Non-parametric Vignetting Correction for Sparse Spatial Transcriptomics Images

Bovey Y. Rao, Alexis M. Peterson, Elena K. Kandror, Stephanie Herrlinger, Attila Losonczy, Liam Paninski, Abbas H. Rizvi, Erdem Varol

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


    Spatial transcriptomics techniques such as STARmap [15] enable the subcellular detection of RNA transcripts within complex tissue sections. The data from these techniques are impacted by optical microscopy limitations, such as shading or vignetting effects from uneven illumination during image capture. Downstream analysis of these sparse spatially resolved transcripts is dependent upon the correction of these artefacts. This paper introduces a novel non-parametric vignetting correction tool for spatial transcriptomic images, which estimates the illumination field and background using an efficient iterative sliced histogram normalization routine. We show that our method outperforms the state-of-the-art shading correction techniques both in terms of illumination and background field estimation and requires fewer input images to perform the estimation adequately. We further demonstrate an important downstream application of our technique, showing that spatial transcriptomic volumes corrected by our method yield a higher and more uniform gene expression spot-calling in the rodent hippocampus. Python code and a demo file to reproduce our results are provided in the supplementary material and at this github page:

    Original languageEnglish (US)
    Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2021 - 24th International Conference, Proceedings
    EditorsMarleen de Bruijne, Philippe C. Cattin, Stéphane Cotin, Nicolas Padoy, Stefanie Speidel, Yefeng Zheng, Caroline Essert
    PublisherSpringer Science and Business Media Deutschland GmbH
    Number of pages10
    ISBN (Print)9783030872366
    StatePublished - 2021
    Event24th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2021 - Virtual, Online
    Duration: Sep 27 2021Oct 1 2021

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume12908 LNCS
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349


    Conference24th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2021
    CityVirtual, Online

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • General Computer Science


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