10x Xenium
Human sural nerve
GSM8714495
bronze Interactive viewer polyneuropathy Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13700, 22775), (1, 6850, 11387), (1, 3425, 5693), (1, 1712, 2846), (1, 856, 1423)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (11551, 20431), (5775, 10215), (2887, 5107), (1443, 2553), (721, 1276)
│ └── 'nucleus_labels': DataTree[yx] (11410, 20291), (5705, 10145), (2852, 5072), (1426, 2536), (713, 1268)
├── Points
│ └── 'transcripts': DataFrame with shape: (252543, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (6411, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (6411, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (6411, 1) (2D shapes)
└── Tables
└── 'table': AnnData (6411, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("YbGmcduOZn2oXkhK0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("YbGmcduOZn2oXkhK") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download YbGmcduOZn2oXkhK0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/YbGmcduOZn2oXkhK
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YbGmcduOZn2oXkhKLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- sural nerve
- Condition
- polyneuropathy
- Modality
- RNA
- Observations (cells)
- 6,411
- Transcripts
- 252,543
- Tier
- bronze
- Size
- 171 MB
- Sample ID
- GSM8714495
- License
- NCBI GEO policy
- Published
- Jun 28, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB