10x Xenium
Mouse spinal cord
GSM9687906
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 78158, 17126), (1, 39079, 8563), (1, 19539, 4281), (1, 9769, 2140), (1, 4884, 1070)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (78158, 15334), (39079, 7667), (19539, 3833), (9769, 1916), (4884, 958)
│ └── 'nucleus_labels': DataTree[yx] (78066, 15195), (39033, 7597), (19516, 3798), (9758, 1899), (4879, 949)
├── Points
│ └── 'transcripts': DataFrame with shape: (10213274, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (21978, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (21978, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (21978, 1) (2D shapes)
└── Tables
└── 'table': AnnData (21978, 300)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ootEpY3GOn3hWg8W0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ootEpY3GOn3hWg8W") # stem uid: Lamin resolves it to the latest version
sdata = artifact.load() # cache, then load into memory
group = artifact.open() # stream without downloading
path = artifact.cache() # sync into the local cache, returns the path Shell
# sddb client: download the .zarr into data/
sddb-cli download ootEpY3GOn3hWg8W0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ootEpY3GOn3hWg8W
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ootEpY3GOn3hWg8WLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- spinal cord
- Modality
- RNA
- Observations (cells)
- 21,978
- Transcripts
- 10,213,274
- Tier
- bronze
- Size
- 982 MB
- Sample ID
- GSM9687906
- License
- NCBI GEO policy
- Published
- Apr 28, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB