10x Xenium
Human common carotid artery plus branches
GSM8907622
bronze Interactive viewer atherosclerosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 34063, 31309), (1, 17031, 15654), (1, 8515, 7827), (1, 4257, 3913), (1, 2128, 1956)
│ └── 'morphology_mip': DataTree[cyx] (1, 34063, 31309), (1, 17031, 15654), (1, 8515, 7827), (1, 4257, 3913), (1, 2128, 1956)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (34063, 31309), (17031, 15654), (8515, 7827), (4257, 3913), (2128, 1956)
│ └── 'nucleus_labels': DataTree[yx] (34063, 31309), (17031, 15654), (8515, 7827), (4257, 3913), (2128, 1956)
├── Points
│ └── 'transcripts': DataFrame with shape: (2199652, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (14547, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (14547, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (14547, 1) (2D shapes)
└── Tables
└── 'table': AnnData (14547, 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("c1ATLQl1nPRGTPW00000")
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("c1ATLQl1nPRGTPW0") # 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 c1ATLQl1nPRGTPW00000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/c1ATLQl1nPRGTPW0
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid c1ATLQl1nPRGTPW0License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- common carotid artery plus branches
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (cells)
- 14,547
- Transcripts
- 2,199,652
- Tier
- bronze
- Size
- 1.7 GB
- Sample ID
- GSM8907622
- License
- NCBI GEO policy
- Published
- Nov 4, 2025
Cite this dataset
doi.org/10.1038/s41467-025-67679-4 ↗ BibTeX
@article{geo:GSM8907622,
doi = {10.1038/s41467-025-67679-4},
title = {GSM8907622},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB