Visium
Human coronary artery
GSM8658915
silver Interactive viewer H&E atherosclerosis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8658915_sample4d1_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8658915_sample4d1_hires_image': DataArray[cyx] (3, 2000, 1887)
│ └── 'GSM8658915_sample4d1_lowres_image': DataArray[cyx] (3, 600, 566)
├── Shapes
│ └── 'GSM8658915_sample4d1': GeoDataFrame shape: (1359, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1359, 18085)
with coordinate systems:
▸ 'GSM8658915_sample4d1', with elements:
GSM8658915_sample4d1_full_image (Images), GSM8658915_sample4d1_hires_image (Images), GSM8658915_sample4d1_lowres_image (Images), GSM8658915_sample4d1 (Shapes)
▸ 'GSM8658915_sample4d1_downscaled_hires', with elements:
GSM8658915_sample4d1_hires_image (Images), GSM8658915_sample4d1 (Shapes)
▸ 'GSM8658915_sample4d1_downscaled_lowres', with elements:
GSM8658915_sample4d1_lowres_image (Images), GSM8658915_sample4d1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("4AhdjBRW4TObInmF0000")
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("4AhdjBRW4TObInmF") # 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 4AhdjBRW4TObInmF0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/4AhdjBRW4TObInmF
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 4AhdjBRW4TObInmFLicense: CC BY 4.0
Part of collection
Spatial Gene Expression of Human Coronary Arteries Revealed the Molecular Features of Diffuse Intimal Thickening in Explanted Hearts→ 6 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- coronary artery
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (spots)
- 1,359
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 1,887 × 2,000 px
- mpp
- 2.490 µm/px
- Size
- 25.7 MB
- Sample ID
- GSM8658915
- License
- CC BY 4.0
- Published
- Feb 11, 2025
Cite this dataset
doi.org/10.3390/ijms26051949 ↗ BibTeX
@article{Li_2025,
title = {Spatial Gene Expression of Human Coronary Arteries Revealed the Molecular Features of Diffuse Intimal Thickening in Explanted Hearts},
volume = {26},
ISSN = {1422-0067},
url = {http://dx.doi.org/10.3390/ijms26051949},
DOI = {10.3390/ijms26051949},
number = {5},
journal = {International Journal of Molecular Sciences},
publisher = {MDPI AG},
author = {Li, Boaz and Leung, Samuel and Elishaev, Maria and Cheng, Wan Hei and Mocci, Giuseppe and Björkegren, Johan L. M. and Lai, Chi and Singh, Amrit and Wang, Ying},
year = {2025},
month = Feb,
pages = {1949}
}Source: NCBI GEO ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB