10x Xenium
Human hypopharynx
GSM9054484
bronze Interactive viewer hypopharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20493, 19975), (1, 10246, 9987), (1, 5123, 4993), (1, 2561, 2496), (1, 1280, 1248)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20254, 19955), (10127, 9977), (5063, 4988), (2531, 2494), (1265, 1247)
│ └── 'nucleus_labels': DataTree[yx] (20079, 19672), (10039, 9836), (5019, 4918), (2509, 2459), (1254, 1229)
├── Points
│ └── 'transcripts': DataFrame with shape: (9435449, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (37878, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (37878, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (37789, 2) (2D shapes)
└── Tables
└── 'table': AnnData (37878, 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("wQfReCBOmH5nMcNt0000")
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("wQfReCBOmH5nMcNt") # 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 wQfReCBOmH5nMcNt0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/wQfReCBOmH5nMcNt
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid wQfReCBOmH5nMcNtLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- hypopharynx
- Condition
- hypopharynx squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 37,878
- Transcripts
- 9,435,449
- Tier
- bronze
- Size
- 765 MB
- Sample ID
- GSM9054484
- 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