DeepSea is an efficient deep-learning model for single-cell segmentation and tracking in time-lapse microscopy.

Journal: Cell reports methods
PMID: 37426758

Abstract

Time-lapse microscopy is the only method that can directly capture the dynamics and heterogeneity of fundamental cellular processes at the single-cell level with high temporal resolution. Successful application of single-cell time-lapse microscopy requires automated segmentation and tracking of hundreds of individual cells over several time points. However, segmentation and tracking of single cells remain challenging for the analysis of time-lapse microscopy images, in particular for widely available and non-toxic imaging modalities such as phase-contrast imaging. This work presents a versatile and trainable deep-learning model, termed DeepSea, that allows for both segmentation and tracking of single cells in sequences of phase-contrast live microscopy images with higher precision than existing models. We showcase the application of DeepSea by analyzing cell size regulation in embryonic stem cells.

Authors

  • Abolfazl Zargari
    School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA.
  • Gerrald A Lodewijk
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Najmeh Mashhadi
    Department of Computer Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Nathan Cook
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Celine W Neudorf
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Kimiasadat Araghbidikashani
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Robert Hays
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Sayaka Kozuki
    Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Stefany Rubio
    Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Eva Hrabeta-Robinson
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Angela Brooks
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Lindsay Hinck
    Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • S Ali Shariati
    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. alish@ucsc.edu.

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