qubit systems inc. & photon systems inc
DESCRIPTION
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)TRANSCRIPT
![Page 1: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/1.jpg)
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
![Page 2: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/2.jpg)
Initial Planswww.qubitphenomics.com
![Page 3: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/3.jpg)
Installation and Trainingwww.qubitphenomics.com
![Page 4: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/4.jpg)
Final Productwww.qubitphenomics.com
![Page 5: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/5.jpg)
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
![Page 6: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/6.jpg)
PlantScreen™ Conveyor Systemswww.qubitphenomics.com
![Page 7: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/7.jpg)
• Remote programming • Monitoring• Controlling• Data storage• Online Analyses• Unified software
Software WEB interfacewww.qubitphenomics.com
![Page 8: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/8.jpg)
XYZ Screening
• RGB Imaging
• Chlorophyll fluorescence Imaging
• Hyperspectral Imaging
www.qubitphenomics.com
![Page 9: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/9.jpg)
PlantScreen™ Field Systemswww.qubitphenomics.com
Submersible System for Flooded Crops (e.g. Rice)
![Page 10: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/10.jpg)
Field Phenotypingwww.qubitphenomics.com
![Page 11: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/11.jpg)
Applications
• Abiotic Stresses
• Biotic Stresses
• Plant Growth Analysis
• Trait Discovery
• Nutrient Stress and Ecotoxicology
• Crop and Field Studies
www.qubitphenomics.com
![Page 12: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/12.jpg)
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
![Page 13: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/13.jpg)
PlantScreen™ Phenotyping Platform
RGB and Morphometric Imaging
Chlorophyll fluorescence Kinetic Imaging
Thermal Imaging
Automated Weighing / Watering
......
![Page 14: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/14.jpg)
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
![Page 15: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/15.jpg)
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
![Page 16: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/16.jpg)
RGB Structural Imaging
Assesed set of morphogenic parametres
• Area
• Perimeter
• Roundness
• Compactness
• Eccentricity
• MLWI
• Green Colour Segmentation
www.qubitphenomics.com
![Page 17: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/17.jpg)
Morphogenic analysis
• Plant genotype pattern • Time development pattern
www.qubitphenomics.com
![Page 18: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/18.jpg)
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
![Page 19: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/19.jpg)
Chlorophyll Fluorescence Kinetics Imagingwww.qubitphenomics.com
Fv/Fm= Fm-Fo/Fm =Quantum Yield in the dark-adapted state
![Page 20: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/20.jpg)
0
50
100
150
200
250
-10 0 10 20 30 40 50 60 70 80
TIME, seconds
FLU
OR
ES
CE
NC
E, r
.u.
F0
FM
FV
FS
FM’
Pixel-to-Pixel Arithmetic Image Operations
![Page 21: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/21.jpg)
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
![Page 22: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/22.jpg)
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)
0 50000000 100000000 150000000 2000000000
1
2
3
4
5
6
Controldrought
Drought Stress: Turfgrasswww.qubitphenomics.com
![Page 23: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/23.jpg)
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
![Page 24: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/24.jpg)
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
![Page 25: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/25.jpg)
• Range 390nm – 2500nm and with 2nm half width
• Resolution 1392 x 870 pixels
• AD conversion 12bits
Hyperspectral Analysiswww.qubitphenomics.com
![Page 26: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/26.jpg)
Hyperspectral Analysiswww.qubitphenomics.com
![Page 27: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/27.jpg)
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
![Page 28: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/28.jpg)
Water Content Estimation via SWIR Hyperspectral Imaging
800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
reflec
tance
www.qubitphenomics.com
![Page 29: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/29.jpg)
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
![Page 30: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/30.jpg)
800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
refle
cta
nce
800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
reflec
tanc
e800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
refle
cta
nce
t = 0.0h t = 0.5h t = 1.0h
Reflectance / Water Content Distribution
![Page 31: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/31.jpg)
800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
refle
cta
nce
800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
refle
cta
nce
800 1000 1200 1400 1600 1800 2000 2200 2400 26000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
wavelength [nm]
refle
cta
nce
t = 2.0h t = 4.0h t = 5.0h
![Page 32: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/32.jpg)
RFID Reader, BAR codes – 2D,3D
• Identification and tracking of the samples
www.qubitphenomics.com
![Page 33: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/33.jpg)
• Nutrient mixing system.
• Very high accuracy
• Watering with full accuracy
Automated Watering and Weighingwww.qubitphenomics.com
![Page 34: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/34.jpg)
• Homogeneous light source
• Light intensity up to 2000uE
• Dark adaptation chamber
• Light adaptation of individual samples
Lighting + Cultivation
www.psi.cz
![Page 35: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/35.jpg)
• Homogeneous light source
• Light intensity up to 2000uE
• Dark adaptation chamber
• Light adaptation of individual samples
Lighting - Cultivation
www.psi.cz
![Page 36: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/36.jpg)
Graphical Control Softwarewww.qubitphenomics.com
![Page 37: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/37.jpg)
Online Operation of the PlantScreen using IP Cameras
www.qubitphenomics.com
![Page 38: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/38.jpg)
PlantScreen Data Analysis Software www.qubitphenomics.com
![Page 39: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/39.jpg)
Automated morphological analysiswww.qubitphenomics.com
![Page 40: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/40.jpg)
Automated analysis of chlorophyll fluorescence parametres
www.qubitphenomics.com
![Page 41: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/41.jpg)
FluorPenwww.qubitphenomics.com
![Page 42: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/42.jpg)
FluorPen Datawww.qubitphenomics.com
![Page 43: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/43.jpg)
FluorPen Datawww.qubitphenomics.com
![Page 44: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/44.jpg)
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
![Page 45: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/45.jpg)
Normalized Difference Greeness Index (NDGI)
NDGI=(R740-R550)/(R740+R550)
95% c onf idenc e interv als
nitrogen c ontent (% )
ND
GI
leaf : 1
2,2 2,4 2,6 2,8 3,0 3,2 3,4 3,6 3,8 4,00,36
0,38
0,40
0,42
0,44
0,46
0,48
0,50
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
0,38
0,40
0,42
0,44
0,46
0,48
0,50
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
![Page 46: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/46.jpg)
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
![Page 47: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/47.jpg)
Photon Systems and Qubit Systems Inc.
www.qubitphenomics.com
![Page 48: Qubit Systems Inc. & Photon Systems Inc](https://reader033.vdocuments.us/reader033/viewer/2022061223/54c4606d4a7959551c8b4581/html5/thumbnails/48.jpg)
Thank you for your attention
http://qubitphenomics.com/