10x Xenium
Human dentate gyrus of hippocampal formation
GSM9471166
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37659, 34251), (1, 18829, 17125), (1, 9414, 8562), (1, 4707, 4281), (1, 2353, 2140)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37423, 34129), (18711, 17064), (9355, 8532), (4677, 4266), (2338, 2133)
│ └── 'nucleus_labels': DataTree[yx] (37409, 34107), (18704, 17053), (9352, 8526), (4676, 4263), (2338, 2131)
├── Points
│ └── 'transcripts': DataFrame with shape: (218276834, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (63657, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (63657, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (63257, 2) (2D shapes)
└── Tables
└── 'table': AnnData (63657, 5011)
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("WMkFUZ5NnzTo5nm90000")
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("WMkFUZ5NnzTo5nm9") # 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 WMkFUZ5NnzTo5nm90000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/WMkFUZ5NnzTo5nm9
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WMkFUZ5NnzTo5nm9License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- dentate gyrus of hippocampal formation
- Modality
- RNA
- Observations (cells)
- 63,657
- Transcripts
- 218,276,834
- Tier
- silver
- Size
- 8.9 GB
- Sample ID
- GSM9471166
- License
- NCBI GEO policy
- Published
- Jan 30, 2026
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