10x Xenium
Mouse lung
GSM9694495
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27281, 36957), (1, 13640, 18478), (1, 6820, 9239), (1, 3410, 4619), (1, 1705, 2309)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (25439, 36890), (12719, 18445), (6359, 9222), (3179, 4611), (1589, 2305)
│ └── 'nucleus_labels': DataTree[yx] (24952, 36855), (12476, 18427), (6238, 9213), (3119, 4606), (1559, 2303)
├── Points
│ └── 'transcripts': DataFrame with shape: (73439745, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (275665, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (275665, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (275599, 2) (2D shapes)
└── Tables
└── 'table': AnnData (275665, 5052)
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("VMjkgzU4MhiumsqQ0000")
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("VMjkgzU4MhiumsqQ") # 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 VMjkgzU4MhiumsqQ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VMjkgzU4MhiumsqQ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VMjkgzU4MhiumsqQLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- lung
- Modality
- RNA
- Observations (cells)
- 275,665
- Transcripts
- 73,439,745
- Tier
- bronze
- Size
- 3.2 GB
- Sample ID
- GSM9694495
- License
- NCBI GEO policy
- Published
- Jun 29, 2026
Cite this dataset
doi.org/10.1038/s41467-026-73516-z ↗ BibTeX
@article{geo:GSM9694495,
doi = {10.1038/s41467-026-73516-z},
title = {GSM9694495},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB