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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("YRGPc82ALjPCsoWE") # 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/YRGPc82ALjPCsoWE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YRGPc82ALjPCsoWE Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["YRGPc82ALjPCsoWE0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 1,323
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 2,000 × 1,968 px
- mpp
- 2.763 µm/px
- Size
- 34 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