10x Xenium
Mouse heart left ventricle
GSM9460461
bronze Interactive viewer heart disorder Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17068, 17049), (8534, 8524), (4267, 4262), (2133, 2131), (1066, 1065)
│ └── 'nucleus_labels': DataTree[yx] (13494, 16867), (6747, 8433), (3373, 4216), (1686, 2108), (843, 1054)
├── Points
│ └── 'transcripts': DataFrame with shape: (13398286, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (38890, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (38903, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (16360, 2) (2D shapes)
└── Tables
└── 'table': AnnData (38903, 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("RXBWt7DkGWOZzQfn0000")
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("RXBWt7DkGWOZzQfn") # 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 RXBWt7DkGWOZzQfn0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/RXBWt7DkGWOZzQfn
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid RXBWt7DkGWOZzQfnLicense: 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
- Condition
- heart disorder
- Modality
- RNA
- Observations (cells)
- 38,903
- Transcripts
- 13,398,286
- Tier
- bronze
- Size
- 282 MB
- Sample ID
- GSM9460461
- License
- NCBI GEO policy
- Published
- Sep 22, 2025
Cite this dataset
doi.org/10.1038/s44161-025-00739-6 ↗ BibTeX
@article{geo:GSM9460461,
doi = {10.1038/s44161-025-00739-6},
title = {GSM9460461},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB