lazyslide.pp.tile_graph

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lazyslide.pp.tile_graph#

tile_graph(wsi, n_neighs=6, n_rings=1, delaunay=False, transform=None, set_diag=False, tile_key='tiles', table_key=None)#

Compute the spatial graph of the tiles.

Parameters:
wsiWSIData

The WSIData object to work on.

n_neighsint, default: 6

The number of neighbors to consider.

n_ringsint, default: 1

The number of rings to consider.

delaunaybool, default: False

Whether to use Delaunay triangulation.

transformstr, default: None

The transformation to apply to the graph.

set_diagbool, default: False

Whether to set the diagonal to 1.

tile_keystr, default: ‘tiles’

The tile key.

table_keystr, default: None

The table key to store the graph.

Returns:
AnnData

The tiles with spatial connectivities and distances in an anndata format. | Added to tile_graph | {key_added} in tables slot of the WSIData object.

Examples

>>> import lazyslide as zs
>>> wsi = zs.datasets.sample()
>>> zs.pp.find_tissues(wsi)
>>> zs.pp.tile_graph(wsi)
>>> wsi['tile_graph']
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