Non invasive computer vision tools to monitor seedling ... · good agreement between manual measurements and fully automated measurements. ... MH. Wagner, S. Besson, S. Ducournau,

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,…