Complete analysis pipeline for the segmentation & classification of structures / cells for LungMap images

This repository is meant to be a demonstration of how the microscopy-analysis-pipeline can be used to integrate with lungmap data to effect instance segmentation and classification of anatomical structures. As such, we provide several python scripts which demonstrate how to use the resources together. But first, to run the scripts, a little setup...

We assume a Python 3 environment with dependencies listed in the requirements.txt file.

pip install -r requirements.txt

For the python scripts to run properly, we assume that the lungmap data has been downloaded and symlinked as data into this repositories parent folder.

cd ~
git clone https://github.com/duke-lungmap-team/lungmap-image-data.git
cd /path/to/lungmap-pipeline
ln -s ~/lungmap-image-data data

Check the top of each script before running. Some scripts assume that other scripts have been run first. This is done to stash model objects or other metadata needed to produce further output.