10x Xenium
Human oropharynx
GSM9589065
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20483, 8653), (1, 10241, 4326), (1, 5120, 2163), (1, 2560, 1081), (1, 1280, 540)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20436, 6311), (10218, 3155), (5109, 1577), (2554, 788), (1277, 394)
│ └── 'nucleus_labels': DataTree[yx] (20296, 6172), (10148, 3086), (5074, 1543), (2537, 771), (1268, 385)
├── Points
│ └── 'transcripts': DataFrame with shape: (2283312, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (18837, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (18837, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (18837, 1) (2D shapes)
└── Tables
└── 'table': AnnData (18837, 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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("jjNvUT1cxYGF0zzY") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/jjNvUT1cxYGF0zzY
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid jjNvUT1cxYGF0zzY Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["jjNvUT1cxYGF0zzY0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oropharynx
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 18,837
- Transcripts
- 2,283,312
- Tier
- bronze
- Size
- 281 MB
- Sample ID
- GSM9589065
- License
- unknown
- Published
- May 11, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB