Visium
Human caudate lobe of liver
GSM5616008
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_hires_image': DataArray[cyx] (3, 2000, 1958)
│ └── 'GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_lowres_image': DataArray[cyx] (3, 600, 587)
├── Shapes
│ └── 'GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix': GeoDataFrame shape: (2265, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2265, 36601)
with coordinate systems:
▸ 'GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix', with elements:
GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_hires_image (Images), GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_lowres_image (Images), GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix (Shapes)
▸ 'GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_downscaled_hires', with elements:
GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_hires_image (Images), GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix (Shapes)
▸ 'GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_downscaled_lowres', with elements:
GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix_lowres_image (Images), GSM5616008_C73_D1_raw_counts_raw_feature_bc_matrix (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("E2O9fFGYbK8m4tPp0000")
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("E2O9fFGYbK8m4tPp") # 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 E2O9fFGYbK8m4tPp0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/E2O9fFGYbK8m4tPp
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid E2O9fFGYbK8m4tPpLicense: NCBI GEO policy
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- caudate lobe of liver
- Modality
- RNA
- Observations (spots)
- 2,265
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,958 × 2,000 px
- mpp
- 3.335 µm/px
- Size
- 25.0 MB
- Sample ID
- GSM5616008
- License
- NCBI GEO policy
- Published
- Oct 13, 2021
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