10x Xenium
Human hypopharynx
GSM9054483
bronze Interactive viewer hypopharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13711, 14306), (1, 6855, 7153), (1, 3427, 3576), (1, 1713, 1788), (1, 856, 894)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13258, 12870), (6629, 6435), (3314, 3217), (1657, 1608), (828, 804)
│ └── 'nucleus_labels': DataTree[yx] (11929, 11941), (5964, 5970), (2982, 2985), (1491, 1492), (745, 746)
├── Points
│ └── 'transcripts': DataFrame with shape: (4832340, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (24109, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (24109, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (23943, 2) (2D shapes)
└── Tables
└── 'table': AnnData (24109, 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("3RYzw6sZ28BlCTFG0000")
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("3RYzw6sZ28BlCTFG") # 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 3RYzw6sZ28BlCTFG0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3RYzw6sZ28BlCTFG
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3RYzw6sZ28BlCTFGLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- hypopharynx
- Condition
- hypopharynx squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 24,109
- Transcripts
- 4,832,340
- Tier
- bronze
- Size
- 439 MB
- Sample ID
- GSM9054483
- 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