Visium
Mouse heart
MEND28
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MEND28_full_image': DataTree[cyx] (3, 23032, 22996), (3, 11516, 11498), (3, 5758, 5749), (3, 2879, 2874)
├── Shapes
│ └── 'MEND28_spots': GeoDataFrame shape: (1835, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1835, 54838)
with coordinate systems:
▸ 'global', with elements:
MEND28_full_image (Images), MEND28_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("pctLKaB96X8JP1ID") # 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/pctLKaB96X8JP1ID
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pctLKaB96X8JP1ID Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["pctLKaB96X8JP1ID0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- heart
- Modality
- RNA
- Observations
- 1,835
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 22,996 × 23,032 px
- mpp
- 0.360 µm/px
- Size
- 477 MB
- Sample ID
- MEND28
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Nov 27, 2021
Cite this dataset
doi.org/10.1038/s44161-022-00138-1 ↗ BibTeX
@article{Mantri_2022,
title = {Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis},
volume = {1},
ISSN = {2731-0590},
url = {http://dx.doi.org/10.1038/s44161-022-00138-1},
DOI = {10.1038/s44161-022-00138-1},
number = {10},
journal = {Nature Cardiovascular Research},
publisher = {Springer Science and Business Media LLC},
author = {Mantri, Madhav and Hinchman, Meleana M. and McKellar, David W. and Wang, Michael F. Z. and Cross, Shaun T. and Parker, John S. L. and De Vlaminck, Iwijn},
year = {2022},
month = Oct,
pages = {946–960}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB