Visium
Human carotid artery segment
GSM7727540
bronze Interactive viewer H&E atherosclerosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7727540_sample2_hires_image': DataArray[cyx] (3, 2000, 1998)
│ └── 'GSM7727540_sample2_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM7727540_sample2': GeoDataFrame shape: (1165, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1165, 17943)
with coordinate systems:
▸ 'GSM7727540_sample2', with elements:
GSM7727540_sample2_hires_image (Images), GSM7727540_sample2_lowres_image (Images), GSM7727540_sample2 (Shapes)
▸ 'GSM7727540_sample2_downscaled_hires', with elements:
GSM7727540_sample2_hires_image (Images), GSM7727540_sample2 (Shapes)
▸ 'GSM7727540_sample2_downscaled_lowres', with elements:
GSM7727540_sample2_lowres_image (Images), GSM7727540_sample2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("1Nz1fJMJLMHsBWXu0000")
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("1Nz1fJMJLMHsBWXu") # 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 1Nz1fJMJLMHsBWXu0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1Nz1fJMJLMHsBWXu
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1Nz1fJMJLMHsBWXuLicense: NCBI GEO policy
Part of collection
A Proteomic Atlas of Atherosclerosis: The Contribution of Proteoglycans to Sex Differences, Plaque Phenotypes and Outcomes→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- carotid artery segment
- Condition
- atherosclerosis
- Modality
- RNA
- Observations (spots)
- 1,165
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,998 × 2,000 px
- mpp
- 3.851 µm/px
- Size
- 6.2 MB
- Sample ID
- GSM7727540
- License
- NCBI GEO policy
- Published
- Aug 29, 2023
Cite this dataset
doi.org/10.1161/CIRCRESAHA.123.322590 ↗ BibTeX
@article{geo:GSM7727540,
doi = {10.1161/CIRCRESAHA.123.322590},
title = {GSM7727540},
year = {2023}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB