10x Xenium
Human common carotid artery plus branches
GSM8907629
bronze Interactive viewer atherosclerosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 37462, 31314), (1, 18731, 15657), (1, 9365, 7828), (1, 4682, 3914), (1, 2341, 1957)
│ └── 'morphology_mip': DataTree[cyx] (1, 37462, 31314), (1, 18731, 15657), (1, 9365, 7828), (1, 4682, 3914), (1, 2341, 1957)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37462, 31314), (18731, 15657), (9365, 7828), (4682, 3914), (2341, 1957)
│ └── 'nucleus_labels': DataTree[yx] (37462, 31314), (18731, 15657), (9365, 7828), (4682, 3914), (2341, 1957)
├── Points
│ └── 'transcripts': DataFrame with shape: (2331333, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (16496, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (16496, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (16496, 1) (2D shapes)
└── Tables
└── 'table': AnnData (16496, 345)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), 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("xmScvMGIoDpW9eC70000")
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("xmScvMGIoDpW9eC7") # 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 xmScvMGIoDpW9eC70000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/xmScvMGIoDpW9eC7
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xmScvMGIoDpW9eC7License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- common carotid artery plus branches
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (cells)
- 16,496
- Transcripts
- 2,331,333
- Tier
- bronze
- Size
- 2.3 GB
- Sample ID
- GSM8907629
- License
- NCBI GEO policy
- Published
- Nov 4, 2025
Cite this dataset
doi.org/10.1038/s41467-025-67679-4 ↗ BibTeX
@article{geo:GSM8907629,
doi = {10.1038/s41467-025-67679-4},
title = {GSM8907629},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB