lazyslide.seg.cell_types

cell_types(wsi, model='nulite', tile_key='tiles', transform=None, batch_size=4, num_workers=0, device=None, pbar=True, key_added='cell_types')

Cell type segmentation for the whole slide image.

Note

Tiles should be prepared before segmentation.

Recommended tile setting:

• nulite: mpp=0.5 or 0.25

Parameters:

wsiWSIData

The WSIData object to work on.

modelstr | SegmentationModel, default: “nulite”

The cell type segmentation model.

tile_keystr, default: “tiles”

The key of the tile table.

transformcallable, default: None

The transformation for the input tiles.

batch_sizeint, default: 4

The batch size for segmentation.

num_workersint, default: 0

The number of workers for data loading.

devicestr, default: None

The device for the model.

pbarbool, default: True

Whether to show a progress bar during segmentation.

key_addedstr, default: “cell_types”

The key for the added cell type shapes.