Visium
Mouse brain
NCBI801
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI801_full_image': DataTree[cyx] (3, 17209, 17546), (3, 8604, 8773), (3, 4302, 4386), (3, 2151, 2193)
├── Shapes
│ └── 'NCBI801_spots': GeoDataFrame shape: (2889, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2889, 32285)
with coordinate systems:
▸ 'global', with elements:
NCBI801_full_image (Images), NCBI801_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("nDlvhxQ2xdUAwgEx0000")
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("nDlvhxQ2xdUAwgEx") # 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 nDlvhxQ2xdUAwgEx0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/nDlvhxQ2xdUAwgEx
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid nDlvhxQ2xdUAwgExLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
A novel model of binge ethanol exposure reveals enhanced neurodegeneration with advanced age→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,889
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 17,546 × 17,209 px
- mpp
- 0.468 µm/px
- Size
- 895 MB
- Sample ID
- NCBI801
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Mar 18, 2024
Cite this dataset
doi.org/10.1016/j.bbi.2023.12.034 ↗ BibTeX
@article{Anton_2024,
title = {Binge ethanol exposure in advanced age elevates neuroinflammation and early indicators of neurodegeneration and cognitive impairment in female mice},
volume = {116},
ISSN = {0889-1591},
url = {http://dx.doi.org/10.1016/j.bbi.2023.12.034},
DOI = {10.1016/j.bbi.2023.12.034},
journal = {Brain, Behavior, and Immunity},
publisher = {Elsevier BV},
author = {Anton, Paige E. and Rutt, Lauren N. and Kaufman, Michael L. and Busquet, Nicolas and Kovacs, Elizabeth J. and McCullough, Rebecca L.},
year = {2024},
month = Feb,
pages = {303–316}
}Source: sciencedirect.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB