EASI-FISH analysis pipeline

Posted on 09.11.2021 - 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.


Wang, Yuhan; Eddison, Mark; Fleishman, Greg; Weigert, Martin; Xu, Shengjin; Wang, Tim; et al. (2021): EASI-FISH analysis pipeline. Janelia Research Campus. Collection. https://doi.org/10.25378/janelia.c.5276708.v2
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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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