10x Xenium
Mouse aorta
GSM9457959
bronze Interactive viewer atherosclerosis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 57816, 31287), (1, 28908, 15643), (1, 14454, 7821), (1, 7227, 3910), (1, 3613, 1955)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (56397, 29061), (28198, 14530), (14099, 7265), (7049, 3632), (3524, 1816)
│ └── 'nucleus_labels': DataTree[yx] (56369, 29059), (28184, 14529), (14092, 7264), (7046, 3632), (3523, 1816)
├── Points
│ └── 'transcripts': DataFrame with shape: (33480530, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (49909, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (49909, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (48979, 2) (2D shapes)
└── Tables
└── 'table': AnnData (49909, 5006)
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("JP3wHYFZ4qnkEJrV0000")
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("JP3wHYFZ4qnkEJrV") # 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 JP3wHYFZ4qnkEJrV0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/JP3wHYFZ4qnkEJrV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JP3wHYFZ4qnkEJrVLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- aorta
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (cells)
- 49,909
- Transcripts
- 33,480,530
- Tier
- bronze
- Size
- 1.6 GB
- Sample ID
- GSM9457959
- License
- NCBI GEO policy
- Published
- May 29, 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