10x Xenium
Human oropharynx
GSM9054475
bronze Interactive viewer oropharynx squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20503, 14303), (1, 10251, 7151), (1, 5125, 3575), (1, 2562, 1787), (1, 1281, 893)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20370, 14008), (10185, 7004), (5092, 3502), (2546, 1751), (1273, 875)
│ └── 'nucleus_labels': DataTree[yx] (19858, 12777), (9929, 6388), (4964, 3194), (2482, 1597), (1241, 798)
├── Points
│ └── 'transcripts': DataFrame with shape: (13152390, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (43759, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (43759, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (45156, 2) (2D shapes)
└── Tables
└── 'table': AnnData (43759, 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("M93Yxjzoczr9ekFO0000")
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("M93Yxjzoczr9ekFO") # 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 M93Yxjzoczr9ekFO0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/M93Yxjzoczr9ekFO
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid M93Yxjzoczr9ekFOLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oropharynx
- Condition
- oropharynx squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 43,759
- Transcripts
- 13,152,390
- Tier
- bronze
- Size
- 756 MB
- Sample ID
- GSM9054475
- 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