10x Xenium
Human subcutaneous adipose tissue
GSM8959878
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23956, 28470), (1, 11978, 14235), (1, 5989, 7117), (1, 2994, 3558), (1, 1497, 1779)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23393, 25969), (11696, 12984), (5848, 6492), (2924, 3246), (1462, 1623)
│ └── 'nucleus_labels': DataTree[yx] (23253, 25830), (11626, 12915), (5813, 6457), (2906, 3228), (1453, 1614)
├── Points
│ └── 'transcripts': DataFrame with shape: (1664803, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (6059, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (6059, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (6059, 1) (2D shapes)
└── Tables
└── 'table': AnnData (6059, 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("kR0wHC5A9hnHGKkM") # 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/kR0wHC5A9hnHGKkM
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kR0wHC5A9hnHGKkM Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["kR0wHC5A9hnHGKkM0000"])[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
- Modality
- RNA
- Observations
- 6,059
- Transcripts
- 1,664,803
- Tier
- bronze
- Size
- 500 MB
- Sample ID
- GSM8959878
- 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