bioptimus.runtime.models.tissue_seg - Bioptimus Documentation

Tissue segmentation server-side model. Loads the exported tissue segmentation checkpoint and produces per-pixel binary masks flattened to a 1-D output vector.

TissueSegModel

class TissueSegModel(checkpoint_name: str,
                     device: str = 'cuda',
                     model_root: Path = MODEL_ROOT)

Tissue segmentation model (512x512, MPP 8.0). Produces a flat (H*W,) binary mask output where each value is the probability of tissue at that pixel.

forward

def forward(requests: list[ModelRequest]) -> torch.Tensor

Runs segmentation returning flattened masks (legacy path).

List of tile requests.

Returns: Flattened mask tensor of shape (N, H*W).