API

This section documents the Application Programming Interface (API) for the spatialdata_io package.

spatialdata-io

I/O for the spatialdata project.

Readers

Spatial technologies

codex(path[, fcs, imread_kwargs])	Read CODEX formatted dataset.
cosmx(path[, dataset_id, transcripts, ...])	Read Cosmx Nanostring data.
curio(path)	Read Curio formatted dataset.
dbit([path, anndata_path, barcode_position, ...])	Read DBiT experiment data (Deterministic Barcoding in Tissue)
experimental.iss(path, raw_relative_path, ...)	Read Sanger ISS formatted dataset.
mcmicro(path[, imread_kwargs, ...])	Read a Mcmicro output into a SpatialData object.
merscope(path[, vpt_outputs, z_layers, ...])	Read MERSCOPE data from Vizgen.
seqfish(path[, load_images, load_labels, ...])	Read seqfish formatted dataset.
steinbock(path[, labels_kind, ...])	Read a Steinbock output into a SpatialData object.
stereoseq(path[, dataset_id, ...])	Read Stereo-seq formatted dataset.
visium(path[, dataset_id, counts_file, ...])	Read 10x Genomics Visium formatted dataset.
visium_hd(path[, dataset_id, ...])	Read 10x Genomics Visium HD formatted dataset.
xenium(path, *[, cells_boundaries, ...])	Read a 10X Genomics Xenium dataset into a SpatialData object.

Data types

generic(input[, data_axes, coordinate_system])	Read a generic shapes or image file and save it as SpatialData zarr.
image(input, data_axes, coordinate_system)	Reads an image file and returns a parsed Image2D spatial element
geojson(input, coordinate_system)	Reads a GeoJSON file and returns a parsed GeoDataFrame spatial element

Conversion functions

experimental.from_legacy_anndata(adata)	Convert (legacy) spatial AnnData object to SpatialData object.
experimental.to_legacy_anndata(sdata[, ...])	Convert a SpatialData object to a (legacy) spatial AnnData object.

Utility functions

xenium_aligned_image(image_path, alignment_file)	Read an image aligned to a Xenium dataset, with an optional alignment file.
xenium_explorer_selection(path[, ...])	Read the coordinates of a selection .csv file exported from the Xenium Explorer.