Visium
Human eye
NCBI595
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI595_full_image': DataTree[cyx] (3, 16616, 17467), (3, 8308, 8733), (3, 4154, 4366), (3, 2077, 2183)
├── Shapes
│ └── 'NCBI595_spots': GeoDataFrame shape: (1303, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1303, 21821)
with coordinate systems:
▸ 'global', with elements:
NCBI595_full_image (Images), NCBI595_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("KIfZBnzaURyWg5aR0000")
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("KIfZBnzaURyWg5aR") # 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 KIfZBnzaURyWg5aR0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/KIfZBnzaURyWg5aR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid KIfZBnzaURyWg5aRLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
GENE EXPRESSION WITHIN A HUMAN CHOROIDAL NEOVASCULAR MEMBRANE USING SPATIAL TRANSCRIPTOMICS→ 5 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- eye
- Modality
- RNA
- Observations (spots)
- 1,303
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 17,467 × 16,616 px
- mpp
- 0.464 µm/px
- Size
- 499 MB
- Sample ID
- NCBI595
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Aug 7, 2023
Cite this dataset
doi.org/10.1101/2023.06.16.544770 ↗ BibTeX
@article{Voigt_2023,
title = {GENE EXPRESSION WITHIN A HUMAN CHOROIDAL NEOVASCULAR MEMBRANE USING SPATIAL TRANSCRIPTOMICS},
url = {http://dx.doi.org/10.1101/2023.06.16.544770},
DOI = {10.1101/2023.06.16.544770},
publisher = {openRxiv},
author = {Voigt, Andrew P. and Mullin, Nathaniel K. and Navratil, Emma M. and Flamme-Wiese, Miles J. and Lin, Li-Chun and Scheetz, Todd E. and Han, Ian C. and Stone, Edwin M. and Tucker, Budd A. and Mullins, Robert F.},
year = {2023},
month = June
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB