Visium
Mouse liver
GSM5764419
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5764419_hires_image': DataArray[cyx] (3, 1923, 2000)
│ └── 'GSM5764419_lowres_image': DataArray[cyx] (3, 577, 600)
├── Shapes
│ └── 'GSM5764419': GeoDataFrame shape: (1279, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1279, 31053)
with coordinate systems:
▸ 'GSM5764419', with elements:
GSM5764419_hires_image (Images), GSM5764419_lowres_image (Images), GSM5764419 (Shapes)
▸ 'GSM5764419_downscaled_hires', with elements:
GSM5764419_hires_image (Images), GSM5764419 (Shapes)
▸ 'GSM5764419_downscaled_lowres', with elements:
GSM5764419_lowres_image (Images), GSM5764419 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("1jad3lRjEfrUavNy0000")
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("1jad3lRjEfrUavNy") # 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 1jad3lRjEfrUavNy0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1jad3lRjEfrUavNy
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1jad3lRjEfrUavNyLicense: NCBI GEO policy
Part of collection
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)→ 15 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- liver
- Modality
- RNA
- Observations (spots)
- 1,279
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,923 px
- mpp
- 3.806 µm/px
- Size
- 24.8 MB
- Sample ID
- GSM5764419
- License
- NCBI GEO policy
- Published
- Jan 11, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB