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A Complete System for 3D Reconstruction of Roots for Phenotypic Analysis

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Signal and Image Analysis for Biomedical and Life Sciences

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 823))

Abstract

Here we present a complete system for 3D reconstruction of roots grown in a transparent gel medium or washed and suspended in water. The system is capable of being fully automated as it is self calibrating. The system starts with detection of root tips in root images from an image sequence generated by a turntable motion. Root tips are detected using the statistics of Zernike moments on image patches centred on high curvature points on root boundary and Bayes classification rule. The detected root tips are tracked in the image sequence using a multi-target tracking algorithm. Conics are fitted to the root tip trajectories using a novel ellipse fitting algorithm which weighs the data points by its eccentricity. The conics projected from the circular trajectory have a complex conjugate intersection which are image of the circular points. Circular points constraint the image of the absolute conics which are directly related to the internal parameters of the camera. The pose of the camera is computed from the image of the rotation axis and the horizon. The silhouettes of the roots and camera parameters are used to reconstruction the 3D voxel model of the roots. We show the results of real 3D reconstruction of roots which are detailed and realistic for phenotypic analysis.

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Authors and Affiliations

  1. School of Information Technology and Mathematical Sciences, Phenomics and Bioinformatics Research Centre, Australian Centre for Plant Functional Genomics, University of South Australia, Mawson Lakes, SA, 5095, Australia

    Pankaj Kumar, Jinhai Cai & Stanley J. Miklavcic

Authors
  1. Pankaj Kumar
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  2. Jinhai Cai
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  3. Stanley J. Miklavcic
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Corresponding author

Correspondence to Pankaj Kumar .

Editor information

Editors and Affiliations

  1. Digital Productivity Flagship, CSIRO, Sydney, New South Wales, Australia

    Changming Sun

  2. Digital Productivity Flagship, CSIRO, Sydney, New South Wales, Australia

    Tomasz Bednarz

  3. The University of Aizu, Fukushima, Japan

    Tuan D. Pham

  4. Digital Productivity Flagship, CSIRO, Sydney, New South Wales, Australia

    Pascal Vallotton

  5. Digital Productivity Flagship, CSIRO, Sydney, New South Wales, Australia

    Dadong Wang

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Kumar, P., Cai, J., Miklavcic, S.J. (2015). A Complete System for 3D Reconstruction of Roots for Phenotypic Analysis. In: Sun, C., Bednarz, T., Pham, T., Vallotton, P., Wang, D. (eds) Signal and Image Analysis for Biomedical and Life Sciences. Advances in Experimental Medicine and Biology, vol 823. Springer, Cham. https://doi.org/10.1007/978-3-319-10984-8_14

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