Visium
Mouse spinal cord
NCBI448
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI448_full_image': DataTree[cyx] (3, 11935, 12368), (3, 5967, 6184), (3, 2983, 3092), (3, 1491, 1546)
├── Shapes
│ └── 'NCBI448_spots': GeoDataFrame shape: (574, 2) (2D shapes)
└── Tables
└── 'table': AnnData (574, 21987)
with coordinate systems:
▸ 'global', with elements:
NCBI448_full_image (Images), NCBI448_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("DMDgkakZCkskV0Ym0000")
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("DMDgkakZCkskV0Ym") # 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 DMDgkakZCkskV0Ym0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/DMDgkakZCkskV0Ym
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid DMDgkakZCkskV0YmLicense: CC BY-NC-SA 4.0 (noncommercial)
Part 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 (spots)
- 574
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 12,368 × 11,935 px
- mpp
- 0.691 µm/px
- Size
- 304 MB
- Sample ID
- NCBI448
- 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