10x Xenium
Human oral cavity
GSM9054478
bronze Interactive viewer oral cavity squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17110, 19970), (1, 8555, 9985), (1, 4277, 4992), (1, 2138, 2496), (1, 1069, 1248)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (16990, 18166), (8495, 9083), (4247, 4541), (2123, 2270), (1061, 1135)
│ └── 'nucleus_labels': DataTree[yx] (16891, 17663), (8445, 8831), (4222, 4415), (2111, 2207), (1055, 1103)
├── Points
│ └── 'transcripts': DataFrame with shape: (15457527, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (31707, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (31707, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (29186, 2) (2D shapes)
└── Tables
└── 'table': AnnData (31707, 476)
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("AqV14pPamZvVQ2GR") # 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/AqV14pPamZvVQ2GR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AqV14pPamZvVQ2GR Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["AqV14pPamZvVQ2GR0000"])[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
- 31,707
- Transcripts
- 15,457,527
- Tier
- bronze
- Size
- 922 MB
- Sample ID
- GSM9054478
- 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