10x Xenium
Human oral cavity
GSM9054479
bronze Interactive viewer oral cavity squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20511, 28491), (1, 10255, 14245), (1, 5127, 7122), (1, 2563, 3561), (1, 1281, 1780)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20044, 28490), (10022, 14245), (5011, 7122), (2505, 3561), (1252, 1780)
│ └── 'nucleus_labels': DataTree[yx] (19980, 28325), (9990, 14162), (4995, 7081), (2497, 3540), (1248, 1770)
├── Points
│ └── 'transcripts': DataFrame with shape: (21368190, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (62220, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (62220, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (59238, 2) (2D shapes)
└── Tables
└── 'table': AnnData (62220, 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("OPromFKVrFqQE87k") # 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/OPromFKVrFqQE87k
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid OPromFKVrFqQE87k Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["OPromFKVrFqQE87k0000"])[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
- 62,220
- Transcripts
- 21,368,190
- Tier
- bronze
- Size
- 1.4 GB
- Sample ID
- GSM9054479
- 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