This repository contains a collection of bash and python scripts to download, preprocess, and classify hematoxylin and eosin (H&E) whole slide image (WSI) breast cancer slides by clinical subtype. This project was contributed to by University of Oregon Knight Campus Bioinformatic and Genomics Master's Program students - Sam Kupp, Davin Marro, Sophia Soriano, Pranav Muthuraman - in collaboration with mentors at the OHSU Knight Cancer Institute Goecks Lab - Cameron Watson and Dr. Allison Creason.
This repository contains the following directories and files:
- Environments: Contains yml files and a md file listing the conda and pip packages used for these scripts.
- Manifests: Contains the two initial The Cancer Genome Atlas (TCGA) manifest files - provided by OHSU project mentors
- final_TCGA_sample_manifest.txt: 875 TCGA H&E breast cancer slides with histological and clinical annotations for each image, along with unique slide IDs. Other breast cancer annotations are also included in this tab-separated file, but these are not used in this project.
- GDC_download_manifest.txt: 875 TCGA image filenames corresponding to each of the 875 slide IDs in the above manifest file.
- README_download_images.md: README file describing how to download TCGA images.
- Scripts: Contains the collection of scripts written for this project, along with accompanying README markdowns describing the usage script, and relevant background/supplementary information. Below is a table summarizing all scripts and READMEs in the order in which they are typically run:
| Script Name | Script README |
|---|---|
| Bash Command - See Manifests | README_download_images.md |
| transform_tile.py | README_transform_tile.md |
| img_preprocessing.py | README_img_preprocessing.md |
| balance.py | README_balance.md |
| resnet_HE_v5.py | README_resnet_HE_v5.md |
- Result_Images: Contains relevant result images generated over the course of the project, which are referenced and described in other markdowns throughout this repository.
- Goecks_BGMP_References.pdf: List of references consulted during this project.