10x Xenium
Human common carotid artery plus branches
GSM8907609
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 23945, 45415), (1, 11972, 22707), (1, 5986, 11353), (1, 2993, 5676), (1, 1496, 2838)
│ └── 'morphology_mip': DataTree[cyx] (1, 23945, 45415), (1, 11972, 22707), (1, 5986, 11353), (1, 2993, 5676), (1, 1496, 2838)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23945, 45415), (11972, 22707), (5986, 11353), (2993, 5676), (1496, 2838)
│ └── 'nucleus_labels': DataTree[yx] (23945, 45415), (11972, 22707), (5986, 11353), (2993, 5676), (1496, 2838)
├── Points
│ └── 'transcripts': DataFrame with shape: (261334, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (6776, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (6776, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (6776, 1) (2D shapes)
└── Tables
└── 'table': AnnData (6776, 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("dPJaB6x2hmJzU7Zl0000")
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("dPJaB6x2hmJzU7Zl") # 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 dPJaB6x2hmJzU7Zl0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/dPJaB6x2hmJzU7Zl
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dPJaB6x2hmJzU7ZlLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- common carotid artery plus branches
- Modality
- RNA
- Observations (cells)
- 6,776
- Transcripts
- 261,334
- Tier
- bronze
- Size
- 1.3 GB
- Sample ID
- GSM8907609
- License
- NCBI GEO policy
- Published
- Nov 4, 2025
Cite this dataset
doi.org/10.1038/s41467-025-67679-4 ↗ BibTeX
@article{geo:GSM8907609,
doi = {10.1038/s41467-025-67679-4},
title = {GSM8907609},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB