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README.md

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 ---
 license: mit
+task_categories:
+- other
+tags:
+- spatial-transcriptomics
+- xenium
+- spatial-omics
+- bioinformatics
+pretty_name: DeepSpaceDB Xenium Preview
 ---
+
+# DeepSpaceDB Xenium Preview
+
+A collection of processed 10x Genomics Xenium spatial transcriptomics samples, curated from public GEO
+depositions and in-house runs, stored as [SpatialData](https://spatialdata.scverse.org/) zarr stores.
+
+**This is a small preview** of the full DeepSpaceDB Xenium collection: 3 human breast cancer samples
+(DSIDX00001-DSIDX00003, GEO series GSE243168). `metadata.csv` lists only these samples.
+
+## Structure
+
+```
+metadata.csv          # one row per sample: organ, condition, species, source, quality, etc.
+data/
+  DSIDX00001.zarr.zip  # one zipped SpatialData zarr store per sample
+  ...
+```
+
+Each `<id>.zarr.zip` is a [SpatialData](https://spatialdata.scverse.org/) store containing (where available):
+- `images`: `morphology_focus` (DAPI/nuclear stain) and `he_image` (H&E, aligned via an `Affine`
+  transform to the same coordinate space as the other elements)
+- `labels`: `cell_labels`, `nucleus_labels` (raster segmentation masks)
+- `shapes`: `cell_boundaries`, `nucleus_boundaries`, `cell_circles`
+- `points`: `transcripts` (per-molecule detections)
+- `tables`: `table` (cell x gene raw count matrix, AnnData)
+
+## Loading a sample
+
+`spatialdata.read_zarr()` cannot currently read directly from a `.zip` (this is an open upstream
+limitation - see [scverse/spatialdata#1141](https://github.com/scverse/spatialdata/pull/1141)) - extract
+first, then read normally:
+
+```python
+import zipfile
+import spatialdata as sd
+
+zipfile.ZipFile("DSIDX00001.zarr.zip").extractall("DSIDX00001.zarr")
+sdata = sd.read_zarr("DSIDX00001.zarr")
+```
+
+## Selecting samples by metadata
+
+`metadata.csv` lets you filter before downloading any zarr data:
+
+```python
+import pandas as pd
+from huggingface_hub import hf_hub_download
+
+meta = pd.read_csv(hf_hub_download(repo_id="vhoncharuk/DeepSpaceDB-Preview", repo_type="dataset", filename="metadata.csv"))
+breast_samples = meta[meta.organ == "breast"]
+
+for dsidx_id in breast_samples["id"]:
+    hf_hub_download(repo_id="vhoncharuk/DeepSpaceDB-Preview", repo_type="dataset", filename=f"data/{dsidx_id}.zarr.zip")
+```
+
+## Metadata columns
+
+`id` (internal accession), `sample_id` (GEO GSM or source sample name), `series_id` (GEO GSE, or
+source collection), `organism`, `condition` / `condition_detailed` (+ Disease Ontology IDs), `organ` /
+`organ_detailed` (+ UBERON IDs), `sex`, `age_or_stage`, `ethnicity_or_strain`, `description`, `source`,
+`URL`, `PMID`, `date_published`, `has_manual_annotation`, `platform`, `quality`.