Visium

Mouse uterus

NCBI788

silver Interactive viewer H&E Zika virus infectious disease ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI788_full_image': DataTree[cyx] (3, 9447, 10136), (3, 4723, 5068), (3, 2361, 2534), (3, 1180, 1267)
├── Shapes
│     └── 'NCBI788_spots': GeoDataFrame shape: (1182, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1182, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI788_full_image (Images), NCBI788_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("6bLtulWAVASecJ7R0000")
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("6bLtulWAVASecJ7R")   # 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 6bLtulWAVASecJ7R0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/6bLtulWAVASecJ7R

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 6bLtulWAVASecJ7R

Install (Python 3.12+) Docs →

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

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics [visium]→

8 datasets · comparison

Metadata

Technology: Visium
Organism: mouse
Tissue: uterus
Condition: Zika virus infectious disease
Modality: RNA
Observations (spots): 1,182
Tier: silver
Chemistry: Visium v1
Resolution: 10,136 × 9,447 px
mpp: 0.910 µm/px
Size: 179 MB
Sample ID: NCBI788
License: CC BY-NC-SA 4.0 NonCommercial
Published: Jun 3, 2023

Cite this dataset

doi.org/10.1016/j.ajog.2023.08.012 ↗

BibTeX

@article{Barrozo_2024,
  title = {Zika virus co-opts microRNA networks to persist in placental niches detected by spatial transcriptomics},
  volume = {230},
  ISSN = {0002-9378},
  url = {http://dx.doi.org/10.1016/j.ajog.2023.08.012},
  DOI = {10.1016/j.ajog.2023.08.012},
  number = {2},
  journal = {American Journal of Obstetrics and Gynecology},
  publisher = {Elsevier BV},
  author = {Barrozo, Enrico R. and Seferovic, Maxim D. and Hamilton, Mark P. and Moorshead, David N. and Jochum, Michael D. and Do, Trang and O’Neil, Derek S. and Suter, Melissa A. and Aagaard, Kjersti M.},
  year = {2024},
  month = Feb,
  pages = {251.e1–251.e17}
}

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