← All datasets
Visium

Human kidney

NCBI702

silver Interactive viewer H&E diabetic kidney disease ✓ Verified publication
Human kidney preview
print(sdata)
SpatialData object
├── Images
│     └── 'NCBI702_full_image': DataTree[cyx] (3, 10474, 11298), (3, 5237, 5649), (3, 2618, 2824), (3, 1309, 1412)
├── Shapes
│     └── 'NCBI702_spots': GeoDataFrame shape: (461, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (461, 36601)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI702_full_image (Images), NCBI702_spots (Shapes)
Load in Python
import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("0Y6QewKoDCORRZiZ")   # 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/0Y6QewKoDCORRZiZ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 0Y6QewKoDCORRZiZ
Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["0Y6QewKoDCORRZiZ0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Metadata

Technology
Visium
Organism
human
Tissue
kidney
Condition
diabetic kidney disease
Modality
RNA
Observations
461
Tier
silver
Chemistry
Visium v1
Resolution
11,298 × 10,474 px
mpp
0.758 µm/px
Size
201 MB
Sample ID
NCBI702
License
CC BY-NC-SA 4.0 NonCommercial
Published
Oct 12, 2022

Cite this dataset

doi.org/10.1038/s41586-023-05769-3 ↗
BibTeX
@article{Lake_2023,
  title = {An atlas of healthy and injured cell states and niches in the human kidney},
  volume = {619},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-023-05769-3},
  DOI = {10.1038/s41586-023-05769-3},
  number = {7970},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Lake, Blue B. and Menon, Rajasree and Winfree, Seth and Hu, Qiwen and Melo Ferreira, Ricardo and Kalhor, Kian and Barwinska, Daria and Otto, Edgar A. and Ferkowicz, Michael and Diep, Dinh and Plongthongkum, Nongluk and Knoten, Amanda and Urata, Sarah and Mariani, Laura H. and Naik, Abhijit S. and Eddy, Sean and Zhang, Bo and Wu, Yan and Salamon, Diane and Williams, James C. and Wang, Xin and Balderrama, Karol S. and Hoover, Paul J. and Murray, Evan and Marshall, Jamie L. and Noel, Teia and Vijayan, Anitha and Hartman, Austin and Chen, Fei and Waikar, Sushrut S. and Rosas, Sylvia E. and Wilson, Francis P. and Palevsky, Paul M. and Kiryluk, Krzysztof and Sedor, John R. and Toto, Robert D. and Parikh, Chirag R. and Kim, Eric H. and Satija, Rahul and Greka, Anna and Macosko, Evan Z. and Kharchenko, Peter V. and Gaut, Joseph P. and Hodgin, Jeffrey B. and Knight, Richard and Lecker, Stewart H. and Stillman, Isaac and Amodu, Afolarin A. and Ilori, Titlayo and Maikhor, Shana and Schmidt, Insa and McMahon, Gearoid M. and Weins, Astrid and Hacohen, Nir and Bush, Lakeshia and Gonzalez-Vicente, Agustin and Taliercio, Jonathan and O’toole, John and Poggio, Emilio and Cooperman, Leslie and Jolly, Stacey and Herlitz, Leal and Nguyen, Jane and Palmer, Ellen and Sendrey, Dianna and Spates-Harden, Kassandra and Appelbaum, Paul and Barasch, Jonathan M. and Bomback, Andrew S. and D’Agati, Vivette D. and Mehl, Karla and Canetta, Pietro A. and Shang, Ning and Balderes, Olivia and Kudose, Satoru and Barisoni, Laura and Alexandrov, Theodore and Cheng, Yinghua and Dunn, Kenneth W. and Kelly, Katherine J. and Sutton, Timothy A. and Wen, Yumeng and Corona-Villalobos, Celia P. and Menez, Steven and Rosenberg, Avi and Atta, Mohammed and Johansen, Camille and Sun, Jennifer and Roy, Neil and Williams, Mark and Azeloglu, Evren U. and He, Cijang and Iyengar, Ravi and Hansen, Jens and Xiong, Yuguang and Rovin, Brad and Parikh, Samir and Madhavan, Sethu M. and Anderton, Christopher R. and Pasa-Tolic, Ljiljana and Velickovic, Dusan and Troyanskaya, Olga and Sealfon, Rachel and Tuttle, Katherine R. and Laszik, Zoltan G. and Nolan, Garry and Sarwal, Minnie and Anjani, Kavya and Sigdel, Tara and Ascani, Heather and Balis, Ulysses G. J. and Lienczewski, Chrysta and Steck, Becky and He, Yougqun and Schaub, Jennifer and Blanc, Victoria M. and Murugan, Raghavan and Randhawa, Parmjeet and Rosengart, Matthew and Tublin, Mitchell and Vita, Tina and Kellum, John A. and Hall, Daniel E. and Elder, Michele M. and Winters, James and Gilliam, Matthew and Alpers, Charles E. and Blank, Kristina N. and Carson, Jonas and De Boer, Ian H. and Dighe, Ashveena L. and Himmelfarb, Jonathan and Mooney, Sean D. and Shankland, Stuart and Williams, Kayleen and Park, Christopher and Dowd, Frederick and McClelland, Robyn L. and Daniel, Stephen and Hoofnagle, Andrew N. and Wilcox, Adam and Bansal, Shweta and Sharma, Kumar and Venkatachalam, Manjeri and Zhang, Guanshi and Pamreddy, Annapurna and Kakade, Vijaykumar R. and Moledina, Dennis and Shaw, Melissa M. and Ugwuowo, Ugochukwu and Arora, Tanima and Ardayfio, Joseph and Bebiak, Jack and Brown, Keith and Campbell, Catherine E. and Saul, John and Shpigel, Anna and Stutzke, Christy and Koewler, Robert and Campbell, Taneisha and Hayashi, Lynda and Jefferson, Nichole and Pinkeney, Roy and Roberts, Glenda V. and Eadon, Michael T. and Dagher, Pierre C. and El-Achkar, Tarek M. and Zhang, Kun and Kretzler, Matthias and Jain, Sanjay},
  year = {2023},
  month = July,
  pages = {585–594}
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB