10x Xenium
Human oropharynx
GSM9054476
bronze Interactive viewer oropharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 10324, 14313), (1, 5162, 7156), (1, 2581, 3578), (1, 1290, 1789), (1, 645, 894)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (10018, 13711), (5009, 6855), (2504, 3427), (1252, 1713), (626, 856)
│ └── 'nucleus_labels': DataTree[yx] (9966, 13300), (4983, 6650), (2491, 3325), (1245, 1662), (622, 831)
├── Points
│ └── 'transcripts': DataFrame with shape: (5547646, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (34060, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (34060, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (35166, 2) (2D shapes)
└── Tables
└── 'table': AnnData (34060, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("JHU3rvlNauk7MMMa0000")
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("JHU3rvlNauk7MMMa") # 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 JHU3rvlNauk7MMMa0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/JHU3rvlNauk7MMMa
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JHU3rvlNauk7MMMaLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oropharynx
- Condition
- oropharynx squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 34,060
- Transcripts
- 5,547,646
- Tier
- bronze
- Size
- 477 MB
- Sample ID
- GSM9054476
- 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