Visium
Mouse liver
GSM5764422
silver Interactive viewer H&E metabolic dysfunction-associated steatotic liver disease No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5764422_hires_image': DataArray[cyx] (3, 1927, 2000)
│ └── 'GSM5764422_lowres_image': DataArray[cyx] (3, 578, 600)
├── Shapes
│ └── 'GSM5764422': GeoDataFrame shape: (2254, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2254, 31053)
with coordinate systems:
▸ 'GSM5764422', with elements:
GSM5764422_hires_image (Images), GSM5764422_lowres_image (Images), GSM5764422 (Shapes)
▸ 'GSM5764422_downscaled_hires', with elements:
GSM5764422_hires_image (Images), GSM5764422 (Shapes)
▸ 'GSM5764422_downscaled_lowres', with elements:
GSM5764422_lowres_image (Images), GSM5764422 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("3D8xAXJmvcyP6iV3") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3D8xAXJmvcyP6iV3
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3D8xAXJmvcyP6iV3 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["3D8xAXJmvcyP6iV30000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)→ 15 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- liver
- Condition
- metabolic dysfunction-associated steatotic liver disease
- Modality
- RNA
- Observations
- 2,254
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,927 px
- mpp
- 3.801 µm/px
- Size
- 38 MB
- Sample ID
- GSM5764422
- License
- unknown
- Published
- Jan 11, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB