10x Xenium
Mouse stomach
GSM9157703
silver Interactive viewer diffuse gastric adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 40881, 37007), (1, 20440, 18503), (1, 10220, 9251), (1, 5110, 4625), (1, 2555, 2312)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (40255, 36674), (20127, 18337), (10063, 9168), (5031, 4584), (2515, 2292)
│ └── 'nucleus_labels': DataTree[yx] (40227, 36627), (20113, 18313), (10056, 9156), (5028, 4578), (2514, 2289)
├── Points
│ └── 'transcripts': DataFrame with shape: (55571217, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (261111, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (261111, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (261111, 2) (2D shapes)
└── Tables
└── 'table': AnnData (261111, 479)
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("5OCfqYA3zQvgWL900000")
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("5OCfqYA3zQvgWL90") # 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 5OCfqYA3zQvgWL900000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5OCfqYA3zQvgWL90
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5OCfqYA3zQvgWL90License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- stomach
- Condition
- diffuse gastric adenocarcinoma
- Modality
- RNA
- Observations (cells)
- 261,111
- Transcripts
- 55,571,217
- Tier
- silver
- Size
- 4.2 GB
- Sample ID
- GSM9157703
- License
- NCBI GEO policy
- Published
- Jul 27, 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