Visium

Human pancreas

NCBI570

silver Interactive viewer H&E pancreatic adenocarcinoma ✓ Verified publication

Preview Download via Python Download via CLI Load via sddb

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)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("oRj9VX1Iis0pYviC")   # 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/oRj9VX1Iis0pYviC

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

Load with the Python client

# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["oRj9VX1Iis0pYviC0000"])[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

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: 3,216
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 14,592 × 14,336 px
mpp: 0.546 µm/px
Size: 397 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