Read Spatial Data

Functions to read spatial transcriptomic data.

Build anndata from Visium data

build_adata_from_transcript_positions(paths_dict)	Builds an AnnData object from a detected_transcripts.csv (Merscope) or transcripts.csv (Xenium) file and saves it to a specified output path.
build_adata_from_visium(paths_dict[, hd])	Processes Visium data from input directories and saves the processed AnnData objects to specified output paths.

Add blank image to AnnData

add_blank_image_to_adata(adata[, platform])

Adds a dummy image to the AnnData object based on the platform specifications.

Other functions used under-the-hood to construct Anndata from spatial data

read_transcript_coords(file_path[, platform])	Reads the transcript locations from a CSV file and ensures it contains the necessary columns.
get_steps_and_coords(df, box_size, step_size)	Computes the number of steps and the top-left coordinates of each box.
populate_sparse_array(df, genes, step_size)	Populates a sparse array with gene counts.
process_gene_counts(file_path, box_size, ...)	Processes the gene counts from the CSV file.
create_anndata(sparse_array, genes, ...)	Creates an AnnData object from the sparse matrix and coordinates.