10x Xenium
Human subcutaneous adipose tissue
GSM8959874
bronze Interactive viewer obesity disorder Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30687, 31329), (1, 15343, 15664), (1, 7671, 7832), (1, 3835, 3916), (1, 1917, 1958)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (28827, 26942), (14413, 13471), (7206, 6735), (3603, 3367), (1801, 1683)
│ └── 'nucleus_labels': DataTree[yx] (28687, 26802), (14343, 13401), (7171, 6700), (3585, 3350), (1792, 1675)
├── Points
│ └── 'transcripts': DataFrame with shape: (1023614, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (7898, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (7898, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (7898, 1) (2D shapes)
└── Tables
└── 'table': AnnData (7898, 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("3XdpFcMccZIoNOjr") # 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/3XdpFcMccZIoNOjr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3XdpFcMccZIoNOjr Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["3XdpFcMccZIoNOjr0000"])[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
- 7,898
- Transcripts
- 1,023,614
- Tier
- bronze
- Size
- 548 MB
- Sample ID
- GSM8959874
- 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