Visium

Mouse unknown

NCBI680

bronze Interactive viewer H&E ✓ Verified publication

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI680_full_image': DataTree[cyx] (3, 2787, 2600), (3, 1393, 1300), (3, 696, 650), (3, 348, 325)
├── Shapes
│     └── 'NCBI680_spots': GeoDataFrame shape: (2772, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2772, 15480)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI680_full_image (Images), NCBI680_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("dyty7Kn9dCAhnuFk")   # 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/dyty7Kn9dCAhnuFk

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dyty7Kn9dCAhnuFk

Load with the Python client

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

ds = Catalog().cohort(uids=["dyty7Kn9dCAhnuFk0000"])[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

Metadata

Technology: Visium
Organism: mouse
Tissue: unknown
Modality: RNA
Observations: 2,772
Tier: bronze
Chemistry: Visium v1
Resolution: 2,600 × 2,787 px
mpp: 3.236 µm/px
Size: 36 MB
Sample ID: NCBI680
License: CC BY-NC-SA 4.0 NonCommercial
Published: May 17, 2022

Cite this dataset

doi.org/10.1016/j.jid.2022.06.014 ↗

BibTeX

@article{Kim_2022,
  title = {Different Molecular Features of Epithelioid and Giant Cells in Foreign Body Reaction Identified by Single-Cell RNA Sequencing},
  volume = {142},
  ISSN = {0022-202X},
  url = {http://dx.doi.org/10.1016/j.jid.2022.06.014},
  DOI = {10.1016/j.jid.2022.06.014},
  number = {12},
  journal = {Journal of Investigative Dermatology},
  publisher = {Elsevier BV},
  author = {Kim, Yoon-Seob and Shin, Sun and Choi, Eun Ji and Moon, Seong Won and Jung, Chan Kwon and Chung, Yeun-Jun and Lee, Sug Hyung},
  year = {2022},
  month = Dec,
  pages = {3232–3242.e16}
}

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