lazyslide.pp.tile_tissues

tile_tissues(wsi, tile_px, *, stride_px=None, overlap=None, edge=False, mpp=None, slide_mpp=None, ops_level=None, background_filter=True, background_fraction=0.3, background_filter_mode='approx', tissue_key='tissues', key_added='tiles', return_tiles=False)

Generate tiles within the tissue contours in the WSI.

If there is no tissue contours, the tiles will generate for the whole image.

Parameters:

wsiWSIData

The WSIData object to work on.

tile_pxint, (int, int)

The size of the tile, if tuple, (W, H).

stride_pxint, (int, int), default: None

The stride of the tile, if tuple, (W, H). If None, use the tile size.

overlapfloat, default: None

The overlap of the tiles, exclusive with stride_px. If in (0, 1), it’s the overlap ratio. If > 1, it’s the overlap in pixels.

edgebool, default: False

Whether to include the edge tiles.

mppfloat, default: None

The requested mpp of the tiles, if None, use the slide mpp.

slide_mppfloat, default: None

This value will override the slide mpp.

ops_levelint, default: None

Which level to use for the actual tile image retrival.

background_filterbool, default: True

Whether to filter the tiles based on the background fraction.

background_fractionfloat, default: 0.3

Only used if background_filter is True. The fraction of background in the tile, if more than this, discard the tile.

background_filter_mode{‘approx’, ‘exact’}, default: ‘approx’

The mode of the background filter. If ‘approx’, it will filter out tiles that are on the border of the tissue. If ‘exact’, it will filter out tiles that are not within the tissue, but it may be much slower for smaller tiles.

tissue_keystr, default ‘tissue’

The key of the tissue contours.

key_addedstr, default ‘tiles’

The key of the tiles. If set to None, the tiles will not be added to the WSIData object.

return_tilesbool, default: False

Return the tiles dataframe.

Returns:

geopandas.GeoDataFrame

The tiles dataframe with columns tissue_id, tile_id, and geometry. Added to shapes.

TileSpec

The tile specification used to create the tiles. Added to attrs with key tile_spec.

Examples

>>> import lazyslide as zs
>>> wsi = zs.datasets.sample()
>>> zs.pp.find_tissues(wsi)
>>> zs.pp.tile_tissues(wsi, 256, mpp=0.5)
>>> zs.pl.tiles(wsi, linewidth=0.5)