CytoCensus, mapping cell identity and division in tissues and organs using machine learning.

Journal: eLife
PMID: 32423529

Abstract

A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends convenient 2D 'point-and-click' user training to 3D detection of cells in challenging datasets with ill-defined cell boundaries. In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection. We used CytoCensus to count stem cells and their progeny, and to quantify individual cell divisions from time-lapse movies of explanted larval brains, comparing wild-type and mutant phenotypes. We further illustrate the general utility and future potential of CytoCensus by analysing the 3D organisation of multiple cell classes in Zebrafish retinal organoids and cell distributions in mouse embryos. CytoCensus opens the possibility of straightforward and robust automated analysis of developmental phenotypes in complex tissues.

Authors

  • Martin Hailstone
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
  • Dominic Waithe
    WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
  • Tamsin J Samuels
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
  • Lu Yang
    Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
  • Ita Costello
    The Dunn School of Pathology,University of Oxford, Oxford, United Kingdom.
  • Yoav Arava
    Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
  • Elizabeth Robertson
    The Dunn School of Pathology,University of Oxford, Oxford, United Kingdom.
  • Richard M Parton
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
  • Ilan Davis
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

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