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Electron Microscopy Solutions

GEVES uses Avizo software to study and control plant seeds

Customer Spotlight

By Ghassen Trigui, Laurence Le Corre, Dominique Honoré and Karima Boudehri-Giresse - 2D/3D Imaging - R&D team, GEVES


At GEVES, Microtomography (micro-CT), which is a technique using X-rays to investigate internal anatomy and morphology of organisms without destruction, is applied to plant seed quality control and phenotyping. Several applications have been developed using micro-CT coupled with Avizo software development, such as for example in:


The Measurements of internal and external sugar beet seed structures for seed phenotyping

Morphological seed characters may be used for the assessment of complex and quantitative traits such as seed resistance, germination potential and other agronomic traits. Examples for such direct measurements are image-based analysis of internal and external seed structures. For the AKER 1 project, we are running an analysis of internal and external sugar beet seed structures using high-resolution micro-CT imaging. The developed image processing pipeline allows 3D- measurements of volume and surface areas of the seed embryo and the seed coat thickness.

Segmentation of high resolution beet seed images acquired with 3D X-ray microtomography. (I) 3D volume rendering with a corner cut showing the structural components of the seed namely E for embryo, P for perisperm and C for seed coat, and with respectively transverse (II) and longitudinal (III) cross-section views. The result of segmentation shows separated components with different labels (blue for embryo, red for perisperm and green for seed coat) respectively showed with a volume rendering (IV), transverse (V) and longitudinal (VI) cross-section views.

The characterization of coated seeds in seed technology

Seeds are coated for seed sizing purposes, and protection against pathogens. Coated seeds are widely used as a standard product for many crops. The developed approach for coated seeds allows virtual separation and individualization of seeds from their coating material. The volume, the sphericity and the surface roughness are then evaluated for coated seed quality purposes.


Virtual cut in 3D volume rendering of a

coated seed showing a sugar beet seed inside

its coating material

 A batch of coated seeds in a Petri dish  after image segmentation showing the separated parts of the coated seeds.


The insect damage quantification

Insects can cause internal and/or external damage by feeding on seed and this infestation can take place before or after harvest. X-ray 3D microtomography and image processing are used to assess quantitative data of the damage without destruction.


The characterization of internal morphology on corn seeds

We also use micro-CT and Avizo software development to study qualitatively and quantitatively the characteristics of the internal morphology of corn seeds. The developed image processing procedure is based on the detection of edges that separate different seed structures (endosperm, embryo and scutellum), and internal cavities. This procedure includes also the detection and quantification of cracks. This analysis addresses issues related to physical and germination seed quality, including industrial processes, treatment products, but also as part of the varietal characterization.

Figure: High-resolution tomography of a corn seed (A) 3D Volume rendering showing the different contrasts. (B) , (C) and (D) virtual slices successively in different planes XY , XZ , YZ and after separation of internal structures showing the albumen (end) , the scutellum (scu ) , the radicle (rad) , Coleoptile (col) and the cavity in the endosperm (c1) the gap characterizing seed filling (c2) and the embryo cavity (c3). Automated crack detection and quantification (E)


GEVES is the French Group for the Study and Control of Varieties and Seeds. It is a Public Interest Group associated with INRA (National Institute of Agricultural Research), the French Ministry of Agriculture and GNIS.



About Amira & Avizo 3D Software

Amira and Avizo are high-performance 3D software for visualizing, analyzing, and understanding scientific and industrial data coming from all types of sources and modalities.



Images and text are courtesy of GEVES



  logo - Investments for the future title=      
This work was sponsored by the French Government through the National Research Agency under the program "Investments for the future" (reference ANR-11-BTBR-0007).


1 AKER aims to improve the competitiveness of sugar beet by 2020 by doubling the annual increase in sugar yield / hectare (4% vs 2%). AKER is part of the "Programme d'Investissements d'Avenir" and is supported by 11 public and private partners, representing the whole of the French sugar beet sector. AKER is an original and innovative programme for research, development and training, confirming sugar beet as a crop and industry reference. 


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