lazyslide.seg.cells

cells(wsi, model='instanseg', tile_key='tiles', transform=None, batch_size=4, num_workers=0, device=None, amp=None, autocast_dtype=None, size_filter=False, nucleus_size=(20, 1000), pbar=True, extract_features=False, key_added='cells', **model_kwargs)

cell segmentation for the whole slide image.

tile should be prepared before segmentation, the tile size should be reasonable (with mpp around 0.5) for the model to work properly

Supported models:

• instanseg [Goldsborough et al., 2024]

• cellpose [Stringer et al., 2021]

Parameters:

wsiWSIData

The WSIData object to work on.

modelstr or SegmentationModelProtocol, default: “instanseg”

The cell 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.

ampbool, optional

Whether to use automatic mixed precision.

autocast_dtypetorch.dtype, optional

The dtype for automatic mixed precision.

size_filterbool, default: False

Whether to filter cells by nucleus size.

nucleus_sizetuple of (int, int), default: (20, 1000)

The (min, max) nucleus size range in pixels for filtering. Only used when size_filter=True.

pbarbool, default: True

Whether to show a progress bar during segmentation.

extract_featuresbool, default: False

Whether to extract per-cell feature vectors from the model’s patch_token_map. Only available for ViT-based segmentation models (e.g. NuLite, HistoPLUS). If the model does not produce a patch_token_map, a warning is emitted and features are skipped.

key_addedstr, default: “cells”

The key for the added cell shapes.

Returns:

None

The cell shapes are added to the shapes slot of the WSIData object.