Visium
Mouse spinal cord
NCBI444
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI444_full_image': DataTree[cyx] (3, 11981, 11792), (3, 5990, 5896), (3, 2995, 2948), (3, 1497, 1474)
├── Shapes
│ └── 'NCBI444_spots': GeoDataFrame shape: (710, 2) (2D shapes)
└── Tables
└── 'table': AnnData (710, 21987)
with coordinate systems:
▸ 'global', with elements:
NCBI444_full_image (Images), NCBI444_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("2MMoD7aMcZYVIvcy") # 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/2MMoD7aMcZYVIvcy
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 2MMoD7aMcZYVIvcy Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["2MMoD7aMcZYVIvcy0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
The neurons that restore walking after paralysis [spatial transcriptomics]→ 16 datasets · publication
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- spinal cord
- Modality
- RNA
- Observations
- 710
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 11,792 × 11,981 px
- mpp
- 0.689 µm/px
- Size
- 273 MB
- Sample ID
- NCBI444
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jun 20, 2022
Cite this dataset
doi.org/10.1038/s41586-022-05385-7 ↗ BibTeX
@article{Kathe_2022,
title = {The neurons that restore walking after paralysis},
volume = {611},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-022-05385-7},
DOI = {10.1038/s41586-022-05385-7},
number = {7936},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Kathe, Claudia and Skinnider, Michael A. and Hutson, Thomas H. and Regazzi, Nicola and Gautier, Matthieu and Demesmaeker, Robin and Komi, Salif and Ceto, Steven and James, Nicholas D. and Cho, Newton and Baud, Laetitia and Galan, Katia and Matson, Kaya J. E. and Rowald, Andreas and Kim, Kyungjin and Wang, Ruijia and Minassian, Karen and Prior, John O. and Asboth, Leonie and Barraud, Quentin and Lacour, Stéphanie P. and Levine, Ariel J. and Wagner, Fabien and Bloch, Jocelyne and Squair, Jordan W. and Courtine, Grégoire},
year = {2022},
month = Nov,
pages = {540–547}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB