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Visium

Mouse uterus

NCBI790

Interactive viewer H&E ✓ Verified publication
Mouse uterus preview
print(sdata) 
SpatialData object
├── Images
│     └── 'NCBI790_full_image': DataTree[cyx] (3, 9362, 9409), (3, 4681, 4704), (3, 2340, 2352), (3, 1170, 1176)
├── Shapes
│     └── 'NCBI790_spots': GeoDataFrame shape: (1625, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1625, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI790_full_image (Images), NCBI790_spots (Shapes)
Load in Python 
import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("g2FPaiGEJaUpYDiG")   # 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/g2FPaiGEJaUpYDiG

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid g2FPaiGEJaUpYDiG
Load with the Python client 
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["g2FPaiGEJaUpYDiG0001"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

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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
Chemistry
Visium v1
Resolution
9,409 × 9,362 px
mpp
0.910 µm/px
Size
170 MB
Sample ID
NCBI790
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