Visium

Human kidney

NCBI565

silver Interactive viewer H&E nephrolithiasis ✓ Verified publication

Preview Client Lamin CLI

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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("uPnF4kwEcckN5w100000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("uPnF4kwEcckN5w10")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download uPnF4kwEcckN5w100000 --dest data/

# or lamin: 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

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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

Part 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 (spots): 1,085
Tier: silver
Chemistry: Visium v1
Resolution: 10,473 × 11,299 px
mpp: 0.758 µm/px
Size: 209 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