spateo-data-io

name	spateo-data-io
description	Read spatial transcriptomics data — 10 platforms + auto-detect

Stage 0: Data IO

Load spatial transcriptomics data from 10+ platforms into standardized AnnData format with .obsm["spatial"].

Quick Start

# Manual read — specify platform
python -m skills.01_data_io.manual_read --platform xenium --data-path ./data/xenium_outs/

# Auto-detect — let the tool figure out the platform
python -m skills.01_data_io.auto_read --data-path ./data/unknown_dataset/

Modules

manual_read.py — Platform-specific readers

Dispatch by platform name. Each reader wraps spateo.io.protocol_io.spatial.*.

from skills.01_data_io.manual_read import read_by_platform

adata = read_by_platform("xenium", "./data/xenium_outs/")
adata = read_by_platform("merfish", "./data/merfish/", counts_file="cell_by_gene.csv")

Supported platforms:

Key	Platform	Key File(s)
merfish	MERFISH	cell_by_gene.csv, cell_metadata.csv
seqfish	seqFISH	CxG CSV, coordinates CSV, DAPI TIFF
slideseq	Slide-seq	Standard output directory
starmap_plus	STARmap+	Expression/spatial CSVs
stereoseq	Stereo-seq	GEM file (binsize default=50)
stereoseq_agg	Stereo-seq agg	GEM file + image file
xenium	Xenium	10x outs directory
visium	Visium	10x Visium output
visium_hd	Visium HD	10x Visium HD binned output
openst	Open-ST	Open-ST output

auto_read.py — Auto-detect + batch read

from skills.01_data_io.auto_read import (
    detect_spatial_platform,
    read_auto_spatial_data,
    read_many_auto,
)

# Detect platform type
platform = detect_spatial_platform("./data/unknown/")

# Auto-detect + read
adata = read_auto_spatial_data("./data/unknown/")

# Batch read multiple directories
results = read_many_auto(["./data/dataset1/", "./data/dataset2/"])

Input/Output

Input: Platform-specific raw data directories/files. Output: AnnData object with .obsm["spatial"] containing 2D/3D coordinates.

Key Parameters

Parameter	Purpose	Default
data_path	Path to raw data directory	—
platform	Platform name (manual_read)	—
counts_file	Gene expression matrix filename	cell_by_gene.csv
binsize	Stereo-seq binning size	50
load_images	Load DAPI/tissue images	True

Troubleshooting

Problem	Fix
ImportError: spateo	Run bash skills/00_env_setup/setup.sh
File not found	Check data_path is absolute or relative to working dir
Platform not detected	Verify input directory contains expected files for the platform