pyXenium.io.XeniumSlide

class XeniumSlide(table: 'ad.AnnData', points: 'dict[str, pd.DataFrame]'=<factory>, shapes: 'dict[str, pd.DataFrame]'=<factory>, images: 'dict[str, XeniumImage]'=<factory>, contour_images: 'dict[str, dict[str, XeniumImage]]'=<factory>, metadata: 'dict[str, Any]'=<factory>, point_sources: 'dict[str, XeniumFrameChunkSource]'=<factory>)

Bases: object

Parameters:

• table (AnnData)

• points (dict[str, DataFrame])

• shapes (dict[str, DataFrame])

• images (dict[str, XeniumImage])

• contour_images (dict[str, dict[str, XeniumImage]])

• metadata (dict[str, Any])

• point_sources (dict[str, XeniumFrameChunkSource])

__init__(table, points=<factory>, shapes=<factory>, images=<factory>, contour_images=<factory>, metadata=<factory>, point_sources=<factory>)

Parameters:

• table (AnnData)

• points (dict[str, DataFrame])

• shapes (dict[str, DataFrame])

• images (dict[str, XeniumImage])

• contour_images (dict[str, dict[str, XeniumImage]])

• metadata (dict[str, Any])

• point_sources (dict[str, XeniumFrameChunkSource])

Return type:

None

Methods

__init__(table[, points, shapes, images, ...])
component_summary()
inspect_wsi([image_key])
to_anndata()
to_spatialdata()
to_wsi_spatialdata([image_key])
to_wsidata([image_key])

Attributes

table
points
shapes
images
contour_images
metadata
point_sources

table: AnnData

points: dict[str, DataFrame]

shapes: dict[str, DataFrame]

images: dict[str, XeniumImage]

contour_images: dict[str, dict[str, XeniumImage]]

metadata: dict[str, Any]

point_sources: dict[str, XeniumFrameChunkSource]

to_anndata()

Return type:

AnnData

inspect_wsi(image_key='he')

Parameters:

image_key (str)

Return type:

dict[str, Any]

to_wsidata(image_key='he')

Parameters:

image_key (str)

to_wsi_spatialdata(image_key='he')

Parameters:

image_key (str)

to_spatialdata()

component_summary()

Return type:

dict[str, list[str]]