Visium
Mouse heart
GSM6613090
silver Interactive viewer H&E myocardial infarction No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6613090_V_Human_STEMI_hires_image': DataArray[cyx] (3, 1836, 2000)
│ └── 'GSM6613090_V_Human_STEMI_lowres_image': DataArray[cyx] (3, 551, 600)
├── Shapes
│ └── 'GSM6613090_V_Human_STEMI': GeoDataFrame shape: (1551, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1551, 36601)
with coordinate systems:
▸ 'GSM6613090_V_Human_STEMI', with elements:
GSM6613090_V_Human_STEMI_hires_image (Images), GSM6613090_V_Human_STEMI_lowres_image (Images), GSM6613090_V_Human_STEMI (Shapes)
▸ 'GSM6613090_V_Human_STEMI_downscaled_hires', with elements:
GSM6613090_V_Human_STEMI_hires_image (Images), GSM6613090_V_Human_STEMI (Shapes)
▸ 'GSM6613090_V_Human_STEMI_downscaled_lowres', with elements:
GSM6613090_V_Human_STEMI_lowres_image (Images), GSM6613090_V_Human_STEMI (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("qjnsdpNx0wnSSIwz0000")
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("qjnsdpNx0wnSSIwz") # 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 qjnsdpNx0wnSSIwz0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/qjnsdpNx0wnSSIwz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qjnsdpNx0wnSSIwzLicense: NCBI GEO policy
Part of collection
Single Cell Spatial Transcriptomics Redefines the Borderzone induced by Myocardial Infarction and Mechanical Injury→ 14 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- heart
- Condition
- myocardial infarction
- Modality
- RNA
- Observations (spots)
- 1,551
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,836 px
- mpp
- 3.861 µm/px
- Size
- 10.9 MB
- Sample ID
- GSM6613090
- License
- NCBI GEO policy
- Published
- Oct 3, 2022
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