Visium

Mouse uterus

NCBI823

bronze Interactive viewer H&E Provisional

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI823_full_image': DataTree[cyx] (3, 9518, 9742), (3, 4759, 4871), (3, 2379, 2435), (3, 1189, 1217)
├── Shapes
│     └── 'NCBI823_spots': GeoDataFrame shape: (875, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (875, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI823_full_image (Images), NCBI823_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("pn7C0oP7pEb1zf16")   # 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/pn7C0oP7pEb1zf16

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pn7C0oP7pEb1zf16

Load with the Python client

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

ds = Catalog().cohort(uids=["pn7C0oP7pEb1zf160000"])[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

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
Modality: RNA
Observations: 875
Tier: bronze
Chemistry: Visium v1
Resolution: 9,742 × 9,518 px
mpp: 0.909 µm/px
Size: 81 MB
Sample ID: NCBI823
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