10x Xenium
Human pleura
GSM9052322
bronze Interactive viewer pleural mesothelioma Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (51044, 37027), (25522, 18513), (12761, 9256), (6380, 4628), (3190, 2314)
│ └── 'nucleus_labels': DataTree[yx] (51003, 36426), (25501, 18213), (12750, 9106), (6375, 4553), (3187, 2276)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (72028, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (72028, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (72688, 2) (2D shapes)
└── Tables
└── 'table': AnnData (72028, 339)
with coordinate systems:
▸ 'global', with elements:
cell_labels (Labels), nucleus_labels (Labels), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("j29ixumEwFN8eB6i0000")
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("j29ixumEwFN8eB6i") # 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 j29ixumEwFN8eB6i0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/j29ixumEwFN8eB6i
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid j29ixumEwFN8eB6iLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- pleura
- Condition
- pleural mesothelioma
- Modality
- RNA
- Observations (cells)
- 72,028
- Tier
- bronze
- Size
- 91.9 MB
- Sample ID
- GSM9052322
- License
- NCBI GEO policy
- Published
- Jun 30, 2025
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