Visium
Human pancreas
GSM7498813
silver Interactive viewer H&E exocrine pancreatic carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_hires_image': DataArray[cyx] (3, 2000, 1972)
│ └── 'GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_lowres_image': DataArray[cyx] (3, 600, 592)
├── Shapes
│ └── 'GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed': GeoDataFrame shape: (4373, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4373, 17943)
with coordinate systems:
▸ 'GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed', with elements:
GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_hires_image (Images), GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_lowres_image (Images), GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed (Shapes)
▸ 'GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_downscaled_hires', with elements:
GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_hires_image (Images), GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed (Shapes)
▸ 'GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_downscaled_lowres', with elements:
GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed_lowres_image (Images), GSM7498813_SS1945070_processed_nfs_SCMGL_srk01_PancCa_GEO_visium_processed_submission_230614_SS1945070_processed (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("iRo7Ep655vyrh7MZ") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/iRo7Ep655vyrh7MZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid iRo7Ep655vyrh7MZ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["iRo7Ep655vyrh7MZ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 4,373
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,972 × 2,000 px
- mpp
- 3.317 µm/px
- Size
- 53 MB
- Sample ID
- GSM7498813
- License
- unknown
- Published
- Nov 17, 2023
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB