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Qubit Systems Inc. & Photon Systems Inc.
 

Qubit Systems Inc. & Photon Systems Inc.

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Remote sensing –Beyond images ...

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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  • Conveyor system in operation at the University of Olomouc. External conveyor is in controlled environment Fytsocope room with LED lighting , temperature and RH control, also provided by Qubit Systems.
  • The GUI for environmental control is easy to operate and read.
  • XYZ imaging system in operation at the University of Olomouc.
  • Concept for screening rice in flooded experimental ponds in Thailand. XYZ system is carried on gantry. All imaging systems are submersible.
  • Features of PlantScreen systems.
  • Sequence of events. Load conveyor. Inform software of chosen protocols. Automated imaging in cabinet automated plant identification. Data collected to data base. Data base accessed to retrieve data displayed in automated graphs.
  • 10 mPixel option also available.
  • RGB image processing to remove objective distortion effects and to detect plants. Binary images can be used as a mask for background exclusion during other image processing.
  • “Spidergrams” allow for easy direct comparison within individual plants and between treatments
  • Monitors chlorophyll fluorescence kinetics, which provide a wealth of information about a plant’s photosynthetic capacity, physiological and metabolic condition, as well as its susceptibility to various stress conditions. 
  • Proof of concept experiments for TAMU conducted with the Qubit PlantScreen
  • Short term differences in chlorophyll fluorescence kinetics between control and droughted plants are most obvious during the fluorescence decline after imposition of actinic irradiance. Other systems (e.g. Lemnatec) have no ability to measure these kinetics.
  • Shows clearly thatdarladapated quantum yield (Fv/Fm) does not distinguish differences between control and droughted plants at early stages of stress whereas NPQ and Rfd show distinct differences. Qubit is the only company that offers measurements of these kinetics in a phenotyping platform.
  • SeparateVNIR (390 – 1000 nm) and SWIR (1000 – 2500 nm) cameras are used to monitor the target range of reflectance values.
  • 3D representation showing reflectance spectrum at each pixel location.
  • Any and all indices may be calculated and visualised as images automatically in software.
  • Its is critical to measure reflectance at water absorption bands in relation to a reference wavelength at which water does not absorb the light. Two absorption bands are shown in the graph.
  • Plants subjected to a protocol that results in rapid water loss.
  • Even after 30 minutes the change in the reflectance at the absorption bands is very obvious and the false colour image showing water as blue, indicates the greatest loss from specific regions. The Lemnatec system does not come even close to this time and spatial resolution.
  • False color images show water loss as reflectance at the absorption bands increases. The system can discriminate water loss of less than 1% of initial plant mass.
  • RFID and bar codes track plants and trays
  • Allows for the imposition of specific drought treatments, or to maintain an accurate watering routine. Nutrient delivery and nutrient analysis is also available.
  • The PlantScreen can be used to cultivate plants within the cabinet, if required. Light levels can be varied between 0 and 100% of maximum in 1% increments. Changes are instantaneous. Spectrum can be varies as required. Very significant advantages compared to HPS lights etc.
  • LEDs available in a wide range to mimic the solar spectrum. Extremely low heat output allows high light cultivation without massive energy expenditure for temperature and RH control. Also minimises heat and RH gradients.
  • The graphical user interface is intuitive. Easy control of lighting and the development of measurement protocols.
  • Internal cameras allow the user to monitor operation remotely.
  • The user may choose to analyse specific trays, groups of trays, specific plants or groups of plants and to collate the data accordingly.
  • Data are processed automatically and presented graphically as one of the options.
  • The user may choose which data to display on the screen out of all the options listed.
  • Over 80 employees including severalPhD level plant scientists.

Qubit Systems Inc. & Photon Systems Inc. Qubit Systems Inc. & Photon Systems Inc. Presentation Transcript

  • 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
  • www.qubitphenomics.com Initial Plans
  • www.qubitphenomics.com Installation and Training
  • www.qubitphenomics.com Final Product
  • 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
  • www.qubitphenomics.com PlantScreen™ Conveyor Systems
  • www.qubitphenomics.com Software WEB interface • • • • • • Remote programming Monitoring Controlling Data storage Online Analyses Unified software
  • www.qubitphenomics.com XYZ Screening • RGB Imaging • Chlorophyll fluorescence Imaging • Hyperspectral Imaging
  • www.qubitphenomics.com PlantScreen™ Field Systems Submersible System for Flooded Crops (e.g. Rice)
  • www.qubitphenomics.com Field Phenotyping
  • www.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
  • PlantScreen™ Phenotyping Platform RGB and Morphometric Imaging Chlorophyll fluorescence Kinetic Imaging Thermal Imaging Automated Weighing / Watering ......
  • 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
  • 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.
  • 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 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
  • www.qubitphenomics.com Chlorophyll Fluorescence Kinetics Imaging Fv/Fm= Fm-Fo/Fm = Quantum Yield in the dark-adapted state
  • 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
  • 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)
  • 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
  • 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.
  • 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
  • www.qubitphenomics.com Hyperspectral Analysis • Range 390nm – 2500nm and with 2nm half width • Resolution 1392 x 870 pixels • AD conversion 12bits
  • www.qubitphenomics.com Hyperspectral Analysis
  • 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)
  • 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
  • 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
  • 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
  • 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
  • www.qubitphenomics.com RFID Reader, BAR codes – 2D,3D • Identification and tracking of the samples
  • www.qubitphenomics.com Automated Watering and Weighing • Nutrient mixing system. • Very high accuracy • Watering with full accuracy
  • www.psi.cz Lighting + Cultivation • Homogeneous light source • Light intensity up to 2000uE • Dark adaptation chamber • Light adaptation of individual samples
  • www.psi.cz Lighting - Cultivation • Homogeneous light source • Light intensity up to 2000uE • Dark adaptation chamber • Light adaptation of individual samples
  • www.qubitphenomics.com Graphical Control Software
  • www.qubitphenomics.com Online Operation of the PlantScreen using IP Cameras
  • www.qubitphenomics.com PlantScreen Data Analysis Software
  • www.qubitphenomics.com Automated morphological analysis
  • www.qubitphenomics.com Automated analysis of chlorophyll fluorescence parametres
  • www.qubitphenomics.com FluorPen
  • www.qubitphenomics.com FluorPen Data
  • www.qubitphenomics.com FluorPen Data
  • 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
  • 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
  • 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.
  • www.qubitphenomics.com Photon Systems and Qubit Systems Inc.
  • Thank you for your attention http://qubitphenomics.com/