Visium
Mouse heart
NCBI787
bronze Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI787_full_image': DataTree[cyx] (3, 12600, 13222), (3, 6300, 6611), (3, 3150, 3305), (3, 1575, 1652)
├── Shapes
│ └── 'NCBI787_spots': GeoDataFrame shape: (2823, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2823, 31899)
with coordinate systems:
▸ 'global', with elements:
NCBI787_full_image (Images), NCBI787_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("rTQo6BzbVNzidqie0000")
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("rTQo6BzbVNzidqie") # 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 rTQo6BzbVNzidqie0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/rTQo6BzbVNzidqie
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rTQo6BzbVNzidqieLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
YAP Drives Assembly of a Spatially Colocalized Cellular Triad Required for Heart Renewal→ 2 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- heart
- Modality
- RNA
- Observations (spots)
- 2,823
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 13,222 × 12,600 px
- mpp
- 0.647 µm/px
- Size
- 461 MB
- Sample ID
- NCBI787
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jan 11, 2024
Cite this dataset
No linked publication found — please cite the data source.
License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB