EASI-FISH analysis pipeline
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.
CITE THIS COLLECTION
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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HHMI Janelia Research Campus
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AUTHORS (18)
ME
Mark Eddison
GF
Greg Fleishman
MW
Martin Weigert
SX
Shengjin Xu
TW
Tim Wang
CG
Cristian Goina
FH
Fredrick E. Henry
AL
Andrew L. Lemire
US
Uwe Schmidt
HY
Hui Yang
EW
Eugene W Myers
SS
Stephan Saalfeld
SS
Scott M. Sternson
PT
Paul W. Tillberg