10x Xenium
Human oral cavity
GSM9054480
bronze Interactive viewer oral cavity squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23906, 22816), (1, 11953, 11408), (1, 5976, 5704), (1, 2988, 2852), (1, 1494, 1426)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23205, 22253), (11602, 11126), (5801, 5563), (2900, 2781), (1450, 1390)
│ └── 'nucleus_labels': DataTree[yx] (21561, 21693), (10780, 10846), (5390, 5423), (2695, 2711), (1347, 1355)
├── Points
│ └── 'transcripts': DataFrame with shape: (26710050, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (86435, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (86435, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (85260, 2) (2D shapes)
└── Tables
└── 'table': AnnData (86435, 477)
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("Hhf1eFqNJMp57rGk0000")
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("Hhf1eFqNJMp57rGk") # 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 Hhf1eFqNJMp57rGk0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Hhf1eFqNJMp57rGk
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Hhf1eFqNJMp57rGkLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oral cavity
- Condition
- oral cavity squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 86,435
- Transcripts
- 26,710,050
- Tier
- bronze
- Size
- 1.7 GB
- Sample ID
- GSM9054480
- License
- NCBI GEO policy
- Published
- Aug 6, 2025
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