Visium

Mouse heart

NCBI543

silver Interactive viewer H&E ischemia reperfusion injury ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI543_full_image': DataTree[cyx] (3, 14336, 14592), (3, 7168, 7296), (3, 3584, 3648), (3, 1792, 1824)
├── Shapes
│     └── 'NCBI543_spots': GeoDataFrame shape: (1962, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1962, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI543_full_image (Images), NCBI543_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("cODKvx39kWejMHry0000")
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("cODKvx39kWejMHry")   # 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 cODKvx39kWejMHry0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/cODKvx39kWejMHry

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cODKvx39kWejMHry

Install (Python 3.12+) Docs →

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

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Part of collection

Single-nucleus Ribonucleic Acid-sequencing and Spatial Transcriptomics Reveal the Cardioprotection of Shexiang Baoxin Pill (MUSKARDIA) in Mice with Myocardial Ischemia-Reperfusion Injury→

2 datasets · comparison

Metadata

Technology: Visium
Organism: mouse
Tissue: heart
Condition: ischemia reperfusion injury
Modality: RNA
Observations (spots): 1,962
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 14,592 × 14,336 px
mpp: 0.547 µm/px
Size: 267 MB
Sample ID: NCBI543
License: CC BY-NC-SA 4.0 NonCommercial
Published: May 9, 2023

Cite this dataset

doi.org/10.3389/fphar.2023.1173649 ↗

BibTeX

@article{Lin_2023,
  title = {Single-nucleus ribonucleic acid-sequencing and spatial transcriptomics reveal the cardioprotection of Shexiang Baoxin Pill (SBP) in mice with myocardial ischemia-reperfusion injury},
  volume = {14},
  ISSN = {1663-9812},
  url = {http://dx.doi.org/10.3389/fphar.2023.1173649},
  DOI = {10.3389/fphar.2023.1173649},
  journal = {Frontiers in Pharmacology},
  publisher = {Frontiers Media SA},
  author = {Lin, Wenyong and Chen, Xin and Wang, Dongyuan and Lu, Ruixia and Zhang, Chunling and Niu, Zhenchao and Chen, Jie and Ruan, Xiaofen and Wang, Xiaolong},
  year = {2023},
  month = May
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB