Visium
Mouse pancreas
GSM7926979
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7926979_A72_hires_image': DataArray[cyx] (3, 2000, 1967)
│ └── 'GSM7926979_A72_lowres_image': DataArray[cyx] (3, 600, 590)
├── Shapes
│ └── 'GSM7926979_A72': GeoDataFrame shape: (3533, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3533, 19465)
with coordinate systems:
▸ 'GSM7926979_A72', with elements:
GSM7926979_A72_hires_image (Images), GSM7926979_A72_lowres_image (Images), GSM7926979_A72 (Shapes)
▸ 'GSM7926979_A72_downscaled_hires', with elements:
GSM7926979_A72_hires_image (Images), GSM7926979_A72 (Shapes)
▸ 'GSM7926979_A72_downscaled_lowres', with elements:
GSM7926979_A72_lowres_image (Images), GSM7926979_A72 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("yW8KtsQT2YLUZkOK0000")
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("yW8KtsQT2YLUZkOK") # 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 yW8KtsQT2YLUZkOK0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/yW8KtsQT2YLUZkOK
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yW8KtsQT2YLUZkOKLicense: NCBI GEO policy
Part of collection
DNA methylation memory of acinar-ductal transition state altering Kras-downstream Pi3k and Rho GTPase signaling [spatial transcriptomics]→ 20 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- pancreas
- Modality
- RNA
- Observations (spots)
- 3,533
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,967 × 2,000 px
- mpp
- 3.478 µm/px
- Size
- 10.7 MB
- Sample ID
- GSM7926979
- License
- NCBI GEO policy
- Published
- Mar 10, 2025
Cite this dataset
doi.org/10.1186/s13073-025-01452-6 ↗ BibTeX
@article{Lo_2025,
title = {DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation},
volume = {17},
ISSN = {1756-994X},
url = {http://dx.doi.org/10.1186/s13073-025-01452-6},
DOI = {10.1186/s13073-025-01452-6},
number = {1},
journal = {Genome Medicine},
publisher = {Springer Science and Business Media LLC},
author = {Lo, Emily K.W. and Idrizi, Adrian and Tryggvadottir, Rakel and Zhou, Weiqiang and Hou, Wenpin and Ji, Hongkai and Cahan, Patrick and Feinberg, Andrew P.},
year = {2025},
month = Mar
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB