Visium
Human placenta
NCBI812
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI812_full_image': DataTree[cyx] (3, 9531, 9760), (3, 4765, 4880), (3, 2382, 2440), (3, 1191, 1220)
├── Shapes
│ └── 'NCBI812_spots': GeoDataFrame shape: (2605, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2605, 36601)
with coordinate systems:
▸ 'global', with elements:
NCBI812_full_image (Images), NCBI812_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("dZTXAOy7eZszgnts0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("dZTXAOy7eZszgnts") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download dZTXAOy7eZszgnts0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/dZTXAOy7eZszgnts
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dZTXAOy7eZszgntsLicense: CC BY-NC-SA 4.0 (noncommercial)
Part 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 (spots)
- 2,605
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 9,760 × 9,531 px
- mpp
- 0.909 µm/px
- Size
- 183 MB
- Sample ID
- NCBI812
- 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