README.md

!!WORK IN PROGESS!!

Preprocessing of Whole Slides Images (WSI) histology data

Preprocess whole slides images and extracting tiles:

• Extracting tiles of H&E histology slides at different magnifications

Project organization

├── README.md
├── config
│   └── config_test.yaml
│
├── data
│   ├── tiles       
│   ├── processed      
│   └── raw  
│
├── images 
│
├── requirements.txt
│
├── setup.py           
│
├── src
│   ├── __init__.py
│   │
│   ├── utils.py
│   │
│   └── visualization
│       └── visualize.py
│
└── ...

Dataset:

Can found test examples on TCGA portal

Table of contents

Getting Started

Prerequisites

• Python >= 3.7.6 (tested)
• OpenSlide [1]
• QuPath [2]

Installation

Documentation

Example

Results

References

• [1] Goode, A., Gilbert, B., Harkes, J., Jukic, D., & Satyanarayanan, M. (2013). OpenSlide: A vendor-neutral software foundation for digital pathology. Journal of pathology informatics, 4. https://doi.org/10.4103/2153-3539.119005
• [2] Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017). https://doi.org/10.1038/s41598-017-17204-5