pyXenium.io.XeniumImage

class XeniumImage(levels: 'list[Any]', axes: 'str', dtype: 'str', source_path: 'str', transform_kind: 'str' = 'affine', image_to_xenium_affine: 'list[list[float]] | None' = None, alignment_csv_path: 'str | None' = None, pixel_size_um: 'float | None' = None, keypoints_validation: 'dict[str, Any] | None'=None, metadata: 'dict[str, Any]'=<factory>)

Bases: object

Parameters:

• levels (list[Any])

• axes (str)

• dtype (str)

• source_path (str)

• transform_kind (str)

• image_to_xenium_affine (list[list[float]] | None)

• alignment_csv_path (str | None)

• pixel_size_um (float | None)

• keypoints_validation (dict[str, Any] | None)

• metadata (dict[str, Any])

__init__(levels, axes, dtype, source_path, transform_kind='affine', image_to_xenium_affine=None, alignment_csv_path=None, pixel_size_um=None, keypoints_validation=None, metadata=<factory>)

Parameters:

• levels (list[Any])

• axes (str)

• dtype (str)

• source_path (str)

• transform_kind (str)

• image_to_xenium_affine (list[list[float]] | None)

• alignment_csv_path (str | None)

• pixel_size_um (float | None)

• keypoints_validation (dict[str, Any] | None)

• metadata (dict[str, Any])

Return type:

None

Methods

__init__(levels, axes, dtype, source_path[, ...])
image_xy_to_xenium_pixel_xy(image_xy)
image_xy_to_xenium_um_xy(image_xy)
infer_level_downsamples(*[, rtol, atol])
level_chunk_shapes()
multiscale_shapes()
to_numpy_levels()
transform_metadata()
wsi_diagnostics(*[, image_key, canonical_source])
xenium_pixel_xy_to_image_xy(xenium_pixel_xy)
xenium_um_to_image_xy(xenium_um_xy)

Attributes

alignment_csv_path
image_to_xenium_affine
keypoints_validation
pixel_size_um
transform_kind
levels
axes
dtype
source_path
metadata

levels: list[Any]

axes: str

dtype: str

source_path: str

transform_kind: str = 'affine'

image_to_xenium_affine: list[list[float]] | None = None

alignment_csv_path: str | None = None

pixel_size_um: float | None = None

keypoints_validation: dict[str, Any] | None = None

metadata: dict[str, Any]

multiscale_shapes()

Return type:

list[tuple[int, …]]

to_numpy_levels()

Return type:

list[ndarray]

level_chunk_shapes()

Return type:

list[tuple[int, …] | None]

infer_level_downsamples(*, rtol=WSI_LEVEL_DOWNSAMPLE_RTOL, atol=WSI_LEVEL_DOWNSAMPLE_ATOL)

Parameters:

• rtol (float)

• atol (float)

Return type:

tuple[list[float] | None, list[str]]

wsi_diagnostics(*, image_key='he', canonical_source='internal_slide_store')

Parameters:

• image_key (str)

• canonical_source (str)

Return type:

dict[str, Any]

transform_metadata()

Return type:

dict[str, Any]

image_xy_to_xenium_pixel_xy(image_xy)

Parameters:

image_xy (Any)

Return type:

ndarray

xenium_pixel_xy_to_image_xy(xenium_pixel_xy)

Parameters:

xenium_pixel_xy (Any)

Return type:

ndarray

image_xy_to_xenium_um_xy(image_xy)

Parameters:

image_xy (Any)

Return type:

ndarray

xenium_um_to_image_xy(xenium_um_xy)

Parameters:

xenium_um_xy (Any)

Return type:

ndarray