10x Xenium
Human lung
GSM9714919
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 68066, 25701), (1, 34033, 12850), (1, 17016, 6425), (1, 8508, 3212), (1, 4254, 1606)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (67554, 23657), (33777, 11828), (16888, 5914), (8444, 2957), (4222, 1478)
│ └── 'nucleus_labels': DataTree[yx] (66542, 23486), (33271, 11743), (16635, 5871), (8317, 2935), (4158, 1467)
├── Points
│ └── 'transcripts': DataFrame with shape: (20155560, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (133729, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (133729, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (133277, 2) (2D shapes)
└── Tables
└── 'table': AnnData (133729, 387)
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("YdljavpeXE4k3fpm0000")
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("YdljavpeXE4k3fpm") # 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 YdljavpeXE4k3fpm0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/YdljavpeXE4k3fpm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YdljavpeXE4k3fpmLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Modality
- RNA
- Observations (cells)
- 133,729
- Transcripts
- 20,155,560
- Tier
- silver
- Size
- 2.3 GB
- Sample ID
- GSM9714919
- License
- NCBI GEO policy
- Published
- Aug 9, 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