1. Plant Biology
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Accurate and versatile 3D segmentation of plant tissues at cellular resolution

  1. Adrian Wolny
  2. Lorenzo Cerrone
  3. Athul Vijayan
  4. Rachele Tofanelli
  5. Amaya Vilches Barro
  6. Marion Louveaux
  7. Christian Wenzl
  8. Sören Strauss
  9. David Wilson-Sánchez
  10. Rena Lymbouridou
  11. Susanne Steigleder
  12. Constantin Pape
  13. Alberto Bailoni
  14. Salva Duran-Nebreda
  15. George Bassel
  16. Jan U Lohmann
  17. Miltos Tsiantis
  18. Fred Hamprecht
  19. Kay Schneitz
  20. Alexis Maizel
  21. Anna Kreshuk  Is a corresponding author
  1. EMBL, Germany
  2. Heidelberg University, Germany
  3. Technical University of Munich, Germany
  4. Max Planck Institute for Plant Breeding Research, Germany
  5. University of Warwick, United Kingdom
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Cite this article as: eLife 2020;9:e57613 doi: 10.7554/eLife.57613

Abstract

Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on 1xed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, acquisition settings even on non plant samples. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface (https://github.com/hci-unihd/plant-seg).

Article and author information

Author details

  1. Adrian Wolny

    Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Lorenzo Cerrone

    Heidelberg Collaboratory for Image Processing, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Athul Vijayan

    School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Rachele Tofanelli

    School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5196-1122
  5. Amaya Vilches Barro

    Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Marion Louveaux

    Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Christian Wenzl

    Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Sören Strauss

    Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. David Wilson-Sánchez

    Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Rena Lymbouridou

    Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Susanne Steigleder

    Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  12. Constantin Pape

    Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  13. Alberto Bailoni

    Heidelberg Collaboratory for Image Processing, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  14. Salva Duran-Nebreda

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  15. George Bassel

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  16. Jan U Lohmann

    Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3667-187X
  17. Miltos Tsiantis

    Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  18. Fred Hamprecht

    Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  19. Kay Schneitz

    School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6688-0539
  20. Alexis Maizel

    Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  21. Anna Kreshuk

    Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
    For correspondence
    anna.kreshuk@embl.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1334-6388

Funding

Deutsche Forschungsgemeinschaft (FOR2581)

  • Jan U Lohmann
  • Miltos Tsiantis
  • Fred Hamprecht
  • Kay Schneitz
  • Alexis Maizel
  • Anna Kreshuk

Leverhulme Trust (RPG-2016-049)

  • George Bassel

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Dominique C Bergmann, Stanford University, United States

Publication history

  1. Received: April 6, 2020
  2. Accepted: July 28, 2020
  3. Accepted Manuscript published: July 29, 2020 (version 1)

Copyright

© 2020, Wolny et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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