Visium
Human intestine
MISC47
silver Interactive viewer H&E colon adenocarcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MISC47_full_image': DataTree[cyx] (3, 40228, 33578), (3, 20114, 16789), (3, 10057, 8394), (3, 5028, 4197)
├── Shapes
│ └── 'MISC47_spots': GeoDataFrame shape: (4818, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4818, 19327)
with coordinate systems:
▸ 'global', with elements:
MISC47_full_image (Images), MISC47_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Za6gMhRyrRrhnKns0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Za6gMhRyrRrhnKns") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download Za6gMhRyrRrhnKns0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Za6gMhRyrRrhnKns
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Za6gMhRyrRrhnKnsLicense: CC BY-NC-SA 4.0 (noncommercial)
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- intestine
- Condition
- colon adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 4,818
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 33,578 × 40,228 px
- mpp
- 0.276 µm/px
- Size
- 4.2 GB
- Sample ID
- MISC47
- 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