Visium

Human pancreas

NCBI570

silver Interactive viewer H&E pancreatic adenocarcinoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI570_full_image': DataTree[cyx] (3, 14336, 14592), (3, 7168, 7296), (3, 3584, 3648), (3, 1792, 1824)
├── Shapes
│     └── 'NCBI570_spots': GeoDataFrame shape: (3216, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3216, 20615)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI570_full_image (Images), NCBI570_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("oRj9VX1Iis0pYviC0000")
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("oRj9VX1Iis0pYviC")   # 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 oRj9VX1Iis0pYviC0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/oRj9VX1Iis0pYviC

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid oRj9VX1Iis0pYviC

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

Schwann Cells Shape Tumor Cells and Cancer-Associated Fibroblasts in the Pancreatic Ductal Adenocarcinoma Microenvironment [ST]→

4 datasets · publication

Metadata

Technology: Visium
Organism: human
Tissue: pancreas
Condition: pancreatic adenocarcinoma
Modality: RNA
Observations (spots): 3,216
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 14,592 × 14,336 px
mpp: 0.546 µm/px
Size: 416 MB
Sample ID: NCBI570
License: CC BY-NC-SA 4.0 NonCommercial
Published: May 30, 2023

Cite this dataset

doi.org/10.1038/s41467-023-40314-w ↗

BibTeX

@article{Xue_2023,
  title = {Schwann cells regulate tumor cells and cancer-associated fibroblasts in the pancreatic ductal adenocarcinoma microenvironment},
  volume = {14},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-023-40314-w},
  DOI = {10.1038/s41467-023-40314-w},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Xue, Meilin and Zhu, Youwei and Jiang, Yongsheng and Han, Lijie and Shi, Minmin and Su, Rui and Wang, Liwen and Xiong, Cheng and Wang, Chaofu and Wang, Ting and Deng, Shijie and Wu, Dong and Cao, Yizhi and Dong, Lei and Bai, Fan and Zhao, Shulin and Deng, Xiaxing and Peng, Chenghong and Li, Hongwei and Chen, Jianjun and Shen, Baiyong and Jiang, Lingxi and Chen, Hao},
  year = {2023},
  month = July
}

Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB