spatial transcriptomics
Human heart
SPA47
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'SPA47_full_image': DataTree[cyx] (3, 8602, 9830), (3, 4301, 4915), (3, 2150, 2457), (3, 1075, 1228)
├── Shapes
│ └── 'SPA47_spots': GeoDataFrame shape: (59, 2) (2D shapes)
└── Tables
└── 'table': AnnData (59, 39739)
with coordinate systems:
▸ 'global', with elements:
SPA47_full_image (Images), SPA47_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("zSRu1XEPESaBrVN1") # 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/zSRu1XEPESaBrVN1
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid zSRu1XEPESaBrVN1 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["zSRu1XEPESaBrVN10001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart→ 19 datasets · comparison
Metadata
- Technology
- spatial transcriptomics
- Organism
- human
- Tissue
- heart
- Modality
- RNA
- Observations
- 59
- Tier
- silver
- Chemistry
- ST 1k
- Resolution
- 9,830 × 8,602 px
- mpp
- 0.913 µm/px
- Size
- 140 MB
- Sample ID
- SPA47
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Dec 16, 2019
Cite this dataset
No linked publication found — please cite the data source: sciencedirect.com ↗.
Source: sciencedirect.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB