Visium
Human intestine
MISC66
silver Interactive viewer H&E colon adenocarcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MISC66_full_image': DataTree[cyx] (3, 30539, 39908), (3, 15269, 19954), (3, 7634, 9977), (3, 3817, 4988)
├── Shapes
│ └── 'MISC66_spots': GeoDataFrame shape: (3970, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3970, 19347)
with coordinate systems:
▸ 'global', with elements:
MISC66_full_image (Images), MISC66_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("N1oeYg3O9wHE68MW") # 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/N1oeYg3O9wHE68MW
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid N1oeYg3O9wHE68MW Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["N1oeYg3O9wHE68MW0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- intestine
- Condition
- colon adenocarcinoma
- Modality
- RNA
- Observations
- 3,970
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 39,908 × 30,539 px
- mpp
- 0.276 µm/px
- Size
- 2.9 GB
- Sample ID
- MISC66
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Dec 7, 2023
Cite this dataset
doi.org/10.1016/j.cell.2023.11.006 ↗ BibTeX
@article{Heiser_2023,
title = {Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors},
volume = {186},
ISSN = {0092-8674},
url = {http://dx.doi.org/10.1016/j.cell.2023.11.006},
DOI = {10.1016/j.cell.2023.11.006},
number = {25},
journal = {Cell},
publisher = {Elsevier BV},
author = {Heiser, Cody N. and Simmons, Alan J. and Revetta, Frank and McKinley, Eliot T. and Ramirez-Solano, Marisol A. and Wang, Jiawei and Kaur, Harsimran and Shao, Justin and Ayers, Gregory D. and Wang, Yu and Glass, Sarah E. and Tasneem, Naila and Chen, Zhengyi and Qin, Yan and Kim, William and Rolong, Andrea and Chen, Bob and Vega, Paige N. and Drewes, Julia L. and Markham, Nicholas O. and Saleh, Nabil and Nikolos, Fotis and Vandekar, Simon and Jones, Angela L. and Washington, M. Kay and Roland, Joseph T. and Chan, Keith S. and Schürpf, Thomas and Sears, Cynthia L. and Liu, Qi and Shrubsole, Martha J. and Coffey, Robert J. and Lau, Ken S.},
year = {2023},
month = Dec,
pages = {5620–5637.e16}
}Source: cell.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB