10x Xenium
Human subcutaneous adipose tissue
GSM8959877
bronze Interactive viewer obesity disorder Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27349, 22862), (1, 13674, 11431), (1, 6837, 5715), (1, 3418, 2857), (1, 1709, 1428)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (25955, 22056), (12977, 11028), (6488, 5514), (3244, 2757), (1622, 1378)
│ └── 'nucleus_labels': DataTree[yx] (25815, 21916), (12907, 10958), (6453, 5479), (3226, 2739), (1613, 1369)
├── Points
│ └── 'transcripts': DataFrame with shape: (620385, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (10372, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (10372, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (10372, 1) (2D shapes)
└── Tables
└── 'table': AnnData (10372, 477)
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("bYJIY2QiAu3tcJcA") # 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/bYJIY2QiAu3tcJcA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid bYJIY2QiAu3tcJcA Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["bYJIY2QiAu3tcJcA0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- subcutaneous adipose tissue
- Condition
- obesity disorder
- Modality
- RNA
- Observations
- 10,372
- Transcripts
- 620,385
- Tier
- bronze
- Size
- 508 MB
- Sample ID
- GSM8959877
- License
- unknown
- Published
- Jun 19, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB