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

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 CODE_ROOT & DATA_ROOT)

$ 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