Extracts tiles from whole slide images.
python tile.py COHORT_PATH -o OUTPATH
COHORT_PATH is a folder containing whole slide images.
| Input Variable name | Description |
|---|---|
| -o or --outdir | Path to the output folder where tiles are saved |
| --tile_size | The size of the output tiles in pixels, default int 224 |
| --um_per_tile | Size each tile spans in µm, default float 256.0 |
| --brightness-cutoff | Brightness past which tiles are rejected as background, default int 224 |
| -f or --force | Overwrite existing tile |
| --no-canny | Disable rejection of edge tiles. Useful for TMAs / sparse slides. |
NAME thumbnail.py - Extracts thumbnails from whole slide images.
SYNOPSIS thumbnail.py COHORT_PATH OUTPATH
DESCRIPTION Extracts thumbnails from whole slide images.
POSITIONAL ARGUMENTS COHORT_PATH Type: PathLike A folder containing whole slide images. OUTPATH Type: PathLike The output folder.
FLAGS --thumbnail_mpp=THUMBNAIL_MPP Type: float Default: 32.0 Micrometers per tile for the thumbnails. --force=FORCE Type: bool Default: False Overwrite already existing thumbnails.