Visium
Human brain
NCBI657
silver Interactive viewer H&E Parkinson disease ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI657_full_image': DataTree[cyx] (3, 47104, 48640), (3, 23552, 24320), (3, 11776, 12160), (3, 5888, 6080)
├── Shapes
│ └── 'NCBI657_spots': GeoDataFrame shape: (3900, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3900, 36601)
with coordinate systems:
▸ 'global', with elements:
NCBI657_full_image (Images), NCBI657_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("15iMIGc3X4XzgKoE") # 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/15iMIGc3X4XzgKoE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 15iMIGc3X4XzgKoE Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["15iMIGc3X4XzgKoE0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section→ 19 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- Parkinson disease
- Modality
- RNA
- Observations
- 3,900
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 48,640 × 47,104 px
- mpp
- 0.172 µm/px
- Size
- 4.5 GB
- Sample ID
- NCBI657
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- May 21, 2023
Cite this dataset
doi.org/10.1038/s41587-023-01937-y ↗ BibTeX
@article{Vicari_2023,
title = {Spatial multimodal analysis of transcriptomes and metabolomes in tissues},
volume = {42},
ISSN = {1546-1696},
url = {http://dx.doi.org/10.1038/s41587-023-01937-y},
DOI = {10.1038/s41587-023-01937-y},
number = {7},
journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
author = {Vicari, Marco and Mirzazadeh, Reza and Nilsson, Anna and Shariatgorji, Reza and Bjärterot, Patrik and Larsson, Ludvig and Lee, Hower and Nilsson, Mats and Foyer, Julia and Ekvall, Markus and Czarnewski, Paulo and Zhang, Xiaoqun and Svenningsson, Per and Käll, Lukas and Andrén, Per E. and Lundeberg, Joakim},
year = {2023},
month = Sept,
pages = {1046–1050}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB