Visium
Mouse cardiac ventricle
Visium_heart_3dPI
silver Interactive viewer H&E myocardial infarction ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7898097_Visium_heart_3dPI_hires_image': DataArray[cyx] (3, 1863, 2000)
│ └── 'GSM7898097_Visium_heart_3dPI_lowres_image': DataArray[cyx] (3, 559, 600)
├── Shapes
│ └── 'GSM7898097_Visium_heart_3dPI': GeoDataFrame shape: (1068, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1068, 19465)
with coordinate systems:
▸ 'GSM7898097_Visium_heart_3dPI', with elements:
GSM7898097_Visium_heart_3dPI_hires_image (Images), GSM7898097_Visium_heart_3dPI_lowres_image (Images), GSM7898097_Visium_heart_3dPI (Shapes)
▸ 'GSM7898097_Visium_heart_3dPI_downscaled_hires', with elements:
GSM7898097_Visium_heart_3dPI_hires_image (Images), GSM7898097_Visium_heart_3dPI (Shapes)
▸ 'GSM7898097_Visium_heart_3dPI_downscaled_lowres', with elements:
GSM7898097_Visium_heart_3dPI_lowres_image (Images), GSM7898097_Visium_heart_3dPI (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("MgK3VcqIbNgGMBV20001")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("MgK3VcqIbNgGMBV2") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download MgK3VcqIbNgGMBV20001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/MgK3VcqIbNgGMBV2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid MgK3VcqIbNgGMBV2License: NCBI GEO policy
Part of collection
Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction→ 4 datasets · other
Metadata
- Technology
- Visium
- Vendor
- 10x Genomics
- Organism
- mouse
- Tissue
- cardiac ventricle
- Condition
- myocardial infarction
- Modality
- RNA
- Observations (spots)
- 1,068
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,863 px
- mpp
- 1.765 µm/px
- Size
- 22.0 MB
- Sample ID
- GSM7898097
- License
- NCBI GEO policy
- Published
- Nov 28, 2023
Cite this dataset
doi.org/10.1038/s41467-023-44227-6 ↗ BibTeX
@article{geo:GSE206787,
doi = {10.1038/s41467-023-44227-6},
title = {Visium_heart_7dPI},
year = {2023}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB