Visium
Human pancreas
GSM8714184
silver Interactive viewer H&E pancreatic ductal adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8714184_PDXPt13_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8714184_PDXPt13_hires_image': DataArray[cyx] (3, 2000, 1367)
│ └── 'GSM8714184_PDXPt13_lowres_image': DataArray[cyx] (3, 600, 410)
├── Shapes
│ └── 'GSM8714184_PDXPt13': GeoDataFrame shape: (2108, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2108, 18085)
with coordinate systems:
▸ 'GSM8714184_PDXPt13', with elements:
GSM8714184_PDXPt13_full_image (Images), GSM8714184_PDXPt13_hires_image (Images), GSM8714184_PDXPt13_lowres_image (Images), GSM8714184_PDXPt13 (Shapes)
▸ 'GSM8714184_PDXPt13_downscaled_hires', with elements:
GSM8714184_PDXPt13_hires_image (Images), GSM8714184_PDXPt13 (Shapes)
▸ 'GSM8714184_PDXPt13_downscaled_lowres', with elements:
GSM8714184_PDXPt13_lowres_image (Images), GSM8714184_PDXPt13 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("5b9tAO4Z6kWxHBGZ0000")
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("5b9tAO4Z6kWxHBGZ") # 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 5b9tAO4Z6kWxHBGZ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5b9tAO4Z6kWxHBGZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5b9tAO4Z6kWxHBGZLicense: NCBI GEO policy
Part of collection
Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer→ 57 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- pancreas
- Condition
- pancreatic ductal adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 2,108
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,367 × 2,000 px
- mpp
- 11.292 µm/px
- Size
- 50.3 MB
- Sample ID
- GSM8714184
- License
- NCBI GEO policy
- Published
- Feb 21, 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