Graphical-model framework for automated annotation of cell identities in dense cellular images

  1. Shivesh Chaudhary
  2. Sol Ah Lee
  3. Yueyi Li
  4. Dhaval S Patel
  5. Hang Lu  Is a corresponding author
  1. Georgia Institute of Technology, United States

Abstract

Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers' experiences. Here we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in C. elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files are provided at https://github.com/shiveshc/CRF_Cell_ID.git.

Article and author information

Author details

  1. Shivesh Chaudhary

    Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sol Ah Lee

    Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Yueyi Li

    Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Dhaval S Patel

    Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Hang Lu

    Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
    For correspondence
    hang.lu@gatech.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6881-660X

Funding

National Institutes of Health (R21DC015652)

  • Hang Lu

National Institutes of Health (R01NS096581)

  • Hang Lu

National Institutes of Health (R01GM088333)

  • Hang Lu

National Science Foundation (1764406)

  • Hang Lu

National Science Foundation (1707401)

  • Hang Lu

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

Reviewing Editor

  1. Ronald L Calabrese, Emory University, United States

Publication history

  1. Received: June 23, 2020
  2. Accepted: February 23, 2021
  3. Accepted Manuscript published: February 24, 2021 (version 1)
  4. Version of Record published: April 8, 2021 (version 2)

Copyright

© 2021, Chaudhary 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. Shivesh Chaudhary
  2. Sol Ah Lee
  3. Yueyi Li
  4. Dhaval S Patel
  5. Hang Lu
(2021)
Graphical-model framework for automated annotation of cell identities in dense cellular images
eLife 10:e60321.
https://doi.org/10.7554/eLife.60321

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