Visium
Mouse liver
GSM5764414
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5764414_hires_image': DataArray[cyx] (3, 2000, 1896)
│ └── 'GSM5764414_lowres_image': DataArray[cyx] (3, 600, 569)
├── Shapes
│ └── 'GSM5764414': GeoDataFrame shape: (1646, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1646, 31053)
with coordinate systems:
▸ 'GSM5764414', with elements:
GSM5764414_hires_image (Images), GSM5764414_lowres_image (Images), GSM5764414 (Shapes)
▸ 'GSM5764414_downscaled_hires', with elements:
GSM5764414_hires_image (Images), GSM5764414 (Shapes)
▸ 'GSM5764414_downscaled_lowres', with elements:
GSM5764414_lowres_image (Images), GSM5764414 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("m1v5TkXIzvkLNFS4") # 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/m1v5TkXIzvkLNFS4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid m1v5TkXIzvkLNFS4 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["m1v5TkXIzvkLNFS40000"])[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
- Modality
- RNA
- Observations
- 1,646
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,896 × 2,000 px
- mpp
- 4.071 µm/px
- Size
- 27 MB
- Sample ID
- GSM5764414
- 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