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Qubit Systems Inc. & Photon Systems Inc.

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Remote sensing –Beyond images
Mexico 14-15 December 2013

The workshop was organized by CIMMYT Global Conservation Agriculture Program (GCAP) and funded by the Bill & Melinda Gates Foundation (BMGF), the Mexican Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), the International Maize and Wheat Improvement Center (CIMMYT), CGIAR Research Program on Maize, the Cereal System Initiative for South Asia (CSISA) and the Sustainable Modernization of the Traditional Agriculture (MasAgro)

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Qubit Systems Inc. & Photon Systems Inc.

  1. 1. Qubit Systems Inc. & Photon Systems Inc. Stephen Hunt (Qubit) Martin Trtilek (PSI) Qubit Systems Inc. Kingston, Ontario, Cana da Photon Systems Inc. Drasov, Czech Republic PLANT PHENOTYPING PLANT PHENOTYPING
  2. 2. www.qubitphenomics.com Initial Plans
  3. 3. www.qubitphenomics.com Installation and Training
  4. 4. www.qubitphenomics.com Final Product
  5. 5. www.qubitphenomics.com PlantScreen™ Conveyor Systems Acclimation chamber/ weighing-watering station IR imaging station/ Hyperspectral imaging station Controlled cultivation environment RGB imaging/Chlorophyll fluorescence imaging station Operation software/PlantScreen database
  6. 6. www.qubitphenomics.com PlantScreen™ Conveyor Systems
  7. 7. www.qubitphenomics.com Software WEB interface • • • • • • Remote programming Monitoring Controlling Data storage Online Analyses Unified software
  8. 8. www.qubitphenomics.com XYZ Screening • RGB Imaging • Chlorophyll fluorescence Imaging • Hyperspectral Imaging
  9. 9. www.qubitphenomics.com PlantScreen™ Field Systems Submersible System for Flooded Crops (e.g. Rice)
  10. 10. www.qubitphenomics.com Field Phenotyping
  11. 11. www.qubitphenomics.com Applications •Abiotic Stresses •Biotic Stresses •Plant Growth Analysis •Trait Discovery •Nutrient Stress and Ecotoxicology •Crop and Field Studies
  12. 12. 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
  13. 13. PlantScreen™ Phenotyping Platform RGB and Morphometric Imaging Chlorophyll fluorescence Kinetic Imaging Thermal Imaging Automated Weighing / Watering ......
  14. 14. www.qubitphenomics.com 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
  15. 15. www.qubitphenomics.com RGB Image Processing A: Barrel distortion correction C: Background subtraction B: Tray detection and cropping D: Binary and RGB Images A. B. C. D.
  16. 16. www.qubitphenomics.com RGB Structural Imaging Assesed set of morphogenic parametres • Area • Perimeter • Roundness • Compactness • Eccentricity • MLWI • Green Colour Segmentation
  17. 17. www.qubitphenomics.com Morphogenic analysis • Plant genotype pattern • Time development pattern
  18. 18. www.qubitphenomics.com Chlorophyll Fluorescence Kinetics Imaging Fluorescence parameters: • Measured parameters : FO, FM, FV, FO', FM', FV', FT • Calculated parameters: FV/FM, FV'/FM', PhiPSII , NPQ, qN, qP, Rfd
  19. 19. www.qubitphenomics.com Chlorophyll Fluorescence Kinetics Imaging Fv/Fm= Fm-Fo/Fm = Quantum Yield in the dark-adapted state
  20. 20. FLUORESCENCE, r.u. Pixel-to-Pixel Arithmetic Image Operations 250 FM 200 150 100 FM’ FV FS 50 0 F0 -10 0 10 20 30 40 50 60 70 80 TIME, seconds
  21. 21. Growth Conditions Drought Stress: Turfgrass Light regime: 12h-12h Light intensity: 150 µE white-LED with addition of infra light Growth conditions: 45% humidity, 22°C 20d old plants  Control plants (normal watering every 3rd day) vs stressed plants (5d without water)
  22. 22. www.qubitphenomics.com Drought Stress: Turfgrass Growth Conditions Light regime: 12h-12h Light intensity: 150 µE white-LED with addition of infra light Growth conditions: 45% humidity, 22°C 20d old plants  Control plants (normal watering every 3rd day) vs stressed plants (5d without water) 6 5 4 3 Control drought 2 1 0 0 50000000 10000000 15000000 20000000
  23. 23. www.qubitphenomics.com Drought Stress: Turfgrass 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.
  24. 24. www.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
  25. 25. www.qubitphenomics.com Hyperspectral Analysis • Range 390nm – 2500nm and with 2nm half width • Resolution 1392 x 870 pixels • AD conversion 12bits
  26. 26. www.qubitphenomics.com Hyperspectral Analysis
  27. 27. www.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)
  28. 28. www.qubitphenomics.com Water Content Estimation via SWIR Hyperspectral Imaging 1 0.9 0.8 reflectance 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 800 1000 1200 1400 1600 1800 2000 wavelength [nm] 2200 2400 2600
  29. 29. 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
  30. 30. Reflectance / Water Content Distribution 0.8 0.8 0.7 0.7 0.7 0.6 0.6 0.6 0.5 0.4 reflectance 1 0.9 reflectance 1 0.9 0.8 reflectance 1 0.9 0.5 0.4 0.5 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.1 0.1 0.1 0 800 1000 1200 1400 1600 1800 2000 wavelength [nm] t = 0.0h 2200 2400 2600 0 800 1000 1200 1400 t = 0.5h 1600 1800 2000 wavelength [nm] 2200 2400 2600 0 800 1000 t = 1.0h 1200 1400 1600 1800 2000 wavelength [nm] 2200 2400 2600
  31. 31. 0.8 0.8 0.7 0.7 0.7 0.6 0.6 0.6 0.5 0.4 reflectance 1 0.9 reflectance 1 0.9 0.8 reflectance 1 0.9 0.5 0.4 0.5 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.1 0.1 0.1 0 800 1000 1200 1400 1600 1800 2000 wavelength [nm] t = 2.0h 2200 2400 2600 0 800 1000 1200 1400 t = 4.0h 1600 1800 2000 wavelength [nm] 2200 2400 2600 0 800 1000 t = 5.0h 1200 1400 1600 1800 2000 wavelength [nm] 2200 2400 2600
  32. 32. www.qubitphenomics.com RFID Reader, BAR codes – 2D,3D • Identification and tracking of the samples
  33. 33. www.qubitphenomics.com Automated Watering and Weighing • Nutrient mixing system. • Very high accuracy • Watering with full accuracy
  34. 34. www.psi.cz Lighting + Cultivation • Homogeneous light source • Light intensity up to 2000uE • Dark adaptation chamber • Light adaptation of individual samples
  35. 35. www.psi.cz Lighting - Cultivation • Homogeneous light source • Light intensity up to 2000uE • Dark adaptation chamber • Light adaptation of individual samples
  36. 36. www.qubitphenomics.com Graphical Control Software
  37. 37. www.qubitphenomics.com Online Operation of the PlantScreen using IP Cameras
  38. 38. www.qubitphenomics.com PlantScreen Data Analysis Software
  39. 39. www.qubitphenomics.com Automated morphological analysis
  40. 40. www.qubitphenomics.com Automated analysis of chlorophyll fluorescence parametres
  41. 41. www.qubitphenomics.com FluorPen
  42. 42. www.qubitphenomics.com FluorPen Data
  43. 43. www.qubitphenomics.com FluorPen Data
  44. 44. www.qubitphenomics.com Hand-Held Screening Devices Normalized Difference Vegetation Index Photochemical Reflectance Index NDVI = (NIR – Red)/(NIR + Red) PRI = (R531 - R570)/(R531 + R570) -indicator of chlorophyll content - Wavelengths: 660 nm, 740 nm -sensitive to changes in carotenoids content as response to light stress -Wavelengths: 531 nm, 570 nm PlantPen PRI 200 & NDVI 300
  45. 45. www.qubitphenomics.com Nitrogen Pen Normalized Difference Greeness Index (NDGI) NDGI=(R740-R550)/(R740+R550) 95% confidence intervals 0,50 Leaf 1 0,48 0,46 0,44 Leaf 2 0,42 0,40 0,38 0,36 2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,0 2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,0 leaf : 1 leaf : 2 0,50 NDGI 0,48 Leaf 3 0,46 0,44 0,42 0,40 0,38 0,36 2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,0 2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,0 leaf : 3 leaf : 4 nitrogen content (%) Leaf 4
  46. 46. www.qubitphenomics.com PolyPen for Hyperspectral Analysis PolyPen RP 400 UVIS Spectral response range: 380 to 780 nm. PolyPen RP 400 NIR Spectral response range: 640 to 1050 nm.
  47. 47. www.qubitphenomics.com Photon Systems and Qubit Systems Inc.
  48. 48. Thank you for your attention http://qubitphenomics.com/

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