Visium
Human pancreas
GSM7498811
silver Interactive viewer H&E exocrine pancreatic carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_hires_image': DataArray[cyx] (3, 2000, 1954)
│ └── 'GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_lowres_image': DataArray[cyx] (3, 600, 586)
├── Shapes
│ └── 'GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed': GeoDataFrame shape: (3947, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3947, 17943)
with coordinate systems:
▸ 'GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed', with elements:
GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_hires_image (Images), GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_lowres_image (Images), GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed (Shapes)
▸ 'GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_downscaled_hires', with elements:
GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_hires_image (Images), GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed (Shapes)
▸ 'GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_downscaled_lowres', with elements:
GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed_lowres_image (Images), GSM7498811_SS1905133_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1905133_processed (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("sKRAm7y8bvdPFzh00000")
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("sKRAm7y8bvdPFzh0") # 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 sKRAm7y8bvdPFzh00000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/sKRAm7y8bvdPFzh0
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid sKRAm7y8bvdPFzh0License: NCBI GEO policy
Part of collection
Integrative single-cell transcriptome analysis of human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis [Spatial]→ 7 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- pancreas
- Condition
- exocrine pancreatic carcinoma
- Modality
- RNA
- Observations (spots)
- 3,947
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,954 × 2,000 px
- mpp
- 3.322 µm/px
- Size
- 63.4 MB
- Sample ID
- GSM7498811
- License
- NCBI GEO policy
- Published
- Nov 17, 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