10x Xenium
Human oropharynx
GSM9054477
bronze Interactive viewer oropharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17112, 11472), (1, 8556, 5736), (1, 4278, 2868), (1, 2139, 1434), (1, 1069, 717)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17112, 11331), (8556, 5665), (4278, 2832), (2139, 1416), (1069, 708)
│ └── 'nucleus_labels': DataTree[yx] (16261, 11112), (8130, 5556), (4065, 2778), (2032, 1389), (1016, 694)
├── Points
│ └── 'transcripts': DataFrame with shape: (8016032, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (29743, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (29743, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (30279, 2) (2D shapes)
└── Tables
└── 'table': AnnData (29743, 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("x5EMLKcBeVtxSFzQ") # 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/x5EMLKcBeVtxSFzQ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid x5EMLKcBeVtxSFzQ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["x5EMLKcBeVtxSFzQ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oropharynx
- Condition
- oropharynx squamous cell carcinoma
- Modality
- RNA
- Observations
- 29,743
- Transcripts
- 8,016,032
- Tier
- bronze
- Size
- 508 MB
- Sample ID
- GSM9054477
- 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