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PLANT PHENOTYPING

Qubit Systems Inc. & Photon Systems Inc.

PLANT PHENOTYPING

Stephen Hunt (Qubit)Martin Trtilek (PSI)

Qubit Systems Inc.Kingston, Ontario, Canada

Photon Systems Inc.Drasov, Czech Republic

Initial Planswww.qubitphenomics.com

Installation and Trainingwww.qubitphenomics.com

Final Productwww.qubitphenomics.com

PlantScreen™ Conveyor Systems

Controlled cultivation environment

Acclimation chamber/ weighing-watering

stationIR imaging station/

Hyperspectral imaging station

RGB imaging/Chlorophyll fluorescence imaging

station

Operation software/PlantScreen

database

www.qubitphenomics.com

PlantScreen™ Conveyor Systemswww.qubitphenomics.com

• Remote programming • Monitoring• Controlling• Data storage• Online Analyses• Unified software

Software WEB interfacewww.qubitphenomics.com

XYZ Screening

• RGB Imaging

• Chlorophyll fluorescence Imaging

• Hyperspectral Imaging


PlantScreen™ Field Systemswww.qubitphenomics.com

Submersible System for Flooded Crops (e.g. Rice)

Field Phenotypingwww.qubitphenomics.com

Applications

• Abiotic Stresses

• Biotic Stresses

• Plant Growth Analysis

• Trait Discovery

• Nutrient Stress and Ecotoxicology

• Crop and Field Studies


PlantScreen™ Conveyor Systems

• RGB and Morphometric Imaging

• Chlorophyll fluorescence Kinetic Imaging

• Near InfraRed (NIR) Imaging

• Hypespectral Imaging

• Thermal Imaging

• Automated Watering and Weighing

• Automated Nutrient Delivery and Analysis

• Automated Light Acclimation of Plants

• Controlled environments for cultivation


PlantScreen™ Phenotyping Platform

RGB and Morphometric Imaging

Chlorophyll fluorescence Kinetic Imaging

Thermal Imaging

Automated Weighing / Watering

......

RGB and structural Imaging

Tracking of growth patterns of plants as they progress through developmental stages and/or through the imposition, onset and recovery from stresses.

RGB structural imaging:

• Minimal resolution 5Mpixels

• Capturing (top and side view)

• Morphological Parameters


RGB Image Processing

A: Barrel distortion correction B: Tray detection and croppingC: Background subtraction D: Binary and RGB Images

A. B.

C. D.


RGB Structural Imaging

Assesed set of morphogenic parametres

• Area

• Perimeter

• Roundness

• Compactness

• Eccentricity

• MLWI

• Green Colour Segmentation


Morphogenic analysis

• Plant genotype pattern • Time development pattern


Fluorescence parameters:

• Measured parameters : FO, FM, FV, FO', FM', FV', FT

• Calculated parameters: FV/FM, FV'/FM', PhiPSII , NPQ, qN, qP, Rfd

Chlorophyll Fluorescence Kinetics Imagingwww.qubitphenomics.com

http://qubitsystems.com/wp-content/uploads/2011/04/imaging-station.jpg

Chlorophyll Fluorescence Kinetics Imagingwww.qubitphenomics.com

Fv/Fm= Fm-Fo/Fm =Quantum Yield in the dark-adapted state

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Pixel-to-Pixel Arithmetic Image Operations

Growth Conditions

Light regime: 12h-12h Light intensity: 150 µE white-LED with addition of infra lightGrowth conditions: 45% humidity, 22°C20d old plants

Control plants (normal watering every 3rd day) vs stressed plants (5d without water)

Drought Stress: Turfgrass

Growth Conditions

Light regime: 12h-12h Light intensity: 150 µE white-LED with addition of infra lightGrowth conditions: 45% humidity, 22°C20d old plants

Control plants (normal watering every 3rd day) vs stressed plants (5d without water)

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Controldrought

Drought Stress: Turfgrasswww.qubitphenomics.com

Control 4D WW 7D WW

FvFm 0.81 0.81 0.74

Rfd_Lss 0.64 0.78 0.9

QY_Lss 0.51 0.43 0.3

NPQ_Lss 0.6 0.89 0.79

NPQ_D1 0.29 0.37 0.58

NPQ_D2 0.2 0.21 0.36

NPQ_D3 0.16 0.16 0.25

Maximum quantum efficiency Fv/Fm does not differ between the variants 4 days after watering.

Parameters such as non-photochemical quenching (NPQ) and Fluorescence Decline Ratio (Rfd_Lss) clearly show differences between the variants during early drought stress.

Drought Stress: Turfgrasswww.qubitphenomics.com

Thermal Imaging

FLIR SC654 (640 x 480 pixels, 25 Hz)

• -20 °C to +650 °C (+2000 °C optionally)• 16 - bit 640 x 480 pixels at 25 Hz• control and image• TCP/IP socket-based FLIR proprietary and GenlCam


• Range 390nm – 2500nm and with 2nm half width

• Resolution 1392 x 870 pixels

• AD conversion 12bits

Hyperspectral Analysiswww.qubitphenomics.com

Hyperspectral Analysiswww.qubitphenomics.com

Plant Reflectance Indices

•Normalized Difference Vegetation Index NDVI = (RNIR - RRED ) / (RNIR + RRED )•Simple Ratio Index (SR) SR = RNIR / RRED•Modified Chlorophyll Absorption in Reflectance Index MCARI1 = 1.2 * [2.5 * (R790- R670) - 1.3 * (R790- R550)]•Optimized Soil-Adjusted Vegetation OSAVI = (1 + 0.16) * (R790- R670) / (R790- R670 + 0.16)•Greenness Index G = R554 / R677•Modified Chlorophyll Absorption in Reflectance MCARI = [(R700- R670) - 0.2 * (R700- R550)] * (R700/ R670)•Transformed CAR Index TCARI = 3 * [(R700- R670) - 0.2 * (R700- R550) * (R700/ R670)]•Triangular Vegetation Index TVI = 0.5 * [120 * (R750- R550) - 200 * (R670- R550)]•Zarco-Tejada & Miller Index ZMI = R750 / R710•Simple Ratio Pigment Index SRPI = R430 / R680•Normalized Phaeophytinization Index NPQI = (R415- R435) / (R415+ R435)•Photochemical Reflectance Index PRI= (R531- R570) / (R531+ R570)•Normalized Pigment Chlorophyll Index NPCI= (R680- R430) / (R680+ R430)


Water Content Estimation via SWIR Hyperspectral Imaging

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Experimental Setup

• 24 plants (A. thaliana)- 12 dried, 12 controls• Measurements:

– t = 0.0h, t = 0.5h (60°C), t = 1.0h (45°C), t = 2.0h (45°C), t = 4.0h (45°C), t = 5.0h (45°C), t = 6.0h (45°C)

• Acquisition parameters

– camera: Headwall SWIR 1000-2500nm, 63Hz, 6ms integration time

– lens: Navitar, 8mm focus– Reflectance correction – Spectralon 99%

reference target– illumination: Ardes infrared heater, 1200W


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Reflectance / Water Content Distribution

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RFID Reader, BAR codes – 2D,3D

• Identification and tracking of the samples


http://qubitsystems.com/wp-content/uploads/2011/04/imaging-station.jpg

• Nutrient mixing system.

• Very high accuracy

• Watering with full accuracy

Automated Watering and Weighingwww.qubitphenomics.com

• Homogeneous light source

• Light intensity up to 2000uE

• Dark adaptation chamber

• Light adaptation of individual samples

Lighting + Cultivation

www.psi.cz

• Homogeneous light source

• Light intensity up to 2000uE

• Dark adaptation chamber

• Light adaptation of individual samples

Lighting - Cultivation

www.psi.cz

Graphical Control Softwarewww.qubitphenomics.com

Online Operation of the PlantScreen using IP Cameras


PlantScreen Data Analysis Software www.qubitphenomics.com

Automated morphological analysiswww.qubitphenomics.com

Automated analysis of chlorophyll fluorescence parametres


FluorPenwww.qubitphenomics.com

FluorPen Datawww.qubitphenomics.com

http://www.qubitbiology.com/wp-content/uploads/2010/04/Z990-Data.jpg

FluorPen Datawww.qubitphenomics.com

Normalized Difference Vegetation Index

NDVI = (NIR – Red)/(NIR + Red)-indicator of chlorophyll content

- Wavelengths: 660 nm, 740 nm

Photochemical Reflectance Index

PRI = (R531 - R570)/(R531 + R570)

-sensitive to changes in carotenoids content as response to light stress-Wavelengths: 531 nm, 570 nm

PlantPen PRI 200 & NDVI 300

Hand-Held Screening Deviceswww.qubitphenomics.com

Normalized Difference Greeness Index (NDGI)

NDGI=(R740-R550)/(R740+R550)

95% c onf idenc e interv als

nitrogen c ontent (% )

ND

GI

leaf : 1

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leaf : 2

2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,0

leaf : 3

2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,00,36

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leaf : 4

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Leaf 1

Leaf 2

Leaf 3

Leaf 4

Nitrogen Penwww.qubitphenomics.com

PolyPen RP 400 UVIS Spectral response range: 380 to 780 nm.

PolyPen RP 400 NIRSpectral response range: 640 to 1050 nm.

PolyPen for Hyperspectral Analysiswww.qubitphenomics.com

Photon Systems and Qubit Systems Inc.


Thank you for your attention

http://qubitphenomics.com/

Download - Qubit Systems Inc. & Photon Systems Inc

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