spatial-loader

name	spatial-loader
description	Load spatial transcriptomics data from 10x Visium, Nanostring MERFISH, BGI Stereo-seq, and generic spatial formats.
allowed-tools	Read, Bash
compatibility	spatial transcriptomics

Spatial Data Loaders

When to Use

To load spatial transcriptomics data into AnnData format for downstream analysis.

Functions

load_visium(path, sample_id=None) -> AnnData

Loads 10x Visium data from the output directory. Expects filtered_feature_bc_matrix/ and spatial/ subdirectories. Uses scanpy.read_visium(). Adds spatial to adata.obsm.

load_merfish(path) -> AnnData

Loads Nanostring MERFISH data from CSV/parquet. Expects gene expression matrix with spatial coordinates (x, y). Returns AnnData with coordinates in adata.obsm["spatial"].

load_stereoseq(path) -> AnnData

Loads BGI Stereo-seq data from GEM file or sparse matrix. Returns AnnData with coordinates in adata.obsm["spatial"].

load_spatial(expression_path, coordinates_path=None, spatial_coords=None) -> AnnData

Generic spatial data loader. Accepts expression matrix (CSV/parquet) and either a coordinates file or numpy array of (x, y) positions.