API

i/o

io.load_merscope(path, slide_name[, ...])	Load vizgen merscope data as SpatialData object
io.load_xenium(path[, index_table, region, ...])	Load xenium data as SpatialData object
io.load_cosmx(path[, dataset_id, feature_key])	Load cosmx data as SpatialData object

Preprocessing

pp.run_scanpy(sdata[, min_counts, ...])	Filter and run scanpy analysis.
pp.scvi_annotate(ad_spatial, ad_ref[, ...])	Annotate anndata spatial cells using anndata cells reference using SCVI.
pp.sync_shape(sdata[, shape_key, table_key])	Synchronize shapes with table

Tools

tl.add_to_shapes(sdata, poly, name[, ...])	Add shape element to SpatialData.
tl.add_shapes_from_hdf5([sdata, path, ...])	Add shapes from cell boundaries hdf5 files to spatialdata object.
tl.add_to_points(sdata[, shape_key, ...])	Add anatomical shapes to sdata.
tl.get_sdata_polygon(sdata[, shape_key, ...])	SpatialData polygon object using sd.polygon_query()
tl.sdata_rotate(sdata[, rotation_angle, ...])	Apply a rotation to sdata object elements + [obs_x,obs_y] sdata.table.obs + sdata.table.obsm[obsm_key]
tl.sdata_querybox(sdata[, xmin, xmax, ymin, ...])	Subset an sdata object to the coordinates box received, then set origin to (x_origin,y_origin)
tl.scis_prop(adata[, group_by, group_only, ...])	Compute per zone celltype proportion between 2 conditions using replicate for statistical testing
tl.shapes_of_cell_type(sdata, celltype[, ...])	Extract shapes from a celltype.

Plotting

pl.plot_qc(sdata)	Plot quality control analysis.
pl.plot_sdata(sdata[, color_key, ...])	Plot sdata object (i.e. embedding and polygons).
pl.plot_multi_sdata(sdata[, color_key, save])	Plot sdata object (i.e. embedding and polygons).
pl.plot_shapes(shape[, title, only_max, ...])
pl.plot_shape_along_axis(sdata[, group_lst, ...])	Analyse cell types occurence and gene expression along x axis of a sdata polygon shape after an evenual rotation
pl.plot_per_groups(adata, clust_key[, size, ...])	Plot UMAP splitted by clust_key