Visium
Mouse heart
GSM5355666
silver Interactive viewer H&E myocardial infarction No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5355666_WT_MI_day7_1_full_image': DataTree[cyx] (3, 3511, 3569), (3, 1755, 1784), (3, 877, 892), (3, 438, 446), (3, 219, 223)
│ └── 'GSM5355666_WT_MI_day7_1_hires_image': DataArray[cyx] (3, 1967, 2000)
├── Shapes
│ └── 'GSM5355666_WT_MI_day7_1': GeoDataFrame shape: (3154, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3154, 32285)
with coordinate systems:
▸ 'GSM5355666_WT_MI_day7_1', with elements:
GSM5355666_WT_MI_day7_1_full_image (Images), GSM5355666_WT_MI_day7_1_hires_image (Images), GSM5355666_WT_MI_day7_1 (Shapes)
▸ 'GSM5355666_WT_MI_day7_1_downscaled_hires', with elements:
GSM5355666_WT_MI_day7_1_hires_image (Images), GSM5355666_WT_MI_day7_1 (Shapes)
▸ 'GSM5355666_WT_MI_day7_1_downscaled_lowres', with elements:
GSM5355666_WT_MI_day7_1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("nQZpCIdUee0B6aNr") # 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/nQZpCIdUee0B6aNr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid nQZpCIdUee0B6aNr Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["nQZpCIdUee0B6aNr0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 3,154
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 3,569 × 3,511 px
- mpp
- 2.064 µm/px
- Size
- 95 MB
- Sample ID
- GSM5355666
- License
- unknown
- Published
- Jul 25, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB