10x Xenium
Mouse heart left ventricle
GSM9460459
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13557, 16982), (6778, 8491), (3389, 4245), (1694, 2122), (847, 1061)
│ └── 'nucleus_labels': DataTree[yx] (13226, 16118), (6613, 8059), (3306, 4029), (1653, 2014), (826, 1007)
├── Points
│ └── 'transcripts': DataFrame with shape: (13596665, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (40747, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (40754, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (17563, 2) (2D shapes)
└── Tables
└── 'table': AnnData (40754, 475)
with coordinate systems:
▸ 'global', with elements:
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("3Yusb5qUV0L8tWzo0000")
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("3Yusb5qUV0L8tWzo") # 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 3Yusb5qUV0L8tWzo0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3Yusb5qUV0L8tWzo
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3Yusb5qUV0L8tWzoLicense: NCBI GEO policy
Part of collection
Spatiotemporal dynamics of the cardioimmune niche during lesion repair [spatial]→ 7 datasets · comparison
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- heart left ventricle
- Modality
- RNA
- Observations (cells)
- 40,754
- Transcripts
- 13,596,665
- Tier
- bronze
- Size
- 288 MB
- Sample ID
- GSM9460459
- License
- NCBI GEO policy
- Published
- Sep 22, 2025
Cite this dataset
doi.org/10.1038/s44161-025-00739-6 ↗ BibTeX
@article{geo:GSM9460459,
doi = {10.1038/s44161-025-00739-6},
title = {GSM9460459},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB