Learning Probabilistic Piecewise Rigid Atlases of Model Organisms via Generative Deep Networks

Amin Nejatbakhsh, Neel Dey, Vivek Venkatachalam, Eviatar Yemini, Liam Paninski, Erdem Varol

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    Atlases are crucial to imaging statistics as they enable the standardization of inter-subject and inter-population analyses. While existing atlas estimation methods based on fluid/elastic/diffusion registration yield high-quality results for the human brain, these deformation models do not extend to a variety of other challenging areas of neuroscience such as the anatomy of C. elegans worms and fruit flies. To this end, this work presents a general probabilistic deep network-based framework for atlas estimation and registration which can flexibly incorporate various deformation models and levels of keypoint supervision that can be applied to a wide class of model organisms. Of particular relevance, it also develops a deformable piecewise rigid atlas model which is regularized to preserve inter-observation distances between neighbors. These modeling considerations are shown to improve atlas construction and key-point alignment across a diversity of datasets with small sample sizes including neuron positions in C. elegans hermaphrodites, fluorescence microscopy of male C. elegans, and images of fruit fly wings. Code is accessible at https://github.com/amin-nejat/Deformable-Atlas.

    Original languageEnglish (US)
    Title of host publicationInformation Processing in Medical Imaging - 28th International Conference, IPMI 2023, Proceedings
    EditorsAlejandro Frangi, Marleen de Bruijne, Demian Wassermann, Nassir Navab
    PublisherSpringer Science and Business Media Deutschland GmbH
    Pages332-343
    Number of pages12
    ISBN (Print)9783031340475
    DOIs
    StatePublished - 2023
    Event28th International Conference on Information Processing in Medical Imaging, IPMI 2023 - San Carlos de Bariloche, Argentina
    Duration: Jun 18 2023Jun 23 2023

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume13939 LNCS
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Conference

    Conference28th International Conference on Information Processing in Medical Imaging, IPMI 2023
    Country/TerritoryArgentina
    CitySan Carlos de Bariloche
    Period6/18/236/23/23

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • General Computer Science

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