10x Xenium
Human pleura
GSM9654049
bronze Interactive viewer pleural mesothelioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23930, 19979), (1, 11965, 9989), (1, 5982, 4994), (1, 2991, 2497), (1, 1495, 1248)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23873, 19744), (11936, 9872), (5968, 4936), (2984, 2468), (1492, 1234)
│ └── 'nucleus_labels': DataTree[yx] (23866, 19294), (11933, 9647), (5966, 4823), (2983, 2411), (1491, 1205)
├── Points
│ └── 'transcripts': DataFrame with shape: (14369196, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (102892, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (102892, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (102875, 2) (2D shapes)
└── Tables
└── 'table': AnnData (102892, 477)
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("Ow1UP2hvxYHn6zfe0000")
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("Ow1UP2hvxYHn6zfe") # 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 Ow1UP2hvxYHn6zfe0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Ow1UP2hvxYHn6zfe
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Ow1UP2hvxYHn6zfeLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- pleura
- Condition
- pleural mesothelioma
- Modality
- RNA
- Observations (cells)
- 102,892
- Transcripts
- 14,369,196
- Tier
- bronze
- Size
- 1.2 GB
- Sample ID
- GSM9654049
- License
- NCBI GEO policy
- Published
- Apr 8, 2026
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