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

www.qubitphenomics.com

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

www.qubitphenomics.com

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

www.qubitphenomics.com

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

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RGB Image Processing

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

A. B.

C. D.

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RGB Structural Imaging

Assesed set of morphogenic parametres

• Area

• Perimeter

• Roundness

• Compactness

• Eccentricity

• MLWI

• Green Colour Segmentation

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Morphogenic analysis

• Plant genotype pattern • Time development pattern

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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

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

www.qubitphenomics.com

• 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)

www.qubitphenomics.com

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

www.qubitphenomics.com

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Reflectance / Water Content Distribution

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RFID Reader, BAR codes – 2D,3D

• Identification and tracking of the samples

www.qubitphenomics.com

• 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

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PlantScreen Data Analysis Software www.qubitphenomics.com

Automated morphological analysiswww.qubitphenomics.com

Automated analysis of chlorophyll fluorescence parametres

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FluorPenwww.qubitphenomics.com

FluorPen Datawww.qubitphenomics.com

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

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leaf : 3

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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.

www.qubitphenomics.com

Thank you for your attention

http://qubitphenomics.com/