Visium
Human skin of body
GSM5531131
silver Interactive viewer H&E diabetes mellitus ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5531131_VS_NS5_hires_image': DataArray[cyx] (3, 2000, 1834)
│ └── 'GSM5531131_VS_NS5_lowres_image': DataArray[cyx] (3, 600, 550)
├── Shapes
│ └── 'GSM5531131_VS_NS5': GeoDataFrame shape: (2603, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2603, 33538)
with coordinate systems:
▸ 'GSM5531131_VS_NS5', with elements:
GSM5531131_VS_NS5_hires_image (Images), GSM5531131_VS_NS5_lowres_image (Images), GSM5531131_VS_NS5 (Shapes)
▸ 'GSM5531131_VS_NS5_downscaled_hires', with elements:
GSM5531131_VS_NS5_hires_image (Images), GSM5531131_VS_NS5 (Shapes)
▸ 'GSM5531131_VS_NS5_downscaled_lowres', with elements:
GSM5531131_VS_NS5_lowres_image (Images), GSM5531131_VS_NS5 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("5ZiTXbXv8HsFlSCK0000")
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("5ZiTXbXv8HsFlSCK") # 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 5ZiTXbXv8HsFlSCK0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5ZiTXbXv8HsFlSCK
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5ZiTXbXv8HsFlSCKLicense: NCBI GEO policy
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- diabetes mellitus
- Modality
- RNA
- Observations (spots)
- 2,603
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,834 × 2,000 px
- mpp
- 3.601 µm/px
- Size
- 14.3 MB
- Sample ID
- GSM5531131
- License
- NCBI GEO policy
- Published
- May 4, 2022
Cite this dataset
doi.org/10.2337/db21-0830 ↗ BibTeX
@article{geo:GSM5531131,
doi = {10.2337/db21-0830},
title = {GSM5531131},
year = {2022}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB