tcga2tile

This code is used to convert TCGA histopathology slide into image tiles.

Preparation

You may need to download the slides from TCGA before using the scripts in this repository.

Download code please refer to https://github.com/MarvinLer/tcga_segmentation

Data format

TCGA-Lung                                 # The directory of the data.
├─ TCGA-63-5128-01A-01-BS1.2635b7d6-bf3d-40b0-89c0-419f0e4d9fb2   
│  ├─ Large                               # The directory of image tiles in Level 0 (40X lens).
│  │  ├─ 0000_0000.jpg                    # The image tile in Row 0 and Column 0.
│  │  ├─ 0000_0001.jpg                    # The image tile in Row 0 and Column 1.
│  │  └─ ...
│  ├─ Medium                              # The directory of image tiles in Level 1 (20X lens).
│  │  ├─ 0000_0000.jpg
│  │  ├─ 0000_0001.jpg
│  │  └─ ...
│  ├─ Small                               # The directory of image tiles in Level 2 (10X lens).
│  │  ├─ 0000_0000.jpg
│  │  ├─ 0000_0001.jpg
│  │  └─ ...
│  ├─ Overview                            # The directory of image tiles in Level 3 (5X lens).
│  │  ├─ 0000_0000.jpg
│  │  ├─ 0000_0001.jpg
│  │  └─ ...
│  ├─ Overview.jpg                        # The thumbnail of the WSI in Level 3.      
│  ├─ Large.txt                           # The information of the WSI in Level 0.   
│  ├─ Medium.txt                          # The information of the WSI in Level 1.   
│  └─ Small.txt                           # The information of the WSI in Level 2.  
├─ TCGA-77-7138-01A-02-BS2.7ebacc9b-2f09-47d1-b3f5-01230b15b6b2
└─ ...

Convert slide to tiles

python main.py --tile-size 512 --overlap 0 --slide-file <path to save slide> <path to save tiles>