Visium
Rat heart
GSM9045886
bronze Interactive viewer H&E myocardial infarction Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9045886_5_1_hires_image': DataArray[cyx] (3, 2000, 1827)
│ └── 'GSM9045886_5_1_lowres_image': DataArray[cyx] (3, 600, 548)
├── Shapes
│ └── 'GSM9045886_5_1': GeoDataFrame shape: (3685, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3685, 25399)
with coordinate systems:
▸ 'GSM9045886_5_1', with elements:
GSM9045886_5_1_hires_image (Images), GSM9045886_5_1_lowres_image (Images), GSM9045886_5_1 (Shapes)
▸ 'GSM9045886_5_1_downscaled_hires', with elements:
GSM9045886_5_1_hires_image (Images), GSM9045886_5_1 (Shapes)
▸ 'GSM9045886_5_1_downscaled_lowres', with elements:
GSM9045886_5_1_lowres_image (Images), GSM9045886_5_1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("VGxhn9YxlxxpNM1y0000")
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("VGxhn9YxlxxpNM1y") # 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 VGxhn9YxlxxpNM1y0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VGxhn9YxlxxpNM1y
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VGxhn9YxlxxpNM1yLicense: NCBI GEO policy
Part of collection
Infusible Extracellular Matrix Biomaterial Enhances and Expedites Cell-Specific Pro-Repair Following Acute Myocardial Infarction→ 12 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- rat
- Tissue
- heart
- Condition
- myocardial infarction
- Modality
- RNA
- Observations (spots)
- 3,685
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,827 × 2,000 px
- mpp
- 4.695 µm/px
- Size
- 31.8 MB
- Sample ID
- GSM9045886
- License
- NCBI GEO policy
- Published
- Nov 30, 2025
Cite this dataset
doi.org/10.1101/2025.11.08.687255 ↗ BibTeX
@article{Mesfin_2025,
title = {Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction},
url = {http://dx.doi.org/10.1101/2025.11.08.687255},
DOI = {10.1101/2025.11.08.687255},
publisher = {openRxiv},
author = {Mesfin, Joshua M. and Chen, Alexander and Lyons, Quincy P. and Nguyen, Michael B. and Karkanitsa, Maria L. and Yu, Justin and Ninh, Van K. and Gardner, Emily and Wong, Elyse G. and Paleti, Sriya N. and Cheng, Julian and Bridgelal, Benjamin D. and Reimold, Kate E. and Cao, Selena and Uhre, Connor and Luo, Colin G. and Fu, Zhenxing and King, Kevin R. and Christman, Karen L.},
year = {2025},
month = Nov
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB