Visium
Mouse heart
GSM7911864
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7911864_A1_hires_image': DataArray[cyx] (3, 1839, 2000)
│ └── 'GSM7911864_A1_lowres_image': DataArray[cyx] (3, 552, 600)
├── Shapes
│ └── 'GSM7911864_A1': GeoDataFrame shape: (1978, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1978, 32285)
with coordinate systems:
▸ 'GSM7911864_A1', with elements:
GSM7911864_A1_hires_image (Images), GSM7911864_A1_lowres_image (Images), GSM7911864_A1 (Shapes)
▸ 'GSM7911864_A1_downscaled_hires', with elements:
GSM7911864_A1_hires_image (Images), GSM7911864_A1 (Shapes)
▸ 'GSM7911864_A1_downscaled_lowres', with elements:
GSM7911864_A1_lowres_image (Images), GSM7911864_A1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("qUqpiK9r69lx03FT0000")
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("qUqpiK9r69lx03FT") # 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 qUqpiK9r69lx03FT0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/qUqpiK9r69lx03FT
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qUqpiK9r69lx03FTLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics to dissect molecular signature of cardiac fibroblasts in experimental autoimmune myocarditis→ 2 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- heart
- Modality
- RNA
- Observations (spots)
- 1,978
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,839 px
- mpp
- 4.342 µm/px
- Size
- 31.6 MB
- Sample ID
- GSM7911864
- License
- NCBI GEO policy
- Published
- Nov 21, 2025
Cite this dataset
doi.org/10.1016/j.bbrep.2025.102344 ↗ BibTeX
@article{Stefa_ska_2025,
title = {Elucidating cardiac fibroblasts heterogeneity and activation during experimental autoimmune myocarditis using spatial transcriptomics},
volume = {44},
ISSN = {2405-5808},
url = {http://dx.doi.org/10.1016/j.bbrep.2025.102344},
DOI = {10.1016/j.bbrep.2025.102344},
journal = {Biochemistry and Biophysics Reports},
publisher = {Elsevier BV},
author = {Stefańska, Monika and Sarad, Katarzyna and Kot, Marta and Ruciński, Marcin and Strzelec, Martyna and Krzysztofik, Daria and Lindberg, Eric L.},
year = {2025},
month = Dec,
pages = {102344}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB