10x Xenium
Human lung
GSM9509137
bronze Interactive viewer squamous cell lung carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 20485, 25612), (4, 10242, 12806), (4, 5121, 6403), (4, 2560, 3201), (4, 1280, 1600)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (19865, 24127), (9932, 12063), (4966, 6031), (2483, 3015), (1241, 1507)
│ └── 'nucleus_labels': DataTree[yx] (19465, 23699), (9732, 11849), (4866, 5924), (2433, 2962), (1216, 1481)
├── Points
│ └── 'transcripts': DataFrame with shape: (33123987, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (64872, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (64872, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (65185, 2) (2D shapes)
└── Tables
└── 'table': AnnData (64872, 5001)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("cOjo8Fe6mVpB4Mu00000")
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("cOjo8Fe6mVpB4Mu0") # 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 cOjo8Fe6mVpB4Mu00000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/cOjo8Fe6mVpB4Mu0
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cOjo8Fe6mVpB4Mu0License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Condition
- squamous cell lung carcinoma
- Modality
- RNA
- Observations (cells)
- 64,872
- Transcripts
- 33,123,987
- Tier
- bronze
- Size
- 2.6 GB
- Sample ID
- GSM9509137
- License
- NCBI GEO policy
- Published
- Mar 27, 2026
Cite this dataset
doi.org/10.1038/s41592-026-03089-8 ↗ BibTeX
@article{geo:GSM9509137,
doi = {10.1038/s41592-026-03089-8},
title = {GSM9509137},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB