Visium
Mouse liver
NCBI841
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI841_full_image': DataTree[cyx] (3, 9992, 9962), (3, 4996, 4981), (3, 2498, 2490), (3, 1249, 1245)
├── Shapes
│ └── 'NCBI841_spots': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 31053)
with coordinate systems:
▸ 'global', with elements:
NCBI841_full_image (Images), NCBI841_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("KoCCEp2MImSg0jWA") # 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/KoCCEp2MImSg0jWA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid KoCCEp2MImSg0jWA Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["KoCCEp2MImSg0jWA0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Multimodal decoding of human liver regeneration [st_mouse]→ 19 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- liver
- Modality
- RNA
- Observations
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 9,962 × 9,992 px
- mpp
- 0.860 µm/px
- Size
- 187 MB
- Sample ID
- NCBI841
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Feb 1, 2023
Cite this dataset
doi.org/10.1038/s41586-024-07376-2 ↗ BibTeX
@article{Matchett_2024,
title = {Multimodal decoding of human liver regeneration},
volume = {630},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-024-07376-2},
DOI = {10.1038/s41586-024-07376-2},
number = {8015},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Matchett, K. P. and Wilson-Kanamori, J. R. and Portman, J. R. and Kapourani, C. A. and Fercoq, F. and May, S. and Zajdel, E. and Beltran, M. and Sutherland, E. F. and Mackey, J. B. G. and Brice, M. and Wilson, G. C. and Wallace, S. J. and Kitto, L. and Younger, N. T. and Dobie, R. and Mole, D. J. and Oniscu, G. C. and Wigmore, S. J. and Ramachandran, P. and Vallejos, C. A. and Carragher, N. O. and Saeidinejad, M. M. and Quaglia, A. and Jalan, R. and Simpson, K. J. and Kendall, T. J. and Rule, J. A. and Lee, W. M. and Hoare, M. and Weston, C. J. and Marioni, J. C. and Teichmann, S. A. and Bird, T. G. and Carlin, L. M. and Henderson, N. C.},
year = {2024},
month = May,
pages = {158–165}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB