Visium
Mouse skin of body
NCBI687
silver Interactive viewer H&E cutaneous melanoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI687_full_image': DataTree[cyx] (3, 9727, 9792), (3, 4863, 4896), (3, 2431, 2448), (3, 1215, 1224)
├── Shapes
│ └── 'NCBI687_spots': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 31053)
with coordinate systems:
▸ 'global', with elements:
NCBI687_full_image (Images), NCBI687_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("70ca9J8pXGdZnTWc") # 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/70ca9J8pXGdZnTWc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 70ca9J8pXGdZnTWc Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["70ca9J8pXGdZnTWc0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
A cellular hierarchy in melanoma uncouples growth and metastasis→ 3 datasets · publication
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- skin of body
- Condition
- cutaneous melanoma
- Modality
- RNA
- Observations
- 4,992
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 9,792 × 9,727 px
- mpp
- 0.949 µm/px
- Size
- 233 MB
- Sample ID
- NCBI687
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jul 12, 2022
Cite this dataset
doi.org/10.1038/s41586-022-05242-7 ↗ BibTeX
@article{Karras_2022,
title = {A cellular hierarchy in melanoma uncouples growth and metastasis},
volume = {610},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-022-05242-7},
DOI = {10.1038/s41586-022-05242-7},
number = {7930},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Karras, Panagiotis and Bordeu, Ignacio and Pozniak, Joanna and Nowosad, Ada and Pazzi, Cecilia and Van Raemdonck, Nina and Landeloos, Ewout and Van Herck, Yannick and Pedri, Dennis and Bervoets, Greet and Makhzami, Samira and Khoo, Jia Hui and Pavie, Benjamin and Lamote, Jochen and Marin-Bejar, Oskar and Dewaele, Michael and Liang, Han and Zhang, Xingju and Hua, Yichao and Wouters, Jasper and Browaeys, Robin and Bergers, Gabriele and Saeys, Yvan and Bosisio, Francesca and van den Oord, Joost and Lambrechts, Diether and Rustgi, Anil K. and Bechter, Oliver and Blanpain, Cedric and Simons, Benjamin D. and Rambow, Florian and Marine, Jean-Christophe},
year = {2022},
month = Sept,
pages = {190–198}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB