lazyslide.seg.cell_types#
- cell_types(wsi, model='nulite', tile_key='tiles', magnification=None, 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='cell_types')#
Cell type 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:
nulite: [Tommasino et al., 2024]
histoplus: [Adjadj et al., 2025]
- Parameters:
- wsi
WSIData 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.
- magnificationstr, default: None
The magnification of the model.
- 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.
- wsi