Visium
Human brain
MISC8
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MISC8_full_image': DataTree[cyx] (3, 13332, 13332), (3, 6666, 6666), (3, 3333, 3333), (3, 1666, 1666)
├── Shapes
│ └── 'MISC8_spots': GeoDataFrame shape: (3661, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3661, 33538)
with coordinate systems:
▸ 'global', with elements:
MISC8_full_image (Images), MISC8_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("AdwRf9R0ZEhhO0p3") # 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/AdwRf9R0ZEhhO0p3
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AdwRf9R0ZEhhO0p3 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["AdwRf9R0ZEhhO0p30000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Modality
- RNA
- Observations
- 3,661
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 13,332 × 13,332 px
- mpp
- 0.726 µm/px
- Size
- 419 MB
- Sample ID
- MISC8
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Feb 8, 2021
Cite this dataset
doi.org/10.1038/s41593-020-00787-0 ↗ BibTeX
@article{Maynard_2021,
title = {Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex},
volume = {24},
ISSN = {1546-1726},
url = {http://dx.doi.org/10.1038/s41593-020-00787-0},
DOI = {10.1038/s41593-020-00787-0},
number = {3},
journal = {Nature Neuroscience},
publisher = {Springer Science and Business Media LLC},
author = {Maynard, Kristen R. and Collado-Torres, Leonardo and Weber, Lukas M. and Uytingco, Cedric and Barry, Brianna K. and Williams, Stephen R. and Catallini, Joseph L. and Tran, Matthew N. and Besich, Zachary and Tippani, Madhavi and Chew, Jennifer and Yin, Yifeng and Kleinman, Joel E. and Hyde, Thomas M. and Rao, Nikhil and Hicks, Stephanie C. and Martinowich, Keri and Jaffe, Andrew E.},
year = {2021},
month = Feb,
pages = {425–436}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB