Visium
Human kidney
NCBI565
silver Interactive viewer H&E nephrolithiasis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI565_full_image': DataTree[cyx] (3, 11299, 10473), (3, 5649, 5236), (3, 2824, 2618), (3, 1412, 1309)
├── Shapes
│ └── 'NCBI565_spots': GeoDataFrame shape: (1085, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1085, 36601)
with coordinate systems:
▸ 'global', with elements:
NCBI565_full_image (Images), NCBI565_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("uPnF4kwEcckN5w10") # 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/uPnF4kwEcckN5w10
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid uPnF4kwEcckN5w10 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["uPnF4kwEcckN5w100000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease→ 7 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- kidney
- Condition
- nephrolithiasis
- Modality
- RNA
- Observations
- 1,085
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 10,473 × 11,299 px
- mpp
- 0.758 µm/px
- Size
- 200 MB
- Sample ID
- NCBI565
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- May 4, 2023
Cite this dataset
doi.org/10.1038/s41467-023-38975-8 ↗ BibTeX
@article{Canela_2023,
title = {A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease},
volume = {14},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-023-38975-8},
DOI = {10.1038/s41467-023-38975-8},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Canela, Victor Hugo and Bowen, William S. and Ferreira, Ricardo Melo and Syed, Farooq and Lingeman, James E. and Sabo, Angela R. and Barwinska, Daria and Winfree, Seth and Lake, Blue B. and Cheng, Ying-Hua and Gaut, Joseph P. and Ferkowicz, Michael and LaFavers, Kaice A. and Zhang, Kun and Coe, Fredric L. and Worcester, Elaine and Jain, Sanjay and Eadon, Michael T. and Williams, James C. and El-Achkar, Tarek M.},
year = {2023},
month = July
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB