Visium

Mouse heart

GSM6756180

bronze Interactive viewer H&E diastolic heart failure Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM6756180_D_Ctrl_HF_hires_image': DataArray[cyx] (3, 1855, 2000)
│     └── 'GSM6756180_D_Ctrl_HF_lowres_image': DataArray[cyx] (3, 557, 600)
├── Shapes
│     └── 'GSM6756180_D_Ctrl_HF': GeoDataFrame shape: (2994, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2994, 19465)
with coordinate systems:
    ▸ 'GSM6756180_D_Ctrl_HF', with elements:
        GSM6756180_D_Ctrl_HF_hires_image (Images), GSM6756180_D_Ctrl_HF_lowres_image (Images), GSM6756180_D_Ctrl_HF (Shapes)
    ▸ 'GSM6756180_D_Ctrl_HF_downscaled_hires', with elements:
        GSM6756180_D_Ctrl_HF_hires_image (Images), GSM6756180_D_Ctrl_HF (Shapes)
    ▸ 'GSM6756180_D_Ctrl_HF_downscaled_lowres', with elements:
        GSM6756180_D_Ctrl_HF_lowres_image (Images), GSM6756180_D_Ctrl_HF (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("rHDLGcpMLGMrfdFm0000")
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("rHDLGcpMLGMrfdFm")   # 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 rHDLGcpMLGMrfdFm0000 --dest data/

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

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

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction [Visium]→

3 datasets · comparison

Metadata

Technology: Visium
Organism: mouse
Tissue: heart
Condition: diastolic heart failure
Modality: RNA
Observations (spots): 2,994
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 1,855 px
mpp: 3.617 µm/px
Size: 37.7 MB
Sample ID: GSM6756180
License: NCBI GEO policy
Published: Dec 14, 2024

Cite this dataset

doi.org/10.1161/circulationaha.123.067504 ↗

BibTeX

@article{Yamada_2025,
  title = {Cardiac Reprogramming and Gata4 Overexpression Reduce Fibrosis and Improve Diastolic Dysfunction in Heart Failure With Preserved Ejection Fraction},
  volume = {151},
  ISSN = {1524-4539},
  url = {http://dx.doi.org/10.1161/circulationaha.123.067504},
  DOI = {10.1161/circulationaha.123.067504},
  number = {6},
  journal = {Circulation},
  publisher = {Ovid Technologies (Wolters Kluwer Health)},
  author = {Yamada, Yu and Sadahiro, Taketaro and Nakano, Koji and Honda, Seiichiro and Abe, Yuto and Akiyama, Tatsuya and Fujita, Ryo and Nakamura, Masashi and Maeda, Takashi and Kuze, Yuta and Onishi, Masaya and Seki, Masahide and Suzuki, Yutaka and Takeuchi, Chikara and Iwasaki, Yuka W. and Murano, Kensaku and Sakata-Yanagimoto, Mamiko and Chiba, Shigeru and Kato, Hideyuki and Sakamoto, Hiroaki and Hiramatsu, Yuji and Ieda, Masaki},
  year = {2025},
  month = Feb,
  pages = {379–395}
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB