Robust non-negative tensor factorization, diffeomorphic motion correction, and functional statistics to understand fixation in fluorescence microscopy

Neel Dey, Jeffrey Messinger, R. Theodore Smith, Christine A. Curcio, Guido Gerig

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

    Abstract

    Fixation is essential for preserving cellular morphology in biomedical research. However, it may also affect spectra captured in multispectral fluorescence microscopy, impacting molecular interpretations. To investigate fixation effects on tissue, multispectral fluorescence microscopy images of pairs of samples with and without fixation are captured. Each pixel might exhibit overlapping spectra, creating a blind source separation problem approachable with linear unmixing. With multiple excitation wavelengths, unmixing is intuitively extended to tensor factorizations. Yet these approaches are limited by nonlinear effects like attenuation. Further, light exposure during image acquisition introduces subtle Brownian motion between image channels of non-fixed tissue. Finally, hypothesis testing for spectral differences due to fixation is non-trivial as retrieved spectra are paired sequential samples. To these ends, we present three contributions, (1) a novel robust non-negative tensor factorization using the β-divergence and L2,1-norm, which decomposes the data into a low-rank multilinear and group-sparse non-multilinear tensor without making any explicit nonlinear modeling choices or assumptions on noise statistics; (2) a diffeomorphic atlas-based strategy for motion correction; (3) a non-parametric hypothesis testing framework for paired sequential data using functional principal component analysis. PyTorch code for robust non-negative tensor factorization is available at https://github.com/neel-dey/robustNTF.

    Original languageEnglish (US)
    Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings
    EditorsDinggang Shen, Pew-Thian Yap, Tianming Liu, Terry M. Peters, Ali Khan, Lawrence H. Staib, Caroline Essert, Sean Zhou
    PublisherSpringer
    Pages658-666
    Number of pages9
    ISBN (Print)9783030322380
    DOIs
    StatePublished - Jan 1 2019
    Event22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019 - Shenzhen, China
    Duration: Oct 13 2019Oct 17 2019

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume11764 LNCS
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Conference

    Conference22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019
    CountryChina
    CityShenzhen
    Period10/13/1910/17/19

    Fingerprint

    Fluorescence Microscopy
    Fluorescence microscopy
    Fixation
    Factorization
    Tensors
    Tensor
    Non-negative
    Statistics
    Motion
    Hypothesis Testing
    Nonparametric Testing
    Functional Principal Component Analysis
    Tissue
    Nonlinear Modeling
    Blind source separation
    Blind Source Separation
    Image Acquisition
    Brownian movement
    Image acquisition
    Atlas

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • Computer Science(all)

    Cite this

    Dey, N., Messinger, J., Smith, R. T., Curcio, C. A., & Gerig, G. (2019). Robust non-negative tensor factorization, diffeomorphic motion correction, and functional statistics to understand fixation in fluorescence microscopy. In D. Shen, P-T. Yap, T. Liu, T. M. Peters, A. Khan, L. H. Staib, C. Essert, ... S. Zhou (Eds.), Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings (pp. 658-666). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11764 LNCS). Springer . https://doi.org/10.1007/978-3-030-32239-7_73

    Robust non-negative tensor factorization, diffeomorphic motion correction, and functional statistics to understand fixation in fluorescence microscopy. / Dey, Neel; Messinger, Jeffrey; Smith, R. Theodore; Curcio, Christine A.; Gerig, Guido.

    Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings. ed. / Dinggang Shen; Pew-Thian Yap; Tianming Liu; Terry M. Peters; Ali Khan; Lawrence H. Staib; Caroline Essert; Sean Zhou. Springer , 2019. p. 658-666 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11764 LNCS).

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

    Dey, N, Messinger, J, Smith, RT, Curcio, CA & Gerig, G 2019, Robust non-negative tensor factorization, diffeomorphic motion correction, and functional statistics to understand fixation in fluorescence microscopy. in D Shen, P-T Yap, T Liu, TM Peters, A Khan, LH Staib, C Essert & S Zhou (eds), Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11764 LNCS, Springer , pp. 658-666, 22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019, Shenzhen, China, 10/13/19. https://doi.org/10.1007/978-3-030-32239-7_73
    Dey N, Messinger J, Smith RT, Curcio CA, Gerig G. Robust non-negative tensor factorization, diffeomorphic motion correction, and functional statistics to understand fixation in fluorescence microscopy. In Shen D, Yap P-T, Liu T, Peters TM, Khan A, Staib LH, Essert C, Zhou S, editors, Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings. Springer . 2019. p. 658-666. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-030-32239-7_73
    Dey, Neel ; Messinger, Jeffrey ; Smith, R. Theodore ; Curcio, Christine A. ; Gerig, Guido. / Robust non-negative tensor factorization, diffeomorphic motion correction, and functional statistics to understand fixation in fluorescence microscopy. Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings. editor / Dinggang Shen ; Pew-Thian Yap ; Tianming Liu ; Terry M. Peters ; Ali Khan ; Lawrence H. Staib ; Caroline Essert ; Sean Zhou. Springer , 2019. pp. 658-666 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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