 750 nm bandpass filters for NDVI 310
PC Communication modules:
Bluetooth and USB
FluorPen Software:
Windows 7 or higher compatible*
Memory Capacity:
Up to 16 Mb
Internal Data Logging:
Up to 100,000 data points
Display:
Graphical display
Keypad:
Sealed, 2-key tactile response
Keypad Escape Time:
Turns off after 5 minutes of no use
Power Supply:
Li-Ion rechargeable battery
Battery Capacity:
2000 mAh
Max. Charging Current:
0.5 A
Charging via USB port:
PC, power bank, USB charger, etc.
Battery Life:
48 hours typical with full operation
Low Battery Detection:
Low battery indication displayed
Size:
135 mm x 65 mm x 33 mm
Weight:
188 g
Sample Holder:
Mechanical leaf clip
Operating Conditions:
Temperature: 0 to +55 ºC, 32 to 130 ºF; Relative humidity: 0 to 95 % (non-condensing)
Storage Conditions:
Temperature: -10 to +60 ºC, 14 to 140 ºF; Relative humidity: 0 to 95 % (non-condensing)
Warranty:
1 year parts and labor (see the last page of this Operation Manual for precise warranty conditions)
* Windows is a registered trademark of Microsoft Corporation.

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3GENERAL INFORMATION
The PlantPen model PRI 210 measures Photochemical Reflectance Index (PRI) in two narrow wavelength bands centered
close to 531 nm and 570 nm. The photochemical reflectance index (PRI = (R531–R570)/(R531+R570)) correlates with the
epoxidation state of xanthophyll cycle pigments and photosystem efficiency in many studies under diverse conditions, such
as different 1. PRI is sensitive to changes in carotenoid pigments that are indicative of photosynthetic light use efficiency,
the rate of carbon dioxide uptake, or as a reliable water-stress index. As such, it is used in studies of vegetation productivity
and stress.
The PlantPen model NDVI 310 measures Normalized Difference Vegetation Index, which is an important indicator of
chlorophyll content in plants. The pigment in plant leaves, chlorophyll, strongly absorbs visible light (from 0.4 to 0.7 µm)
for use in photosynthesis. The cell structure of the leaves, on the other hand, strongly reflects near-infrared light (from 0.7
to 1.1 µm). The differences in plant reflectance in the visible and near-infrared wavelengths is used to calculate NDVI index
as follows: NDVI=((NIR-VIS)/((NIR+VIS)), where VIS and NIR stand for the spectral reflectance measurements acquired in
the visible (red) and near-infrared regions, respectively. NDVI is directly related to the photosynthetic capacity and hence
energy absorption of plant canopies 2. The NDVI 310 device compares reflected light at two distinct wavelengths, 635 and
760 nm.
PlantPen can be operated as a stand-alone instrument and thus is ideal for field studies. Measured data are sequentially
stored in the internal PlantPen memory. Data transfer is via USB or Bluetooth communication. Comprehensive FluorPen
1.1 software provides data transfer routines and many additional features for data presentation in tables and graphs.
1John Gamon, Josep Penuelas, and Christopher Field (1992). A narrow-waveband spectral index that tracks diurnal changes in
photosynthetic efficiency. Remote Sensing of environment, 41, 35-44.
2Sellers, P. J. (1985) 'Canopy reflectance, photosynthesis, and transpiration', International Journal of Remote Sensing, 6, 1335-1372.

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3.1 DEVICE DESCRIPTION
Fig. 1 Device description.

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4LIST OF EQUIPMENT AND CUSTOMER INFORMATION
Standard version of the PlantPen device package consists:
•PlantPen PRI 210 or PlantPen NDVI 310
•Carrying Case
•FluorPen software and driver (on a USB flash disc)
•Operation Manual (PDF on a USB flash disc)
•USB Cable
•Self-Adhesive Rubber Pads for Optics Protection
•Other Accessories or Optional Features (according to your specific order)
For USB connection you need to have the USB driver installed in your PC. You find the driver on the
installation disk (USB driver folder). For more information go to
If any item is missing, please, contact the manufacturer. Also check the carton for any visible external
damage. If you find any damage, notify the carrier and the manufacturer immediately. The carton and
all packing materials should be retained for inspection by the carrier or insurer.
For customer support, please write to: [e-mail]

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5CARE AND MAINTENANCE
•Never submerge the device in water!
•The device should not come in contact with any organic solvents, strong acids or bases.
•Keep the optical part clean and dry. If cleaning is needed, use soft, non-abrasive tissue.
•Battery life is approximately 48 hours when the FluorPen is operated continuously.

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6PRINCIPLE OF MEASUREMENT
PlantPen is a reflectance-based device that provides a convenient method of measuring the relative chlorophyll content
of a leaf sample.
The PlantPen model PRI 210 (Fig. 2)measures Photochemical Reflectance Index (PRI) by comparing leaf reflectance in two
narrow wavelength bands centered close to 531 nm and 570 nm. PRI is sensitive to changes in carotenoid pigments that
are indicative of changes in photosynthetic light use efficiency, the rate of CO2uptake and as a reliable water-stress index.
As such, it is used in studies of vegetation productivity and stress.
Fig. 2 PlantPen PRI 210.
The PlantPen model NDVI 310 (Fig. 3) measures Normalized Difference Vegetation Index (NDVI), which is an important
indicator of chlorophyll content in plants. The pigment in plant leaves, chlorophyll, strongly absorbs visible light (from 0.4
to 0.7 µm) for use in photosynthesis. The cell structure of the leaves, on the other hand, strongly reflects near-infrared
light (from 0.7 to 1.1 µm). The differences in plant reflectance in the visible and near-infrared wavelengths are used to
calculate NDVI index. NDVI is directly related to the photosynthetic capacity and hence energy absorption of plant
canopies.
Fig. 3 PlantPen NDVI 310.

