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Cecelia: a multifunctional image analysis toolbox for decoding spatial cellular interactions and behaviour

Author

Listed:
  • Dominik Schienstock

    (The University of Melbourne, The Peter Doherty Institute for Infection and Immunity)

  • Jyh Liang Hor

    (The University of Melbourne, The Peter Doherty Institute for Infection and Immunity
    NIAID, NIH)

  • Sapna Devi

    (The University of Melbourne, The Peter Doherty Institute for Infection and Immunity)

  • Scott N. Mueller

    (The University of Melbourne, The Peter Doherty Institute for Infection and Immunity)

Abstract

With the ever-increasing complexity of microscopy modalities, it is imperative to have computational workflows that enable researchers to process and perform in-depth quantitative analysis of the resulting images. However, workflows that allow flexible, interactive and intuitive analysis from raw images to analysed data are lacking for many experimental use-cases. Notably, integrated software solutions for analysis of complex 3D and live cell images are sorely needed. To address this, we present Cecelia, a toolbox that integrates various open-source packages into a coherent data management suite to make quantitative multidimensional image analysis accessible for non-specialists. We describe the application of Cecelia to several immunologically relevant scenarios and the development of an unbiased approach to distinguish dynamic cell behaviours from live imaging data. Cecelia is available as a software package with a Shiny app interface ( https://github.com/schienstockd/cecelia ). We envision that this framework and its approaches will be of broad use for biological researchers.

Suggested Citation

  • Dominik Schienstock & Jyh Liang Hor & Sapna Devi & Scott N. Mueller, 2025. "Cecelia: a multifunctional image analysis toolbox for decoding spatial cellular interactions and behaviour," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57193-y
    DOI: 10.1038/s41467-025-57193-y
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    1. Amanda Janesick & Robert Shelansky & Andrew D. Gottscho & Florian Wagner & Stephen R. Williams & Morgane Rouault & Ghezal Beliakoff & Carolyn A. Morrison & Michelli F. Oliveira & Jordan T. Sicherman &, 2023. "High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Thomas Gebhardt & Paul G. Whitney & Ali Zaid & Laura K. Mackay & Andrew G. Brooks & William R. Heath & Francis R. Carbone & Scott N. Mueller, 2011. "Different patterns of peripheral migration by memory CD4+ and CD8+ T cells," Nature, Nature, vol. 477(7363), pages 216-219, September.
    3. Visser, Ingmar & Speekenbrink, Maarten, 2010. "depmixS4: An R Package for Hidden Markov Models," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 36(i07).
    4. J. A. Hartigan & M. A. Wong, 1979. "A K‐Means Clustering Algorithm," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 28(1), pages 100-108, March.
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