HEImagingDataset#

class spora_io.datasets.he.HEImagingDataset(name, resolution, path=None, load_cell_metadata=False, verbose=True, mean_std_type='imagenet', tile_size=None, tile_strategy=None, split=None, **kwargs)[source]#

Bases: BaseImagingDataset

Class for handling H&E stained imaging datasets.

Parameters:

  • name (str)

  • resolution (float | str)

  • path (os.PathLike | str | None)

  • load_cell_metadata (bool)

  • verbose (bool)

  • mean_std_type (str)

  • tile_size (Optional[int])

  • tile_strategy (Optional[str])

  • split (Optional[str])

IMAGENET_MEAN#

The mean values for ImageNet normalization.

Type:

torch.Tensor

IMAGENET_STD#

The standard deviation values for ImageNet normalization.

Type:

torch.Tensor

HIBOU_MEAN#

The mean values for HIBOU normalization.

Type:

torch.Tensor

HIBOU_STD#

The standard deviation values for HIBOU normalization.

Type:

torch.Tensor

IDENTITY_MEAN#

The mean values for identity normalization.

Type:

torch.Tensor

IDENTITY_STD#

The standard deviation values for identity normalization.

Type:

torch.Tensor

mean_std_type#

The type of mean and standard deviation to use for normalization. Valid options are “imagenet”, “hibou”, and “identity”.

Type:

str

get_tissue(tissue_id, kind='complete', preprocess=True, image_mode='CHW')[source]#

Get the normalized tissue image post filtering channels for a given tissue id.

Parameters:

  • tissue_id (str) – The tissue ID to retrieve the image for.

  • kind (str) – The kind of tissue image to retrieve. Only “complete” is supported for H&E datasets since there is only one modality channel. Default is “complete”.

  • preprocess (bool) – If True, preprocess the image (normalize). Default is True.

Returns:

HETissue: The normalized tissue image as an HETissue instance.

get_tile_by_coordinates(tissue_id, row, col, kind='complete', image_mode='CHW', preprocess=True)[source]#

Get a specific tile based on the tissue id and tile id

Parameters:

  • tissue_id (str) – The tissue ID to retrieve the tile for.

  • row (int) – The row coordinate of the tile.

  • col (int) – The column coordinate of the tile.

  • kind (str) – The kind of tile image to retrieve. Default is “complete”.

  • image_mode (str) – The image mode of the tile image. Valid options are “CHW” and “HWC”. Default is “CHW”.

  • preprocess (bool) – If True, preprocess the image (normalize). Default is True.

Returns:

HETissue: The specific tile as an HETissue instance.

get_tile(tissue_id, tile_id, kind='complete', image_mode='CHW', preprocess=True)[source]#

Get a specific tile based on the tissue id and tile id

Parameters:

  • tissue_id (str) – The tissue ID to retrieve the tile for.

  • tile_id (int) – The tile ID to retrieve.

  • kind (str)

  • image_mode (str)

  • preprocess (bool)

Returns:

HETissue: The specific tile as an HETissue instance.