10x Xenium
Human sural nerve
GSM8714496
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13699, 11456), (1, 6849, 5728), (1, 3424, 2864), (1, 1712, 1432), (1, 856, 716)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (11222, 9259), (5611, 4629), (2805, 2314), (1402, 1157), (701, 578)
│ └── 'nucleus_labels': DataTree[yx] (11082, 9119), (5541, 4559), (2770, 2279), (1385, 1139), (692, 569)
├── Points
│ └── 'transcripts': DataFrame with shape: (81983, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (4784, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (4784, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (4784, 1) (2D shapes)
└── Tables
└── 'table': AnnData (4784, 99)
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("cvEI7e9W4bsd7lgm") # 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/cvEI7e9W4bsd7lgm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cvEI7e9W4bsd7lgm Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["cvEI7e9W4bsd7lgm0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- sural nerve
- Modality
- RNA
- Observations
- 4,784
- Transcripts
- 81,983
- Tier
- bronze
- Size
- 163 MB
- Sample ID
- GSM8714496
- License
- unknown
- Published
- Jun 28, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB