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EASI-FISH analysis pipeline

Version 2 2021-11-09, 16:07
Version 1 2021-03-05, 18:52
Posted on 2021-11-09 - 16:07 authored by Yuhan Wang
Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. The analysis pipeline includes automated image stitching, distributed fast deformable multi-round image registration, 3D deep-learning based cell segmentation, and distributed highly accurate FISH spot detection. This pipeline can also be adapted for analysis of other image-based spatial transcriptomic datasets.

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AUTHORS (18)

  • Mark Eddison
    Greg Fleishman
    Martin Weigert
    Shengjin Xu
    Tim Wang
    Cristian Goina
    Fredrick E. Henry
    Andrew L. Lemire
    Uwe Schmidt
    Hui Yang
    Eugene W Myers
    Stephan Saalfeld
    Scott M. Sternson
    Paul W. Tillberg
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