Visium
Human pancreas
NCBI572
silver Interactive viewer H&E pancreatic adenocarcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI572_full_image': DataTree[cyx] (3, 14848, 14592), (3, 7424, 7296), (3, 3712, 3648), (3, 1856, 1824)
├── Shapes
│ └── 'NCBI572_spots': GeoDataFrame shape: (3794, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3794, 20615)
with coordinate systems:
▸ 'global', with elements:
NCBI572_full_image (Images), NCBI572_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("B29NR7Ts0SVORISV") # 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/B29NR7Ts0SVORISV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid B29NR7Ts0SVORISV Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["B29NR7Ts0SVORISV0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 3,794
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 14,592 × 14,848 px
- mpp
- 0.547 µm/px
- Size
- 478 MB
- Sample ID
- NCBI572
- 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