Visium
Human pancreas
GSM8443453
silver Interactive viewer H&E pancreatic ductal adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8443453_PDAC-p5_hires_image': DataArray[cyx] (3, 1911, 2000)
│ └── 'GSM8443453_PDAC-p5_lowres_image': DataArray[cyx] (3, 574, 600)
├── Shapes
│ └── 'GSM8443453_PDAC-p5': GeoDataFrame shape: (4952, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4952, 17943)
with coordinate systems:
▸ 'GSM8443453_PDAC-p5', with elements:
GSM8443453_PDAC-p5_hires_image (Images), GSM8443453_PDAC-p5_lowres_image (Images), GSM8443453_PDAC-p5 (Shapes)
▸ 'GSM8443453_PDAC-p5_downscaled_hires', with elements:
GSM8443453_PDAC-p5_hires_image (Images), GSM8443453_PDAC-p5 (Shapes)
▸ 'GSM8443453_PDAC-p5_downscaled_lowres', with elements:
GSM8443453_PDAC-p5_lowres_image (Images), GSM8443453_PDAC-p5 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("CQudwo3X2zDrKlOf0000")
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("CQudwo3X2zDrKlOf") # 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 CQudwo3X2zDrKlOf0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/CQudwo3X2zDrKlOf
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CQudwo3X2zDrKlOfLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics on treatment-naïve pancreatic ductal adenocarcinoma (PDAC) patients→ 5 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- pancreas
- Condition
- pancreatic ductal adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 4,952
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,911 px
- mpp
- 3.787 µm/px
- Size
- 48.3 MB
- Sample ID
- GSM8443453
- License
- NCBI GEO policy
- Published
- Feb 1, 2025
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