Tiles in wsidata#

Tiles in wsidata is stored as a GeoDataFrame with an associated TileSpec object.

To extract tiles from a non-existing magnification level, the tiling operation in wsidata is recorded with following information:

  • User specifies the tile size and magnification level.

  • The actual tile size and magnification level are used to create the tiles.

  • The tile size at the level 0.

Noted that wsidata cannot create tiles, it can only record the information for generating tiles. Please use LazySlide to create tiles.

from huggingface_hub import hf_hub_download

s = hf_hub_download("RendeiroLab/LazySlide-data", "sample.svs", repo_type="dataset")

from wsidata import TileSpec, open_wsi

wsi = open_wsi(s)

wsi.properties

Slide Properties

FieldValue
shape[2967, 2220]
n_level1
level_shape[[2967, 2220]]
level_downsample[1.0]
mpp0.499
magnification20.0
bounds[0, 0, 2220, 2967]

Here we have a wsi with only one level with mpp=0.5

If we want to request a tile size of 100x100 at level 0, the tile operation will be performed at level 0 with a tile size of 100x100.

TileSpec.from_wsidata(wsi, 100)

Tile 1

Tile 2

Tile 3

Tile at: 0.499 mpp
Tile size: 100×100 (h×w)
Stride: 100×100 (0×0 overlap)
Operation size: 100×100, level=0
Base size: 100×100, level=0
Target tissue: 'None'

However, if we request a tile size of 100x100 at mpp=1, but mpp=1 doesn’t exist in the original image. The tile operation will be performed at level 0 with a tile size of 200x200 and rescaled to 100x100.

TileSpec.from_wsidata(wsi, 100, mpp=1)

Tile 1

Tile 2

Tile 3

Tile at: 1 mpp
Tile size: 100×100 (h×w)
Stride: 100×100 (0×0 overlap)
Operation size: 200×200, level=0
Base size: 200×200, level=0
Target tissue: 'None'

Of course, tiles with overlapping is also supported

TileSpec.from_wsidata(wsi, 100, stride_px=50)

Tile 1

Tile 2

Tile 3

Tile at: 0.499 mpp
Tile size: 100×100 (h×w)
Stride: 50×50 (50×50 overlap)
Operation size: 100×100, level=0
Base size: 100×100, level=0
Target tissue: 'None' 
TileSpec.from_wsidata(wsi, 100, overlap=0.1)

Tile 1

Tile 2

Tile 3

Tile at: 0.499 mpp
Tile size: 100×100 (h×w)
Stride: 90×90 (10×10 overlap)
Operation size: 100×100, level=0
Base size: 100×100, level=0
Target tissue: 'None'

If you want to create a new tile table manually, please remember to synchronize the TileSpec with it.

import numpy as np

from wsidata.io import add_tiles, sync_tile_spec

add_tiles(
    wsi,
    "tiles",
    np.random.randint(0, 255, (100, 2), dtype=np.int32),
    tile_spec=TileSpec.from_wsidata(wsi, 25),
    tissue_ids=np.random.randint(0, 2, 100),
)

wsi["new_tiles"] = wsi["tiles"].sample(10)
sync_tile_spec(wsi, "tiles", "new_tiles")