10x Xenium
Human larynx
GSM9054482
bronze Interactive viewer laryngeal squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30688, 22821), (1, 15344, 11410), (1, 7672, 5705), (1, 3836, 2852), (1, 1918, 1426)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30562, 22788), (15281, 11394), (7640, 5697), (3820, 2848), (1910, 1424)
│ └── 'nucleus_labels': DataTree[yx] (29751, 21391), (14875, 10695), (7437, 5347), (3718, 2673), (1859, 1336)
├── Points
│ └── 'transcripts': DataFrame with shape: (16244332, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (59995, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (59995, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (59482, 2) (2D shapes)
└── Tables
└── 'table': AnnData (59995, 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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("WfoM2TpWiuVb5gC9") # 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/WfoM2TpWiuVb5gC9
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WfoM2TpWiuVb5gC9 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["WfoM2TpWiuVb5gC90000"])[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
- laryngeal squamous cell carcinoma
- Modality
- RNA
- Observations
- 59,995
- Transcripts
- 16,244,332
- Tier
- bronze
- Size
- 1.3 GB
- Sample ID
- GSM9054482
- License
- unknown
- Published
- Aug 6, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB