Visium
Human pancreas
GSM7021871
silver Interactive viewer H&E pancreatic ductal adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7021871_PanIN_PanIN_full_image': DataTree[cyx] (4, 1134, 2000), (4, 567, 1000), (4, 283, 500), (4, 141, 250), (4, 70, 125)
│ ├── 'GSM7021871_PanIN_PanIN_hires_image': DataArray[cyx] (3, 1134, 2000)
│ └── 'GSM7021871_PanIN_PanIN_lowres_image': DataArray[cyx] (3, 340, 600)
├── Shapes
│ └── 'GSM7021871_PanIN_PanIN': GeoDataFrame shape: (1872, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1872, 17943)
with coordinate systems:
▸ 'GSM7021871_PanIN_PanIN', with elements:
GSM7021871_PanIN_PanIN_full_image (Images), GSM7021871_PanIN_PanIN_hires_image (Images), GSM7021871_PanIN_PanIN_lowres_image (Images), GSM7021871_PanIN_PanIN (Shapes)
▸ 'GSM7021871_PanIN_PanIN_downscaled_hires', with elements:
GSM7021871_PanIN_PanIN_hires_image (Images), GSM7021871_PanIN_PanIN (Shapes)
▸ 'GSM7021871_PanIN_PanIN_downscaled_lowres', with elements:
GSM7021871_PanIN_PanIN_lowres_image (Images), GSM7021871_PanIN_PanIN (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("eV4esKGltygysVdz0000")
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("eV4esKGltygysVdz") # 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 eV4esKGltygysVdz0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/eV4esKGltygysVdz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid eV4esKGltygysVdzLicense: NCBI GEO policy
Part of collection
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces→ 3 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- pancreas
- Condition
- pancreatic ductal adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 1,872
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,134 px
- mpp
- 5.916 µm/px
- Size
- 30.6 MB
- Sample ID
- GSM7021871
- License
- NCBI GEO policy
- Published
- Apr 19, 2023
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