Visium
Mouse heart
GSM6756178
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6756178_A_Ctrl_hires_image': DataArray[cyx] (3, 1855, 2000)
│ └── 'GSM6756178_A_Ctrl_lowres_image': DataArray[cyx] (3, 557, 600)
├── Shapes
│ └── 'GSM6756178_A_Ctrl': GeoDataFrame shape: (1935, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1935, 19465)
with coordinate systems:
▸ 'GSM6756178_A_Ctrl', with elements:
GSM6756178_A_Ctrl_hires_image (Images), GSM6756178_A_Ctrl_lowres_image (Images), GSM6756178_A_Ctrl (Shapes)
▸ 'GSM6756178_A_Ctrl_downscaled_hires', with elements:
GSM6756178_A_Ctrl_hires_image (Images), GSM6756178_A_Ctrl (Shapes)
▸ 'GSM6756178_A_Ctrl_downscaled_lowres', with elements:
GSM6756178_A_Ctrl_lowres_image (Images), GSM6756178_A_Ctrl (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("lMG5vIbdBPW9A1VS") # 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/lMG5vIbdBPW9A1VS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lMG5vIbdBPW9A1VS Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["lMG5vIbdBPW9A1VS0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- Modality
- RNA
- Observations
- 1,935
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,855 px
- mpp
- 3.619 µm/px
- Size
- 26 MB
- Sample ID
- GSM6756178
- License
- unknown
- Published
- Dec 14, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB