Visium

Mouse lung

NCBI727

silver Interactive viewer H&E influenza ✓ Verified publication

Preview Client Lamin CLI

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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("XiBG5525zu1EZhwU0000")
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("XiBG5525zu1EZhwU")   # 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 XiBG5525zu1EZhwU0000 --dest data/

# or lamin: 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

Install (Python 3.12+) Docs →

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

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Metadata

Technology: Visium
Organism: mouse
Tissue: lung
Condition: influenza
Modality: RNA
Observations (spots): 1,899
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 18,035 × 17,103 px
mpp: 0.490 µm/px
Size: 412 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