Visium
Human brain
GSM5420751
silver Interactive viewer H&E lung adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5420751_hires_image': DataArray[cyx] (3, 1867, 2000)
│ └── 'GSM5420751_lowres_image': DataArray[cyx] (3, 560, 600)
├── Shapes
│ └── 'GSM5420751': GeoDataFrame shape: (946, 2) (2D shapes)
└── Tables
└── 'table': AnnData (946, 36601)
with coordinate systems:
▸ 'GSM5420751', with elements:
GSM5420751_hires_image (Images), GSM5420751_lowres_image (Images), GSM5420751 (Shapes)
▸ 'GSM5420751_downscaled_hires', with elements:
GSM5420751_hires_image (Images), GSM5420751 (Shapes)
▸ 'GSM5420751_downscaled_lowres', with elements:
GSM5420751_lowres_image (Images), GSM5420751 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("dEcKdGwpfTXxAqcR") # 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/dEcKdGwpfTXxAqcR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dEcKdGwpfTXxAqcR Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["dEcKdGwpfTXxAqcR0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- lung adenocarcinoma
- Modality
- RNA
- Observations
- 946
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,867 px
- mpp
- 3.919 µm/px
- Size
- 15 MB
- Sample ID
- GSM5420751
- License
- unknown
- Published
- Aug 4, 2021
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB