Visium

Human placenta

NCBI815

silver Interactive viewer H&E COVID-19 ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI815_full_image': DataTree[cyx] (3, 9238, 9564), (3, 4619, 4782), (3, 2309, 2391), (3, 1154, 1195)
├── Shapes
│     └── 'NCBI815_spots': GeoDataFrame shape: (369, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (369, 36601)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI815_full_image (Images), NCBI815_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("W3RgxmAp6qJJQoYV0000")
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("W3RgxmAp6qJJQoYV")   # 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 W3RgxmAp6qJJQoYV0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/W3RgxmAp6qJJQoYV

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid W3RgxmAp6qJJQoYV

Install (Python 3.12+) Docs →

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

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Part of collection

SARS-CoV-2 Niches in Human Placenta Revealed by Spatial Transcriptomics→

15 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: placenta
Condition: COVID-19
Modality: RNA
Observations (spots): 369
Tier: silver
Chemistry: Visium v1
Resolution: 9,564 × 9,238 px
mpp: 0.911 µm/px
Size: 101 MB
Sample ID: NCBI815
License: CC BY-NC-SA 4.0 NonCommercial
Published: Jul 5, 2023

Cite this dataset

doi.org/10.1016/j.medj.2023.06.003 ↗

BibTeX

@article{Barrozo_2023,
  title = {SARS-CoV-2 niches in human placenta revealed by spatial transcriptomics},
  volume = {4},
  ISSN = {2666-6340},
  url = {http://dx.doi.org/10.1016/j.medj.2023.06.003},
  DOI = {10.1016/j.medj.2023.06.003},
  number = {9},
  journal = {Med},
  publisher = {Elsevier BV},
  author = {Barrozo, Enrico R. and Seferovic, Maxim D. and Castro, Eumenia C.C. and Major, Angela M. and Moorshead, David N. and Jochum, Michael D. and Rojas, Ricardo Ferral and Shope, Cynthia D. and Aagaard, Kjersti M.},
  year = {2023},
  month = Sept,
  pages = {612–634.e4}
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB