Visium

Mouse lung

NCBI727

silver Interactive viewer H&E influenza ✓ Verified publication

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI727_full_image': DataTree[cyx] (3, 17103, 18035), (3, 8551, 9017), (3, 4275, 4508), (3, 2137, 2254)
├── Shapes
│     └── 'NCBI727_spots': GeoDataFrame shape: (1899, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1899, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI727_full_image (Images), NCBI727_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("XiBG5525zu1EZhwU")   # 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/XiBG5525zu1EZhwU

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid XiBG5525zu1EZhwU

Load with the Python client

# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["XiBG5525zu1EZhwU0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Metadata

Technology: Visium
Organism: mouse
Tissue: lung
Condition: influenza
Modality: RNA
Observations: 1,899
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 18,035 × 17,103 px
mpp: 0.490 µm/px
Size: 393 MB
Sample ID: NCBI727
License: CC BY-NC-SA 4.0 NonCommercial
Published: Aug 8, 2023

Cite this dataset

doi.org/10.1038/s41467-023-41387-3 ↗

BibTeX

@article{Beppu_2023,
  title = {Epithelial plasticity and innate immune activation promote lung tissue remodeling following respiratory viral infection},
  volume = {14},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-023-41387-3},
  DOI = {10.1038/s41467-023-41387-3},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Beppu, Andrew K. and Zhao, Juanjuan and Yao, Changfu and Carraro, Gianni and Israely, Edo and Coelho, Anna Lucia and Drake, Katherine and Hogaboam, Cory M. and Parks, William C. and Kolls, Jay K. and Stripp, Barry R.},
  year = {2023},
  month = Sept
}

Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB