API

spatialdata-io

I/O for the spatialdata project.

Readers

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)
mcmicro(path[, imread_kwargs, ...])	Read a Mcmicro output into a SpatialData object.
merscope(path[, vpt_outputs, z_layers, ...])	Read MERSCOPE data from Vizgen.
steinbock(path[, labels_kind, ...])	Read a Steinbock output into a SpatialData object.
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[, n_jobs, cells_as_circles, ...])	Read a 10X Genomics Xenium dataset into a SpatialData object.

Experimental readers

iss(path, raw_relative_path, ...[, ...])

Read Sanger ISS formatted dataset.

Conversion functions

Experimental conversion functions

from_legacy_anndata(adata)	Convert (legacy) spatial AnnData object to SpatialData object.
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.