10x Xenium
Human oropharynx
GSM9589062
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37408, 14360), (1, 18704, 7180), (1, 9352, 3590), (1, 4676, 1795), (1, 2338, 897)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (35419, 13134), (17709, 6567), (8854, 3283), (4427, 1641), (2213, 820)
│ └── 'nucleus_labels': DataTree[yx] (35280, 13013), (17640, 6506), (8820, 3253), (4410, 1626), (2205, 813)
├── Points
│ └── 'transcripts': DataFrame with shape: (2163805, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (11845, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (11845, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (11845, 1) (2D shapes)
└── Tables
└── 'table': AnnData (11845, 377)
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("cKr2RfvttFU1zvy10000")
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("cKr2RfvttFU1zvy1") # 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 cKr2RfvttFU1zvy10000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/cKr2RfvttFU1zvy1
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cKr2RfvttFU1zvy1License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oropharynx
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 11,845
- Transcripts
- 2,163,805
- Tier
- bronze
- Size
- 441 MB
- Sample ID
- GSM9589062
- License
- NCBI GEO policy
- Published
- May 11, 2026
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