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7HOW TO GET STARTED
For more detailed information on particular steps of PlantPen operation please refer to chapter 8.
The device works on Li-Ion battery or is charged via USB cable from PC or grid.
The PlantPen is controlled using two buttons:
•Use the MENU key to scroll through sequential menu options on the digital display.
•Use the SET key to select a menu option based on cursor (>) position.
7.1 PRI MEASUREMENT
7.1.1 CALIBRATION
Calibration assures you that your measurements are accurate within the specification limits that led you to select the
instrument in the first place. It is better to calibrate your device before every set of samples. For Calibration of PlantPen
use white reflectance standard. The calibration of the white reflectance standard is an indispensable part of a correct
calculation of PRI.
Prior PRI measurement perform the calibration as follows:
•For calibration use white reflectance standard (It is part of leaf clip)
•Turn ON device –hold SET button for 1 sec.
•Close the leaf clip (white standard is on bottom part of the leaf clip)
•Go to Calibration (“Insert white sample”appears on display)
•Press SET button to confirm the calibration and wait until the calibration step is completed.
•Calibration is automatically stored into the device memory.
•The device is now ready to measure other samples.
7.1.2 MEASUREMENT
The PlantPen model PRI 210measures The PlantPen model PRI 210 measures Photochemical Reflectance Index (PRI) in
two narrow wavelength bands centred close to 531 nm and 570 nm. The photochemical reflectance index (PRI = (R531–
R570)/(R531+R570)) correlates with the epoxidation state of xanthophyll cycle pigments and photosystem efficiency in
many studies under diverse conditions, such as different. PRI is sensitive to changes in carotenoid pigments that are
indicative of photosynthetic light use efficiency, the rate of carbon dioxide uptake, or as a reliable water-stress index. As
such, it is used in studies of vegetation productivity and stress.
Please follow these instructions to perform a measurement:
•Insert a leaf sample into the leaf clip. The leaf clip is important for the sample stabilization.
•Go to Measurement
It is necessary to calibrate PlantPen after every switch ON.

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•Press SET to confirm.
•PlantPen measure PRI
•Value of PRI appears on display after measuring.
•During the measurement all data are stored into the device memory.
7.2 NDVI MEASUREMENT
7.2.1 CALIBRATION
Calibration assures you that your measurements are accurate within the specification limits that led you to select the
instrument in the first place. It is better to calibrate your device before every set of samples. For Calibration of PlantPen
use white reflectance standard. The calibration of the white reflectance standard is an indispensable part of a correct
calculation of NDVI.
Prior NDVI measurement perform the calibration as follows:
•For calibration use white reflectance standard (It is part of leaf clip)
•Turn ON device –hold SET button for 1 sec.
•Close the leaf clip (white standard is on bottom part of the leaf clip)
•Go to Calibration (“Insert white sample”appears on display)
•Press SET button to confirm the calibration and wait until the calibration step is completed.
•Calibration is automatically stored into the device memory.
•The device is now ready to measure other samples.
7.2.2 MEASUREMENT
The PlantPen model NDVI 310 measures Normalized Difference Vegetation Index, which is an important indicator of
chlorophyll content in plants. The pigment in plant leaves, chlorophyll, strongly absorbs visible light (from 0.4 to 0.7 µm)
for use in photosynthesis. The cell structure of the leaves, on the other hand, strongly reflects near-infrared light (from 0.7
to 1.1 µm). The NDVI 310 device compares reflected light at two distinct wavelengths, 635 and 760 nm.
Please follow these instructions to perform a measurement:
•Insert a leaf sample into the leaf clip. The leaf clip is important for the sample stabilization.
•Go to Measurement
•Press SET to confirm.
•PlantPen measure NDVI
•Value of NDVI appears on display after measuring.
•During the measurement all data are stored into the device memory.
It is necessary to calibrate PlantPen after every switch ON.

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8CONTROL MENU TREE
The next pages show the structure of the operation scheme, which includes the Main Menu, first-level Sub-Menus and
second-level Sub-Menus.
•The blue color represents the Main Menu and its Options.
•The yellow color represents the first-level Sub-Menus and their Options.
•The green color represents the second-level Sub-Menus and their Options.
•Full-line arrows are used for the SET key.
•Dashed-line arrows are used for the MENU key.

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9USB CONNECTION
Connect the USB cable with the PlantPen device. Please note that lock in system is used.
Pay attention when connecting the USB cable not to damage the outlet connector on the Pen
device. Make sure that you orient the cable correctly prior connecting the inlet with the outlet and
the cable is upright towards the device.
To connect PlantPen with your computer please follow steps below in Fig. 4:
Fig. 4 How to connect PlantPen with PC.
A) Outlet connector on PlantPen device. B) Inlet part on the USB cable. C –E) Position the cable horizontally, plug in the
inlet and screw the securing screw. F) Correct connection of the USB cable and Pen device.
Connect the USB cable to a computer. The PlantPen switches ON automatically after connecting the cable to the PC. For
USB connection you need to have the USB driver installed in your PC. You find the driver on the installation disk (USB driver
folder). If you check the Device Manager in Windows you should see the USB serial port in the device tree. In case of
missing driver, you may download it from PSI websites. When the driver is installed correctly you should be able to connect
to the device in the FluorPen software menu Setup > Device ID.
For more information about FluorPen software see chapter 11.