hutaobo/pyxenium-gsm9116572

GSM9116572 Xenium Demo (for pyXenium)

Source: NCBI GEO Sample GSM9116572 (Series GSE303048), originally distributed as GSM9116572_SSc_2_1_1_raw.tar.gz. This repo repackages the Xenium out/ subfolders into single-file archives (*.zarr.zip) for fast remote loading.

Attribution: Please cite the original GEO Series/Sample and associated publication(s).

Files

• analysis.zarr.zip
• cells.zarr.zip
• transcripts.zarr.zip
• (optional) mex/:
  • matrix.mtx.gz
  • features.tsv.gz
  • barcodes.tsv.gz

Load with pyXenium (remote URLs)

# Requires the v2 loader that supports base_url (partial_xenium_loader_v2.py)
from pyXenium.io.partial_xenium_loader import load_anndata_from_partial

BASE = "https://huggingface.co/datasets/hutaobo/pyxenium-gsm9116572/resolve/main"

adata = load_anndata_from_partial(
    base_url=BASE,
    analysis_name="analysis.zarr.zip",
    cells_name="cells.zarr.zip",
    transcripts_name="transcripts.zarr.zip",
    # If you also uploaded a MEX triplet:
    # mex_dir=BASE + "/mex",
    # mex_matrix_name="matrix.mtx.gz",
    # mex_features_name="features.tsv.gz",
    # mex_barcodes_name="barcodes.tsv.gz",
    build_counts_if_missing=True,
)
print(adata)