Visium
Mouse heart
GSM5355668
silver Interactive viewer H&E myocardial infarction No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5355668_WT_MI_day14_1_full_image': DataTree[cyx] (3, 3674, 3411), (3, 1837, 1705), (3, 918, 852), (3, 459, 426), (3, 229, 213)
│ └── 'GSM5355668_WT_MI_day14_1_hires_image': DataArray[cyx] (3, 2000, 1857)
├── Shapes
│ └── 'GSM5355668_WT_MI_day14_1': GeoDataFrame shape: (1153, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1153, 32285)
with coordinate systems:
▸ 'GSM5355668_WT_MI_day14_1', with elements:
GSM5355668_WT_MI_day14_1_full_image (Images), GSM5355668_WT_MI_day14_1_hires_image (Images), GSM5355668_WT_MI_day14_1 (Shapes)
▸ 'GSM5355668_WT_MI_day14_1_downscaled_hires', with elements:
GSM5355668_WT_MI_day14_1_hires_image (Images), GSM5355668_WT_MI_day14_1 (Shapes)
▸ 'GSM5355668_WT_MI_day14_1_downscaled_lowres', with elements:
GSM5355668_WT_MI_day14_1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("FlFiWGv5Hn1Skulx0000")
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("FlFiWGv5Hn1Skulx") # 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 FlFiWGv5Hn1Skulx0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/FlFiWGv5Hn1Skulx
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FlFiWGv5Hn1SkulxLicense: NCBI GEO policy
Part of collection
Spatiotemporal transcriptome analysis reveals critical roles for mechano-sensing genes at the border zone in remodeling after myocardial infarction→ 14 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- heart
- Condition
- myocardial infarction
- Modality
- RNA
- Observations (spots)
- 1,153
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 3,411 × 3,674 px
- mpp
- 1.968 µm/px
- Size
- 42.7 MB
- Sample ID
- GSM5355668
- License
- NCBI GEO policy
- Published
- Jul 25, 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