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https://github.com/cpathology/lungevolutionpathomics

Lung Preneoplasia Progression via Pathomics

https://github.com/cpathology/lungevolutionpathomics

Science Score: 13.0%

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    Found 2 DOI reference(s) in README
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    Low similarity (4.7%) to scientific vocabulary

Keywords

biomedical-image-analysis computational-pathology lung-cancer lung-preneoplasia neoplasm-evolution pathology-image pathomics
Last synced: 10 months ago · JSON representation

Repository

Lung Preneoplasia Progression via Pathomics

Basic Info
  • Host: GitHub
  • Owner: cpathology
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 18.5 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
biomedical-image-analysis computational-pathology lung-cancer lung-preneoplasia neoplasm-evolution pathology-image pathomics
Created over 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

LungEvolutionPathomics

Pipeline of investigating lung preneoplasia evolution via pathomics

  • Data to reproduce the results was deposited in Mendeley Data
  • NucleiSegHE was used to generate ROI-level nuclei segmentation
  • Pipeline illustrating the general study design of lung preneoplasia evolution via pathomics Pipeline of Lung Evolution Pathomics

Environment Configurations

a. Prepare docker image

  • Build from Dockerfile $ docker build -t lung_evolution_pathomics:chen .
  • Or pull from Docker Hub $ docker pull pingjunchen/lung_evolution_pathomics:chen $ docker tag pingjunchen/lung_evolution_pathomics:chen lung_evolution_pathomics:chen

b. Setup docker container

  • Start docker container (specify CODEROOT & DATAROOT) $ docker run -it --rm --user $(id -u):$(id -g) \ -v ${CODE_ROOT}:/App/LungEvolutionPathomics \ -v ${DATA_ROOT}:/Data \ --shm-size=168G --gpus '"device=0"' --cpuset-cpus=10-39 \ --name lung_evolution_pathomics_chen lung_evolution_pathomics:chen

Pathomic Features Evaluating Lung Preneoplasia Evolution

1. Evolution trends along with pathological stage progression

2. Correlation with a series of molecular markers

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