Visium
Human lung
GSM5255579
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5255579_L1_hires_image': DataArray[cyx] (3, 2000, 1960)
│ └── 'GSM5255579_L1_lowres_image': DataArray[cyx] (3, 600, 588)
├── Shapes
│ └── 'GSM5255579_L1': GeoDataFrame shape: (1591, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1591, 36601)
with coordinate systems:
▸ 'GSM5255579_L1', with elements:
GSM5255579_L1_hires_image (Images), GSM5255579_L1_lowres_image (Images), GSM5255579_L1 (Shapes)
▸ 'GSM5255579_L1_downscaled_hires', with elements:
GSM5255579_L1_hires_image (Images), GSM5255579_L1 (Shapes)
▸ 'GSM5255579_L1_downscaled_lowres', with elements:
GSM5255579_L1_lowres_image (Images), GSM5255579_L1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("UoJkW2aDLjuKKhSa0000")
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("UoJkW2aDLjuKKhSa") # 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 UoJkW2aDLjuKKhSa0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/UoJkW2aDLjuKKhSa
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid UoJkW2aDLjuKKhSaLicense: NCBI GEO policy
Part of collection
Cell type inference in human lung tissue by domain adaptation of single-cell and spatial transcriptomic data→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lung
- Modality
- RNA
- Observations (spots)
- 1,591
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,960 × 2,000 px
- mpp
- 3.332 µm/px
- Size
- 21.3 MB
- Sample ID
- GSM5255579
- License
- NCBI GEO policy
- Published
- Jun 15, 2022
Cite this dataset
doi.org/10.1093/nar/gkac084 ↗ BibTeX
@article{geo:GSM5255579,
doi = {10.1093/nar/gkac084},
title = {GSM5255579},
year = {2022}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB