Version 2 2021-11-09, 16:07Version 2 2021-11-09, 16:07
Version 1 2021-03-05, 18:52Version 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 SituHybridization (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.