Using positional information to provide context for biological image analysis with MorphoGraphX 2.0

  1. Sören Strauss
  2. Adam Runions
  3. Brendan Lane
  4. Dennis Eschweiler
  5. Namrata Bajpai
  6. Nicola Trozzi
  7. Anne-Lise Routier-Kierzkowska
  8. Saiko Yoshida
  9. Sylvia Rodrigues da Silveira
  10. Athul Vijayan
  11. Rachele Tofanelli
  12. Mateusz Majda
  13. Emillie Echevin
  14. Constance Le Gloanec
  15. Hana Bertrand-Rakusova
  16. Milad Adibi
  17. Kay Schneitz
  18. George Bassel
  19. Daniel Kierzkowski
  20. Johannes Stegmaier
  21. Miltos Tsiantis
  22. Richard S Smith  Is a corresponding author
  1. Max Planck Institute for Plant Breeding Research, Germany
  2. John Innes Centre, United Kingdom
  3. RWTH Aachen University, Germany
  4. Université de Montréal, Canada
  5. University of Montreal, Canada
  6. Technical University of Munich, Germany
  7. University of Warwick, United Kingdom

Abstract

Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially-coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here we present recent advances in the MorphoGraphX software (Barbier de Reuille et al., 2015)⁠ that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.

Data availability

Datasets and software are available at www.MorphoGraphX.org and Dryad

The following data sets were generated

Article and author information

Author details

  1. Sören Strauss

    Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Adam Runions

    Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7758-7423
  3. Brendan Lane

    John Innes Centre, Norwich, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Dennis Eschweiler

    Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Namrata Bajpai

    Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Nicola Trozzi

    John Innes Centre, Norwich, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3951-6533
  7. Anne-Lise Routier-Kierzkowska

    Department of Biological Sciences, Université de Montréal, Montréal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0383-0811
  8. Saiko Yoshida

    Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Sylvia Rodrigues da Silveira

    Department of Biological Sciences, University of Montreal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  10. Athul Vijayan

    School of Life Sciences, 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:" 0000-0003-1837-6359
  11. Rachele Tofanelli

    School of Life Sciences, 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
  12. Mateusz Majda

    John Innes Centre, Norwich, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  13. Emillie Echevin

    Department of Biological Sciences, University of Montreal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  14. Constance Le Gloanec

    Department of Biological Sciences, University of Montreal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7959-6307
  15. Hana Bertrand-Rakusova

    Department of Biological Sciences, University of Montreal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  16. Milad Adibi

    Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  17. Kay Schneitz

    School of Life Sciences, 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
  18. George Bassel

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  19. Daniel Kierzkowski

    Department of Biological Sciences, University of Montreal, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1947-8691
  20. Johannes Stegmaier

    Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4072-3759
  21. Miltos Tsiantis

    Max Planck Institute for Plant Breeding Research, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  22. Richard S Smith

    John Innes Centre, Norwich, United Kingdom
    For correspondence
    Richard.Smith@jic.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9220-0787

Funding

Deutsche Forschungsgemeinschaft (Forschunggruppe 2581)

  • Kay Schneitz
  • Miltos Tsiantis
  • Richard S Smith

Human Frontiers Science Program (RGP0002/2020)

  • George Bassel

Max Planck Society (Core grant)

  • Miltos Tsiantis

Fonds Nature et Technologies (282285)

  • Anne-Lise Routier-Kierzkowska
  • Daniel Kierzkowski

Deutsche Forschungsgemeinschaft (ERA-CAPS V-Morph)

  • Richard S Smith

Biotechnology and Biological Sciences Research Council (ISP to John Innes Centre)

  • Richard S Smith

Bundesministerium für Bildung und Forschung (031A494 & 031A492)

  • Richard S Smith

Deutsche Forschungsgemeinschaft (STE2802/2-1)

  • Dennis Eschweiler

New Frontiers in Research Fund (2018-00953)

  • Anne-Lise Routier-Kierzkowska
  • Daniel Kierzkowski

Natural Sciences and Engineering Research Council of Canada (RGPIN-2018-04897)

  • Daniel Kierzkowski

Natural Sciences and Engineering Research Council of Canada (RGPIN-2018-05762)

  • Anne-Lise Routier-Kierzkowska

Leverhulme Trust (RPG-2019-267)

  • George Bassel

Biotechnology and Biological Sciences Research Council (BB/S002804/1)

  • 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: August 12, 2021
  2. Preprint posted: August 13, 2021 (view preprint)
  3. Accepted: May 3, 2022
  4. Accepted Manuscript published: May 5, 2022 (version 1)
  5. Version of Record published: June 1, 2022 (version 2)

Copyright

© 2022, Strauss 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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  1. Sören Strauss
  2. Adam Runions
  3. Brendan Lane
  4. Dennis Eschweiler
  5. Namrata Bajpai
  6. Nicola Trozzi
  7. Anne-Lise Routier-Kierzkowska
  8. Saiko Yoshida
  9. Sylvia Rodrigues da Silveira
  10. Athul Vijayan
  11. Rachele Tofanelli
  12. Mateusz Majda
  13. Emillie Echevin
  14. Constance Le Gloanec
  15. Hana Bertrand-Rakusova
  16. Milad Adibi
  17. Kay Schneitz
  18. George Bassel
  19. Daniel Kierzkowski
  20. Johannes Stegmaier
  21. Miltos Tsiantis
  22. Richard S Smith
(2022)
Using positional information to provide context for biological image analysis with MorphoGraphX 2.0
eLife 11:e72601.
https://doi.org/10.7554/eLife.72601

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