Visium
Mouse pancreas
GSM8972906
silver Interactive viewer H&E pancreatitis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8972906_Test_24h_284_2m_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8972906_Test_24h_284_2m_hires_image': DataArray[cyx] (3, 1968, 2000)
│ └── 'GSM8972906_Test_24h_284_2m_lowres_image': DataArray[cyx] (3, 591, 600)
├── Shapes
│ └── 'GSM8972906_Test_24h_284_2m': GeoDataFrame shape: (1323, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1323, 19465)
with coordinate systems:
▸ 'GSM8972906_Test_24h_284_2m', with elements:
GSM8972906_Test_24h_284_2m_full_image (Images), GSM8972906_Test_24h_284_2m_hires_image (Images), GSM8972906_Test_24h_284_2m_lowres_image (Images), GSM8972906_Test_24h_284_2m (Shapes)
▸ 'GSM8972906_Test_24h_284_2m_downscaled_hires', with elements:
GSM8972906_Test_24h_284_2m_hires_image (Images), GSM8972906_Test_24h_284_2m (Shapes)
▸ 'GSM8972906_Test_24h_284_2m_downscaled_lowres', with elements:
GSM8972906_Test_24h_284_2m_lowres_image (Images), GSM8972906_Test_24h_284_2m (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("YRGPc82ALjPCsoWE0000")
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("YRGPc82ALjPCsoWE") # 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 YRGPc82ALjPCsoWE0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/YRGPc82ALjPCsoWE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YRGPc82ALjPCsoWELicense: NCBI GEO policy
Part of collection
HMG Box-Containing Protein 1 (HBP1) Protects Against Pancreatic Injury in Acute Pancreatitis but Promotes Neoplastic Progression→ 6 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- pancreas
- Condition
- pancreatitis
- Modality
- RNA
- Observations (spots)
- 1,323
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 2,000 × 1,968 px
- mpp
- 2.763 µm/px
- Size
- 35.5 MB
- Sample ID
- GSM8972906
- License
- NCBI GEO policy
- Published
- Jul 16, 2025
Cite this dataset
doi.org/10.1016/j.jcmgh.2025.101536 ↗ BibTeX
@article{Lee_2025,
title = {HMG Box-containing Protein 1 (HBP1) Protects Against Pancreatic Injury in Acute Pancreatitis but Promotes Neoplastic Progression},
volume = {19},
ISSN = {2352-345X},
url = {http://dx.doi.org/10.1016/j.jcmgh.2025.101536},
DOI = {10.1016/j.jcmgh.2025.101536},
number = {9},
journal = {Cellular and Molecular Gastroenterology and Hepatology},
publisher = {Elsevier BV},
author = {Lee, Seung-Won and Ekstrom, Taelor and Manalo, Elise C. and Ye, Shangyuan and Berry, Mark and Grygoryev, Dmytro and Szczepaniak, Malwina and Lee, Jinho and Marmolejo, Carlos Origel and Haverlack, Syber and Lee, Juyoung and Shah, Vidhi M. and Keith, Dove and Muschler, John L. and Chin, Koei and Sears, Rosalie C. and Weisberg, Stuart P. and Morgan, Terry and Kim, Jungsun},
year = {2025},
pages = {101536}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB