10x Xenium
Mouse lung
GSM9694502
bronze Interactive viewer cryptococcosis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37462, 39814), (1, 18731, 19907), (1, 9365, 9953), (1, 4682, 4976), (1, 2341, 2488)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37397, 39493), (18698, 19746), (9349, 9873), (4674, 4936), (2337, 2468)
│ └── 'nucleus_labels': DataTree[yx] (37319, 37655), (18659, 18827), (9329, 9413), (4664, 4706), (2332, 2353)
├── Points
│ └── 'transcripts': DataFrame with shape: (94102756, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (261309, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (261309, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (261038, 2) (2D shapes)
└── Tables
└── 'table': AnnData (261309, 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("3KkVQvS5BrVPsplw0000")
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("3KkVQvS5BrVPsplw") # 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 3KkVQvS5BrVPsplw0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3KkVQvS5BrVPsplw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3KkVQvS5BrVPsplwLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- lung
- Condition
- cryptococcosis
- Modality
- RNA
- Observations (cells)
- 261,309
- Transcripts
- 94,102,756
- Tier
- bronze
- Size
- 3.9 GB
- Sample ID
- GSM9694502
- License
- NCBI GEO policy
- Published
- Jun 29, 2026
Cite this dataset
doi.org/10.1038/s41467-026-73516-z ↗ BibTeX
@article{geo:GSM9694502,
doi = {10.1038/s41467-026-73516-z},
title = {GSM9694502},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB