10x Xenium
Human oral cavity
GSM9054485
bronze Interactive viewer oral cavity squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34070, 19996), (1, 17035, 9998), (1, 8517, 4999), (1, 4258, 2499), (1, 2129, 1249)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (33924, 19906), (16962, 9953), (8481, 4976), (4240, 2488), (2120, 1244)
│ └── 'nucleus_labels': DataTree[yx] (30802, 19638), (15401, 9819), (7700, 4909), (3850, 2454), (1925, 1227)
├── Points
│ └── 'transcripts': DataFrame with shape: (18131543, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (88466, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (88466, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (86474, 2) (2D shapes)
└── Tables
└── 'table': AnnData (88466, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("osgHwu8APbESFh3C0000")
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("osgHwu8APbESFh3C") # 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 osgHwu8APbESFh3C0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/osgHwu8APbESFh3C
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid osgHwu8APbESFh3CLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oral cavity
- Condition
- oral cavity squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 88,466
- Transcripts
- 18,131,543
- Tier
- bronze
- Size
- 1.6 GB
- Sample ID
- GSM9054485
- 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