Visium
Human placenta
NCBI576
silver Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI576_full_image': DataTree[cyx] (3, 9371, 9722), (3, 4685, 4861), (3, 2342, 2430), (3, 1171, 1215)
├── Shapes
│ └── 'NCBI576_spots': GeoDataFrame shape: (470, 2) (2D shapes)
└── Tables
└── 'table': AnnData (470, 36601)
with coordinate systems:
▸ 'global', with elements:
NCBI576_full_image (Images), NCBI576_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("fheRN6YV1yMJQpzV") # 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/fheRN6YV1yMJQpzV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid fheRN6YV1yMJQpzV Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["fheRN6YV1yMJQpzV0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
SARS-CoV-2 Niches in Human Placenta Revealed by Spatial Transcriptomics→ 15 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- placenta
- Modality
- RNA
- Observations
- 470
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 9,722 × 9,371 px
- mpp
- 0.912 µm/px
- Size
- 125 MB
- Sample ID
- NCBI576
- 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