Visium
Mouse cardiac ventricle
GSM7898098
silver Interactive viewer H&E myocardial infarction No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7898098_Visium_heart_7dPI_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM7898098_Visium_heart_7dPI_hires_image': DataArray[cyx] (3, 2000, 1930)
│ └── 'GSM7898098_Visium_heart_7dPI_lowres_image': DataArray[cyx] (3, 600, 579)
├── Shapes
│ └── 'GSM7898098_Visium_heart_7dPI': GeoDataFrame shape: (1245, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1245, 19465)
with coordinate systems:
▸ 'GSM7898098_Visium_heart_7dPI', with elements:
GSM7898098_Visium_heart_7dPI_full_image (Images), GSM7898098_Visium_heart_7dPI_hires_image (Images), GSM7898098_Visium_heart_7dPI_lowres_image (Images), GSM7898098_Visium_heart_7dPI (Shapes)
▸ 'GSM7898098_Visium_heart_7dPI_downscaled_hires', with elements:
GSM7898098_Visium_heart_7dPI_hires_image (Images), GSM7898098_Visium_heart_7dPI (Shapes)
▸ 'GSM7898098_Visium_heart_7dPI_downscaled_lowres', with elements:
GSM7898098_Visium_heart_7dPI_lowres_image (Images), GSM7898098_Visium_heart_7dPI (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("vM2MYyDv1V9A8ddm0000")
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("vM2MYyDv1V9A8ddm") # 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 vM2MYyDv1V9A8ddm0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/vM2MYyDv1V9A8ddm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid vM2MYyDv1V9A8ddmLicense: NCBI GEO policy
Part of collection
Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- cardiac ventricle
- Condition
- myocardial infarction
- Modality
- RNA
- Observations (spots)
- 1,245
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,930 × 2,000 px
- mpp
- 2.078 µm/px
- Size
- 43.6 MB
- Sample ID
- GSM7898098
- License
- NCBI GEO policy
- Published
- Nov 28, 2023
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB