non invasive computer vision tools to monitor seedling ... · good agreement between manual...
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E. Belin1, D. Rousseau2, D. Demilly3 and C. Dürr4
1 : Laboratoire d'Ingénierie des Systèmes Automatisés (LISA), Université d'Angers, Angers, France.2 : Université de Lyon, CREATIS, Lyon, France.
3 : GEVES - Station Nationale d'Essais de Semences (SNES), Beaucouzé, France. 4 : INRA - Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, France.
Non invasive computer vision tools to monitor seedling elongation
INTERNATIONAL SEED TESTING ASSOCIATION (ISTA) ANNUAL MEETING 2012VENLO – THE NETHERLANDS
A multi-disciplinary collaboration
Development of an automated phenotyping of seeds and seedlings within the Federative Research Institute in Angers (www.ifrquasav-angers.org)
Collaboration with research teams in:
• plant sciences
• information sciences
within the Phenotic research project:
www.istia.univ-angers.fr/LISA/PHENOTIC
2/16
Context: elongation phase
Monitoring the elongation of 2parts of seedlings during growth
-hypocotyl-radicle
Currently:-visible light = actinic-experts notations
⇒ Outperform currentmeasurements withnon invasive computervision tools
Hypocotyl
Radicle
Cotyledons
Visible images acquisition device
backlighting system
Petri dish with seedlings
cameraresolution: 3200x2400 pixels
t = 40ht = 0h t = 80hEx.: monitoring of Medicago truncatula seedlings during 80h
Visible images processing
- based on gray-levels images- segmentation by active contour detection
radiclehypocotyl
radicle
Automated extraction of organs curve length
- based on biological prior knowledge. Separation ofhypocotyl and radicle = line done by the germination point
- curve length computed on skeletonof organs
Results for visible images processing- Tested on 50 seedlings monitored during 50 hours after apparition of embryonicaxis at freq. 2h = 1250 processed images- Comparison between results computed by algorithm (solid line) and resultsobtained by 3 experts notations (dotted line with errorbars)
Ex.: monitoring of hypocotyl (A,C) and radicle (B,D) for 2 seedlings of Medicago truncatula
Upgrading previous device with thermal imaging
Multimodal imaging acquisition device
t = 70ht = 40ht = 30h
Ex.: monitoring of Medicago truncatula seedlings during 70h
blotter with seedlings
LED lighting system
infrared cooled cameraspectral range: 2,5 – 5 µmresolution: 320x240
visible camera (for visual diagnostic by experts on images)
E. Belin, D. Rousseau, J. Rojas-Varela, D. Demilly, M.H. Wagner, M.H. Cathala, C. Dürr. “Thermography as non invasivefunctional imaging for monitoring seedling growth”; Computers and Electronics in Agriculture, Vol. 79, n° 2, p. 236-240 (2011).
Thermal images processing n°1
Ex. : monitoring of 4 seedlingsof Mtr during 70h.
Algorithm developed: demonstrate the feasibility of transposing from visible to dark conditions the monitoring of total curve length of roots elongation seedling
18 seedlings monitored during 70h atfreq. 2h30 + apparition of embryonic axis35h after sowing ≈ 250 images
Observations of multimodal images
Specific contrast on thermal imaging
No influence of the blotter.No contact between root (radicle + hypocotyl) withblotter: specific contrast on thermal images
⇒ Separation: radicle / hypocotyl ?
- Algorithm developed to extractradicle and hypocotyl curve lengthfrom the separation of specificcontrast.
- Registration of thermal and visibleimages.
- Comparison with notations of 3experts on 250 images.
Thermal images processing n°2 (1/2)
• Results in good agreement / according to the relative deviation(errorbars) of experts notations• Thermal imaging may be predictive: hypocotyl seen before expertsnotations (panel A)
• Physiological hypothesis: fluxes exchanges during heterotrophgrowth
Thermal images processing n°2 (2/2)
Ex.: monitoring of hypocotyl and radicle of 1 seedling of Mtr during 70h.
Conclusion & perspectives
2 non invasive computers vision tools to perform organs segmentationof seedlings during elongation.
Focus on thermal imaging device:good agreement between manual measurements and fully automatedmeasurements.
Main interest of thermal imaging: working in dark conditions.
Questions about the functional origin of thermal contrast in seedlingsduring elongation.
These tools will be used in different research projects:AKER, Convigour, plant KBBE,…
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