A framework for the extraction of quantitative traits from 2D images of mature Arabidopsis thaliana

In this work, we propose an image-based phenotyping framework for the determination of quantitative traits from mature Arabidopsis thaliana plants. Two-dimensional (2D) images taken from the dried and flattened plants are analyzed regarding their geometry as well as their branching topology. The rea...

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Bibliographic Details
Published in:Machine vision and applications 2016-07, Vol.27 (5), p.647-661
Main Authors: Augustin, Marco, Haxhimusa, Yll, Busch, Wolfgang, Kropatsch, Walter G.
Format: Article
Language:English
Subjects:
Communications Engineering
Computer Science
Continuity (mathematics)
Extraction
Flattening
Image acquisition
Image Processing and Computer Vision
Image reconstruction
Machine vision
Manuals
Networks
Pattern Recognition
Segments
Special Issue Paper
Topology
Two-dimensional analysis
Vision systems
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Summary:In this work, we propose an image-based phenotyping framework for the determination of quantitative traits from mature Arabidopsis thaliana plants. Two-dimensional (2D) images taken from the dried and flattened plants are analyzed regarding their geometry as well as their branching topology. The realistic branching architecture is hereby reconstructed from a single 2D image using a tracing approach with a semi-circular search window. The centerline segments of the tracing procedure are subsequently merged and labeled based on a hierarchical approach combining continuity properties with geometrical and topological information determined during tracing. This paper covers a detailed description of the proposed plant phenotyping pipeline from the image acquisition process until the extraction of the quantitative traits. The framework is evaluated using a set of 106 images and compared to a manual phenotyping approach as well as a semi-automatic image-based approach. The most relevant results of this evaluation are presented.
ISSN:0932-8092
1432-1769
DOI:10.1007/s00138-015-0720-z