API

Preprocessing

pp.create_grid_squares(sdata[, layer, ...])	Generate a grid of square polygons covering the transcript space.
pp.aggregate_urna(sdata[, layer, gene_key, ...])	Aggregate urna transcript counts into a grid of squares.
pp.compute_extracellular_counts(data_extracell)	Compute observed, expected, and fold ratio for extracellular transcript counts.
pp.define_urna(sdata[, layer, method, ...])	Identifies unassigned transcripts based on the specified method and updates the spatial data object accordingly.
pp.filter_urna(sdata[, min_counts, ...])	Filters xRNA based on specified criteria and updates the sdata object.
pp.format_adata(input_path, outpath_dummy, ...)	Processes and formats AnnData and transcripts by loading data, merging cell information,applying spatial filters, and saving the processed data to a dummy output directory.