CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC
Kyu Sang Han, Pei-Hsun Wu, Sashank Reddy, Denis Wirtz, Joel Sunshine, Ashley Kiemen
Published: 2024-04-02 DOI: 10.17504/protocols.io.kqdg324xpv25/v1
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Abstract
CODA pipeline with 6 parts
Steps
Setting up CODA environment and preparing sample dataset
1.
dx.doi.org/10.17504/protocols.io.q26g71rpkgwz/v1
Calculate registration on low-resolution tissue images
2.
dx.doi.org/10.17504/protocols.io.kxygxym3dl8j/v1
Deep learning multi-labelling of tissue structures using training on manual annotations
3.
dx.doi.org/10.17504/protocols.io.81wgbz1x3gpk/v1
Register the deep learning labelled images and Construct 3D tissue matrix
4.
dx.doi.org/10.17504/protocols.io.yxmvme7eog3p/v1
Nuclear coordinate generation
5.
dx.doi.org/10.17504/protocols.io.dm6gpz8z8lzp/v1
Register the nuclear coordinates and Construct 3D cell matrix
6.
dx.doi.org/10.17504/protocols.io.n2bvjnrnxgk5/v1
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