Visium

Mouse heart

NCBI543

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

Preview Download via Python Download via CLI Load via sddb

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)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("cODKvx39kWejMHry")   # 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/cODKvx39kWejMHry

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

Load with the Python client

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

ds = Catalog().cohort(uids=["cODKvx39kWejMHry0000"])[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

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: 1,962
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 14,592 × 14,336 px
mpp: 0.547 µm/px
Size: 255 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