Visium

Human pancreas

NCBI569

silver Interactive viewer H&E pancreatic adenocarcinoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI569_full_image': DataTree[cyx] (3, 14592, 14336), (3, 7296, 7168), (3, 3648, 3584), (3, 1824, 1792)
├── Shapes
│     └── 'NCBI569_spots': GeoDataFrame shape: (3493, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3493, 20615)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI569_full_image (Images), NCBI569_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("UrwO68jLUIz6iDm20000")
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("UrwO68jLUIz6iDm2")   # 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 UrwO68jLUIz6iDm20000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/UrwO68jLUIz6iDm2

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid UrwO68jLUIz6iDm2

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): 3,493
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 14,336 × 14,592 px
mpp: 0.547 µm/px
Size: 472 MB
Sample ID: NCBI569
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