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Visium

Mouse unknown

NCBI680

bronze Interactive viewer H&E ✓ Verified publication
Mouse unknown preview
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)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("dyty7Kn9dCAhnuFk0000")
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("dyty7Kn9dCAhnuFk")   # 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 dyty7Kn9dCAhnuFk0000 --dest data/

# or lamin: 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
Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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Metadata

Technology
Visium
Organism
mouse
Tissue
unknown
Modality
RNA
Observations (spots)
2,772
Tier
bronze
Chemistry
Visium v1
Resolution
2,600 × 2,787 px
mpp
3.236 µm/px
Size
37.5 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