10x Xenium
Mouse submandibular gland
GSM9401279
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27290, 34149), (1, 13645, 17074), (1, 6822, 8537), (1, 3411, 4268), (1, 1705, 2134)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (25695, 29849), (12847, 14924), (6423, 7462), (3211, 3731), (1605, 1865)
│ └── 'nucleus_labels': DataTree[yx] (25671, 29819), (12835, 14909), (6417, 7454), (3208, 3727), (1604, 1863)
├── Points
│ └── 'transcripts': DataFrame with shape: (33864567, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (171943, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (171943, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (168689, 2) (2D shapes)
└── Tables
└── 'table': AnnData (171943, 5006)
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("40pnlPN6rhVJwP4l0000")
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("40pnlPN6rhVJwP4l") # 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 40pnlPN6rhVJwP4l0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/40pnlPN6rhVJwP4l
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 40pnlPN6rhVJwP4lLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- submandibular gland
- Modality
- RNA
- Observations (cells)
- 171,943
- Transcripts
- 33,864,567
- Tier
- bronze
- Size
- 1.9 GB
- Sample ID
- GSM9401279
- License
- NCBI GEO policy
- Published
- Aug 23, 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