10x Xenium
Human larynx
GSM9589059
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 10330, 45430), (1, 5165, 22715), (1, 2582, 11357), (1, 1291, 5678), (1, 645, 2839)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (8975, 42924), (4487, 21462), (2243, 10731), (1121, 5365), (560, 2682)
│ └── 'nucleus_labels': DataTree[yx] (8835, 42784), (4417, 21392), (2208, 10696), (1104, 5348), (552, 2674)
├── Points
│ └── 'transcripts': DataFrame with shape: (2843520, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (8377, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (8377, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (8377, 1) (2D shapes)
└── Tables
└── 'table': AnnData (8377, 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("28kZ7wLmuzgGW0SP") # 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/28kZ7wLmuzgGW0SP
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 28kZ7wLmuzgGW0SP Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["28kZ7wLmuzgGW0SP0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- larynx
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 8,377
- Transcripts
- 2,843,520
- Tier
- bronze
- Size
- 440 MB
- Sample ID
- GSM9589059
- 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