10x Xenium
Human common carotid artery plus branches
GSM8907630
bronze Interactive viewer atherosclerosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 27277, 25660), (1, 13638, 12830), (1, 6819, 6415), (1, 3409, 3207), (1, 1704, 1603)
│ └── 'morphology_mip': DataTree[cyx] (1, 27277, 25660), (1, 13638, 12830), (1, 6819, 6415), (1, 3409, 3207), (1, 1704, 1603)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (27277, 25660), (13638, 12830), (6819, 6415), (3409, 3207), (1704, 1603)
│ └── 'nucleus_labels': DataTree[yx] (27277, 25660), (13638, 12830), (6819, 6415), (3409, 3207), (1704, 1603)
├── Points
│ └── 'transcripts': DataFrame with shape: (636217, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (16417, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (16417, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (16417, 1) (2D shapes)
└── Tables
└── 'table': AnnData (16417, 314)
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("5KN1QUU9pV7idkjQ0000")
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("5KN1QUU9pV7idkjQ") # 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 5KN1QUU9pV7idkjQ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5KN1QUU9pV7idkjQ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5KN1QUU9pV7idkjQLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- common carotid artery plus branches
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (cells)
- 16,417
- Transcripts
- 636,217
- Tier
- bronze
- Size
- 1.5 GB
- Sample ID
- GSM8907630
- License
- NCBI GEO policy
- Published
- Nov 4, 2025
Cite this dataset
doi.org/10.1038/s41467-025-67679-4 ↗ BibTeX
@article{geo:GSM8907630,
doi = {10.1038/s41467-025-67679-4},
title = {GSM8907630},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB