10x Xenium
Human subcutaneous adipose tissue
GSM8959873
bronze Interactive viewer obesity disorder Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23902, 22879), (1, 11951, 11439), (1, 5975, 5719), (1, 2987, 2859), (1, 1493, 1429)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (19635, 20204), (9817, 10102), (4908, 5051), (2454, 2525), (1227, 1262)
│ └── 'nucleus_labels': DataTree[yx] (19495, 20068), (9747, 10034), (4873, 5017), (2436, 2508), (1218, 1254)
├── Points
│ └── 'transcripts': DataFrame with shape: (754748, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (2663, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (2663, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (2663, 1) (2D shapes)
└── Tables
└── 'table': AnnData (2663, 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("sWGt2t3ml8nkWP0l") # 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/sWGt2t3ml8nkWP0l
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid sWGt2t3ml8nkWP0l Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["sWGt2t3ml8nkWP0l0000"])[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
- 2,663
- Transcripts
- 754,748
- Tier
- bronze
- Size
- 346 MB
- Sample ID
- GSM8959873
- 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