CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC

Kyu Sang Han, Pei-Hsun Wu, Sashank Reddy, Denis Wirtz, Joel Sunshine, Ashley Kiemen

Published: 2024-04-17 DOI: 10.17504/protocols.io.kqdg324xpv25/v2

CODA

deeplearning

semanticsegmentation

tissuemapping

annotation

machinelearning

AI 解读
浏览 1096

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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