10x Xenium
Mouse submandibular gland
GSM9401283
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37498, 31248), (1, 18749, 15624), (1, 9374, 7812), (1, 4687, 3906), (1, 2343, 1953)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37170, 30510), (18585, 15255), (9292, 7627), (4646, 3813), (2323, 1906)
│ └── 'nucleus_labels': DataTree[yx] (36994, 30070), (18497, 15035), (9248, 7517), (4624, 3758), (2312, 1879)
├── Points
│ └── 'transcripts': DataFrame with shape: (83306566, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (224696, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (224696, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (218935, 2) (2D shapes)
└── Tables
└── 'table': AnnData (224696, 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("umWjLIdogbVejDce0000")
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("umWjLIdogbVejDce") # 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 umWjLIdogbVejDce0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/umWjLIdogbVejDce
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid umWjLIdogbVejDceLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- submandibular gland
- Modality
- RNA
- Observations (cells)
- 224,696
- Transcripts
- 83,306,566
- Tier
- bronze
- Size
- 3.3 GB
- Sample ID
- GSM9401283
- License
- NCBI GEO policy
- Published
- Aug 23, 2026
Cite this dataset
doi.org/10.1016/j.isci.2026.117494 ↗ BibTeX
@article{geo:GSM9401283,
doi = {10.1016/j.isci.2026.117494},
title = {GSM9401283},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB