Very simple, parallel Whole-Slide-Imaging Tiler for Digital Histopathology built using histolab and ray.
conda create -n wsi_env python=3.8
conda activate wsi_env
conda install -c conda-forge openslide
pip install -r requirements.txt
python wsi_tiler.py -h
usage: wsi_tiler.py [-h] [--tile_size TILE_SIZE] [--tissue_percent TISSUE_PERCENT] wsi_dir out_dir
Split Whole-Slide-Images into a set of smaller tiles.
positional arguments:
wsi_dir (Possibly nested) directory containing input WSIs.
out_dir Directory for tiles, reports, thumbnails, ray logs.
optional arguments:
-h, --help show this help message and exit
--tile_size TILE_SIZE
Specifies height and width of the resulting square tiles.
--tissue_percent TISSUE_PERCENT
Reject tiles containing less then `tissue_percent` tissue.
The tiler creates three separate directories tiles, score_reports, tiler_thumbnails in the user-specified out_dir directory.
The tiles directory contains all generated tiles from all WSIs found in wsi_dir. Tiles are saved with the pattern {slide.name}_tile_{tiles_counter}_level{level}_{x_ul_wsi}-{y_ul_wsi}-{x_br_wsi}-{y_br_wsi}.jpg where x_ul_wsi, y_ul_wsi, x_br_wsi, y_br_wsi describe the top-left and bottom-right pixel coordinates of the tile in the WSI.
The score_reports directory contains one .csv file for each WSI. For a given WSI, the table contains URIs to the resulting tiles associated with a combined Nuclei-Tissue-Detection score. This score can be useful for sampling images during training.
| Index | filename | score | scaled_score |
|---|---|---|---|
| 0 | C3L-00004-21_tile_0_level0_5450-14577-5962-15089.png | 0.156751 | 1 |
| 1 | C3L-00004-21_tile_1_level0_6986-13041-7498-13553.png | 0.154509 | 0.982271 |
| 2 | C3L-00004-21_tile_2_level0_7498-12017-8010-12529.png | 0.154412 | 0.9815 |
| 3 | C3L-00004-21_tile_3_level0_18762-10481-19274-10993.png | 0.153387 | 0.973393 |
| ... | ... | ... | ... |
The tiler_thumbnails directory contains a thumbnail for each WSI with extracted tiles as bounding boxes:
slide_status.csv is saved in the out_dir directory and indicates whether the tiling succeeded or failed for a given WSI. This can be handy when working with a large set of images.
Finally, all ray logs are saved by default in the temporary directory /tmp/wsi_tiler_ray_logs.