Stellaromics Pyxa demo dataset

Output from the Stellaromics Pyxa platform, used as a demo dataset for the spatialdata-io pyxa reader (experimental). No patient-identifiable information.

Datasets

Each folder is a self-contained dataset with the same layout.

Folder	Extent (x × y × z)	Cells	Transcripts	Size	Purpose
small/	~1310 × 443 × 130 µm	4,372	395,667	~290 MB	full demo region
xsmall/	100 × 100 × 100 µm crop	187	23,495	~8 MB	CI tests and quick visual checks

xsmall/ is generated from small/ by scripts/make_xsmall.py: the cube spans x ∈ [900, 1000), y ∈ [-5140, -5040), z ∈ [20, 120) µm. Cells whose centroid falls inside the cube are kept whole (all of their segmentation polygons and assigned transcripts, so the per-cell counts stay consistent with the transcripts); unassigned transcripts and the DAPI mosaic are cropped to the cube.

Files

• cell_assigned_gene_v1.csv: transcript-level gene assignments (points layer). Unassigned transcripts have a cell_id ending in _-1.
• cell_by_gene_v1.csv: per-cell gene expression counts (table layer).
• cell_metadata_v1.csv: per-cell metadata (volume, spatial coordinates).
• segmentation_geometries_v1.parquet: per-cell, per-z-plane segmentation polygons (shapes layer), in pixel units.
• mosaic_3d.ome.zarr.zip: multiscale DAPI mosaic image (OME-Zarr v0.5, zipped per Hugging Face's Zarr storage guidance).

Usage

import zipfile

from huggingface_hub import snapshot_download
from spatialdata_io.experimental import pyxa

local_dir = snapshot_download("Stellaromics/demo", repo_type="dataset", allow_patterns="xsmall/*")
data_dir = f"{local_dir}/xsmall"
zipfile.ZipFile(f"{data_dir}/mosaic_3d.ome.zarr.zip").extractall(data_dir)

sdata = pyxa(data_dir, image_path=f"{data_dir}/mosaic_3d.ome.zarr")

Replace xsmall with small for the full region.

License

BSD 3-Clause.