Visium
Mouse skeletal muscle tissue
NCBI652
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI652_full_image': DataTree[cyx] (3, 14602, 15111), (3, 7301, 7555), (3, 3650, 3777), (3, 1825, 1888)
├── Shapes
│ └── 'NCBI652_spots': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 55414)
with coordinate systems:
▸ 'global', with elements:
NCBI652_full_image (Images), NCBI652_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("IUhWZylkhiwgE93e") # 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/IUhWZylkhiwgE93e
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid IUhWZylkhiwgE93e Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["IUhWZylkhiwgE93e0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial Total RNA-Sequencing of regenerating mouse hindlimb muscle and Type 1-Lang reovirus-infected mouse heart→ 7 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- skeletal muscle tissue
- Modality
- RNA
- Observations
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 15,111 × 14,602 px
- mpp
- 0.562 µm/px
- Size
- 463 MB
- Sample ID
- NCBI652
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Apr 20, 2022
Cite this dataset
doi.org/10.1038/s41587-022-01517-6 ↗ BibTeX
@article{McKellar_2022,
title = {Spatial mapping of the total transcriptome by in situ polyadenylation},
volume = {41},
ISSN = {1546-1696},
url = {http://dx.doi.org/10.1038/s41587-022-01517-6},
DOI = {10.1038/s41587-022-01517-6},
number = {4},
journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
author = {McKellar, David W. and Mantri, Madhav and Hinchman, Meleana M. and Parker, John S. L. and Sethupathy, Praveen and Cosgrove, Benjamin D. and De Vlaminck, Iwijn},
year = {2022},
month = Nov,
pages = {513–520}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB