10x Xenium
Human common carotid artery plus branches
GSM8907604
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 17102, 28466), (1, 8551, 14233), (1, 4275, 7116), (1, 2137, 3558), (1, 1068, 1779)
│ └── 'morphology_mip': DataTree[cyx] (1, 17102, 28466), (1, 8551, 14233), (1, 4275, 7116), (1, 2137, 3558), (1, 1068, 1779)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17102, 28466), (8551, 14233), (4275, 7116), (2137, 3558), (1068, 1779)
│ └── 'nucleus_labels': DataTree[yx] (17102, 28466), (8551, 14233), (4275, 7116), (2137, 3558), (1068, 1779)
├── Points
│ └── 'transcripts': DataFrame with shape: (505947, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (6576, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (6576, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (6576, 1) (2D shapes)
└── Tables
└── 'table': AnnData (6576, 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("CHrkJwH1CT4qyYxA0000")
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("CHrkJwH1CT4qyYxA") # 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 CHrkJwH1CT4qyYxA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/CHrkJwH1CT4qyYxA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CHrkJwH1CT4qyYxALicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- common carotid artery plus branches
- Modality
- RNA
- Observations (cells)
- 6,576
- Transcripts
- 505,947
- Tier
- bronze
- Size
- 799 MB
- Sample ID
- GSM8907604
- License
- NCBI GEO policy
- Published
- Nov 4, 2025
Cite this dataset
doi.org/10.1038/s41467-025-67679-4 ↗ BibTeX
@article{geo:GSM8907604,
doi = {10.1038/s41467-025-67679-4},
title = {GSM8907604},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB