TileDBOpenSlide

bioimg.openslide.TileDBOpenSlide(self, uri, *, attr=ATTR_NAME, config=None, ctx=None)

Attributes

Name	Description
dimensions	A (width, height) tuple for level 0 of the slide.
level_count	Number of levels in the slide
level_dimensions	A sequence of (width, height) tuples, one for each level of the slide.
level_downsamples	A sequence of downsample factors for each level of the slide.
levels	Sequence of level numbers in the slide.
properties	Metadata about the slide

Methods

Name	Description
get_best_level_for_downsample	Return the best level for displaying the given downsample filtering by factor.
level_properties	Metadata about the given slide level
read_level	Return an image containing the contents of the specified level as NumPy array.
read_level_dask	Return an image containing the contents of the specified level as Dask array.
read_region	Return an image containing the contents of the specified region as NumPy array.

get_best_level_for_downsample

bioimg.openslide.TileDBOpenSlide.get_best_level_for_downsample(factor)

Return the best level for displaying the given downsample filtering by factor.

Parameters

Name	Type	Description	Default
factor	float	The factor of downsamples. Above this value downsamples are filtered out.	required

Returns

Type	Description
int	The number corresponding to a level

level_properties

bioimg.openslide.TileDBOpenSlide.level_properties(level)

Metadata about the given slide level

read_level

bioimg.openslide.TileDBOpenSlide.read_level(level, to_original_axes=False)

Return an image containing the contents of the specified level as NumPy array.

Parameters

Name	Type	Description	Default
level	int	the level number	required
to_original_axes	bool	If True return the image in the original axes, otherwise return it in YXC (height, width, channel) axes.	False

read_level_dask

bioimg.openslide.TileDBOpenSlide.read_level_dask(level, to_original_axes=False)

Return an image containing the contents of the specified level as Dask array.

Parameters

Name	Type	Description	Default
level	int	the level number	required
to_original_axes	bool	If True return the image in the original axes, otherwise return it in YXC (height, width, channel) axes.	False

read_region

bioimg.openslide.TileDBOpenSlide.read_region(location, level, size)

Return an image containing the contents of the specified region as NumPy array.

Parameters

Name	Type	Description	Default
location	Tuple[int, int]	(x, y) tuple giving the top left pixel in the level 0 reference frame	required
level	int	the level number	required
size	Tuple[int, int]	(width, height) tuple giving the region size	required

Returns

Type	Description
np.ndarray	3D (height, width, channel) Numpy array