Data Types

Tissue Types

class spora_io.datasets._types.HETissue(*, image, tissue_id, channels='RGB', kind='tissue')[source]

HETissue class to represent a H&E Tissue sample.

Parameters:

  • image (torch.Tensor | NDArray[np.float32])

  • tissue_id (str)

  • channels (str)

  • kind (str)

class spora_io.datasets._types.MultiplexTissue(*, image, tissue_id, kind='tissue', measured_mask, image_loading_mask, channel_names=None, uniprot_ids=None)[source]

MultiplexTissue class to represent a Multiplex Tissue sample.

Parameters:

  • image (torch.Tensor | NDArray[np.float32])

  • tissue_id (str)

  • kind (str)

  • measured_mask (NDArray[np.bool_] | None)

  • image_loading_mask (NDArray[np.bool_] | None)

  • channel_names (NDArray[np.str_] | None)

  • uniprot_ids (NDArray[np.object_] | None)

class spora_io.datasets._types.IHCTissue(*, image, tissue_id, channels='RGB', kind='tissue')[source]

IHCTissue class to represent an IHC Tissue sample.

Parameters:

  • image (torch.Tensor | NDArray[np.float32])

  • tissue_id (str)

  • channels (str)

  • kind (str)

class spora_io.datasets._types.ComposedTissue(*, tissue_id, modalities)[source]

ComposedTissue class to represent a tissue sample composed of multiple modalities.

Parameters:

Masks

class spora_io.datasets._types.TissueMask(*, mask, tissue_id)[source]

TissueMask class to represent a Tissue Mask sample.

Parameters:

  • mask (ndarray[tuple[Any, ...], dtype[bool]])

  • tissue_id (str)

class spora_io.datasets._types.CellMask(*, mask, tissue_id, mapping=None)[source]

Cell Segmentation/Instance Mask class to represent a Cell Segmentation/Instance Mask sample.

Parameters:

  • mask (ndarray[tuple[Any, ...], dtype[int64]])

  • tissue_id (str)

  • mapping (Dict[int, str] | None)