Visium
Mouse liver
NCBI621
silver Interactive viewer H&E hepatoblastoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI621_full_image': DataTree[cyx] (3, 10000, 9896), (3, 5000, 4948), (3, 2500, 2474), (3, 1250, 1237)
├── Shapes
│ └── 'NCBI621_spots': GeoDataFrame shape: (4989, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4989, 31053)
with coordinate systems:
▸ 'global', with elements:
NCBI621_full_image (Images), NCBI621_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("IrxNuPqyc0VnwdjU") # 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/IrxNuPqyc0VnwdjU
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid IrxNuPqyc0VnwdjU Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["IrxNuPqyc0VnwdjU0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- liver
- Condition
- hepatoblastoma
- Modality
- RNA
- Observations
- 4,989
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 9,896 × 10,000 px
- mpp
- 0.890 µm/px
- Size
- 191 MB
- Sample ID
- NCBI621
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jun 9, 2023
Cite this dataset
doi.org/10.1038/s41467-023-39717-6 ↗ BibTeX
@article{Fang_2023,
title = {Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma},
volume = {14},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-023-39717-6},
DOI = {10.1038/s41467-023-39717-6},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Fang, Jie and Singh, Shivendra and Cheng, Changde and Natarajan, Sivaraman and Sheppard, Heather and Abu-Zaid, Ahmed and Durbin, Adam D. and Lee, Ha Won and Wu, Qiong and Steele, Jacob and Connelly, Jon P. and Jin, Hongjian and Chen, Wenan and Fan, Yiping and Pruett-Miller, Shondra M. and Rehg, Jerold E. and Koo, Selene C. and Santiago, Teresa and Emmons, Joseph and Cairo, Stefano and Wang, Ruoning and Glazer, Evan S. and Murphy, Andrew J. and Chen, Taosheng and Davidoff, Andrew M. and Armengol, Carolina and Easton, John and Chen, Xiang and Yang, Jun},
year = {2023},
month = July
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB