lazyslide.seg.cells#
- cells(wsi, model='instanseg', tile_key='tiles', transform=None, batch_size=4, num_workers=0, device=None, size_filter=False, nucleus_size=(20, 1000), pbar=True, key_added='cells', **model_kwargs)#
Cell segmentation for the whole slide image.
Tiles 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:
- wsi
WSIData The WSIData object to work on.
- modelstr | SegmentationModel, 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.
- pbarbool, default: True
Whether to show a progress bar during segmentation.
- key_addedstr, default: “cells”
The key for the added cell shapes.
- wsi