This repository is designed to provide an in-depth introduction to deep learning on whole slide images. It assumes the user is familiar with the basics of Python, PyTorch and deep learning. The full walkthrough is provided in this notebook, and a related slideshow walkthrough is provided in microsoft powerpoint and PDF formats.
The notebook walkthrough uses a toy dataset made up of four TCGA WSI files. All TCGA .svs slide files can be downloaded from the TCGA data portal https://portal.gdc.cancer.gov/. The four used for this notebook are:
WSIs/
.../MSI-H/
.../.../TCGA-5M-AAT6-01Z-00-DX1.8834C952-14E3-4491-8156-52FC917BB014.svs
.../.../TCGA-5M-AATE-01Z-00-DX1.483FFD2F-61A1-477E-8F94-157383803FC7.svs
.../MSS/
.../.../TCGA-3L-AA1B-01Z-00-DX1.8923A151-A690-40B7-9E5A-FCBEDFC2394F.svs
.../.../TCGA-4N-A93T-01Z-00-DX1.82E240B1-22C3-46E3-891F-0DCE35C43F8B.svs