Visium

Human skin of body

NCBI480

silver Interactive viewer H&E lichen planus ✓ Verified publication

Preview Client Lamin CLI

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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("60U29Be78Hbq6aKX0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("60U29Be78Hbq6aKX")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download 60U29Be78Hbq6aKX0000 --dest data/

# or lamin: 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

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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Part 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 (spots): 695
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 15,983 × 16,224 px
mpp: 0.526 µm/px
Size: 510 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