fetch-spatial 0.1.0

A regex-fueled parser that tries to let you input a single GEO Experiment accession number and get SpatialData objects for each of its Samples.

Fetch-Spatial: A SpatialData builder from GEO Experiment entries

Fetch-Spatial is a helper package to try and make downloading and using spatial transcriptomics data from GEO less painful.

After installing it, you should be able to call python -m fetch_spatial GSE123456 path/to/outdir and get an organized folder with the raw input data, one SpatialData.zarr object for each Sample in the Experiment, and a single Report.json file that tells you what pieces of the SpatialData were and were not parse-able.

Note: Currently, only Xenium data is supported, but we hope to add more formats soon

This function returns SpatialData objects even if they are missing images, boundaries, or expression data, so make sure you check the Report.json file to see what actually happened before trying to use the files. We do this because most of the time, if a file is "missing", it's because the Sample had a strange naming convention that we couldn't anticipate, but you can probably figure out which file it is on your own. Then, you have a somewhat-complete SpatialData object that you can just add whatever is missing to using the spatialdata_io package.

Note that spatial transcriptomics files are very large sometimes, so make sure you have enough disk space to write everything. Additionally, this script writes many intermediate files to your /tmp directory (and then cleans them up); if your /tmp is not big enough, you can set SPATIAL_TMP as an environment variable to override where temporary files are written.