Visium
Human skin of body
NCBI480
silver Interactive viewer H&E lichen planus ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI480_full_image': DataTree[cyx] (3, 16224, 15983), (3, 8112, 7991), (3, 4056, 3995), (3, 2028, 1997)
├── Shapes
│ └── 'NCBI480_spots': GeoDataFrame shape: (695, 2) (2D shapes)
└── Tables
└── 'table': AnnData (695, 19850)
with coordinate systems:
▸ 'global', with elements:
NCBI480_full_image (Images), NCBI480_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("60U29Be78Hbq6aKX") # 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/60U29Be78Hbq6aKX
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 60U29Be78Hbq6aKX Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["60U29Be78Hbq6aKX0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial transcriptomics landscape of non-communicable inflammatory skin diseases→ 59 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- lichen planus
- Modality
- RNA
- Observations
- 695
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 15,983 × 16,224 px
- mpp
- 0.526 µm/px
- Size
- 487 MB
- Sample ID
- NCBI480
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Nov 14, 2022
Cite this dataset
doi.org/10.1038/s41467-022-35319-w ↗ BibTeX
@article{Sch_bitz_2022,
title = {Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases},
volume = {13},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-022-35319-w},
DOI = {10.1038/s41467-022-35319-w},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Schäbitz, A. and Hillig, C. and Mubarak, M. and Jargosch, M. and Farnoud, A. and Scala, E. and Kurzen, N. and Pilz, A. C. and Bhalla, N. and Thomas, J. and Stahle, M. and Biedermann, T. and Schmidt-Weber, C. B. and Theis, F. and Garzorz-Stark, N. and Eyerich, K. and Menden, M. P. and Eyerich, S.},
year = {2022},
month = Dec
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB