Qubit Systems Inc. & Photon Systems Inc.
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Transcript of Qubit Systems Inc. & Photon Systems Inc.
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
www.qubitphenomics.com
RGB Image Processing
A: Barrel distortion correction B: Tray detection and croppingC: Background subtraction D: Binary and RGB Images
A. B.
C. D.
www.qubitphenomics.com
RGB Structural Imaging
Assesed set of morphogenic parametres
• Area
• Perimeter
• Roundness
• Compactness
• Eccentricity
• MLWI
• Green Colour Segmentation
www.qubitphenomics.com
Morphogenic analysis
• Plant genotype pattern • Time development pattern
www.qubitphenomics.com
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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www.qubitphenomics.com
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
www.qubitphenomics.com
PlantScreen Data Analysis Software www.qubitphenomics.com
Automated morphological analysiswww.qubitphenomics.com
Automated analysis of chlorophyll fluorescence parametres
www.qubitphenomics.com
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
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
2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,0
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/