Spatial functions

Tissue segmentation

detect_tissue_threshold(adata[, size, low, high])	Detect the tissue boundary using a thresholding method.
get_approx_tissue_boundary(adata[, size, ...])	Compute approx tissue.
get_tissue_boundary(adata[, threshold_low, ...])	Detect the tissue boundary.
get_tissue_contour_score(cntr, adata[, size])	Get the score of a contour.

Geometries

get_geom(adata[, threshold, inplace, res])	Get the tissue polygons and tissue boundary from the sample image.
get_spot_coords(adata[, subset, as_tuple, ...])	Get the spot coordinates in the image.
get_visium_spots(adata[, with_radius, res])	Return a GeoSeries of the spots in the Visium slide.
set_geometry(adata, geom[, values, index, ...])	Set the geometry of the AnnData object.
to_points(x, y[, data, scale, radius])	Create a GeoSeries from x and y coordinates.
to_spatial_weights(adata[, graph_name])	Convert a graph adjacency matrix to a spatial weights matrix.

Image transformation

These functions allow rotating and mirroring the tissue images. These functions perform the same transformations on the spot coordinates.

apply_transforms(adata)	Apply unapplied image transforms.
cancel_transforms(adata)	Cancel unapplied image transforms.
mirror_img(adata[, apply, k, axis])	Mirror the image along an axis.
rollback_transforms(adata[, apply])	Rollback all transformations.
rotate_img90(adata[, apply, k, axis])	Rotate the image by 90 degrees k times.

Metrics and neighbours

compute_spatial_lag(adata, feature[, ...])	Compute the spatial lag of a feature.
local_moran(adata, feature[, inplace, ...])	Compute local Moran's I for a feature.
losh(adata, feature[, graph_name, ...])	Compute LOSH for a feature.
moran(adata, feature[, graph_name, layer, ...])	Compute Moran's I.

Graphs

compute_correlogram(adata, feature[, ...])	Compute the correlogram of a feature.
compute_higher_order_neighbors(adata[, ...])	Compute higher order neighbors of graph.
get_default_graph(adata)	Get the default graph for spatial operations.
set_default_graph(adata, graph_name)	Set the default graph for spatial operations.