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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Hhf1eFqNJMp57rGk") # 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 Load from the CLI
# one-shot: 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 Hhf1eFqNJMp57rGk Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Hhf1eFqNJMp57rGk0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oral cavity
- Condition
- oral cavity squamous cell carcinoma
- Modality
- RNA
- Observations
- 86,435
- Transcripts
- 26,710,050
- Tier
- bronze
- Size
- 1.6 GB
- Sample ID
- GSM9054480
- License
- unknown
- Published
- Aug 6, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB