Visium
Human coronary artery
GSM7780296
bronze Interactive viewer H&E atherosclerosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7780296_Sample_1_hires_image': DataArray[cyx] (3, 1993, 2000)
│ └── 'GSM7780296_Sample_1_lowres_image': DataArray[cyx] (3, 598, 600)
├── Shapes
│ └── 'GSM7780296_Sample_1': GeoDataFrame shape: (2615, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2615, 17943)
with coordinate systems:
▸ 'GSM7780296_Sample_1', with elements:
GSM7780296_Sample_1_hires_image (Images), GSM7780296_Sample_1_lowres_image (Images), GSM7780296_Sample_1 (Shapes)
▸ 'GSM7780296_Sample_1_downscaled_hires', with elements:
GSM7780296_Sample_1_hires_image (Images), GSM7780296_Sample_1 (Shapes)
▸ 'GSM7780296_Sample_1_downscaled_lowres', with elements:
GSM7780296_Sample_1_lowres_image (Images), GSM7780296_Sample_1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("xfnllvs3p3mxlswc0000")
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("xfnllvs3p3mxlswc") # 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 xfnllvs3p3mxlswc0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/xfnllvs3p3mxlswc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xfnllvs3p3mxlswcLicense: NCBI GEO policy
Part of collection
Clonal proliferation of smooth muscle cell in human atherosclerosis→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- coronary artery
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (spots)
- 2,615
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,993 px
- mpp
- 3.576 µm/px
- Size
- 5.9 MB
- Sample ID
- GSM7780296
- License
- NCBI GEO policy
- Published
- Dec 4, 2023
Cite this dataset
doi.org/10.1161/ATVBAHA.123.319479 ↗ BibTeX
@article{geo:GSM7780296,
doi = {10.1161/ATVBAHA.123.319479},
title = {GSM7780296},
year = {2023}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB