Visium
Human skin of body
MEND40
silver Interactive viewer H&E skin squamous cell carcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MEND40_full_image': DataTree[cyx] (3, 47104, 48640), (3, 23552, 24320), (3, 11776, 12160), (3, 5888, 6080)
├── Shapes
│ └── 'MEND40_spots': GeoDataFrame shape: (2793, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2793, 33538)
with coordinate systems:
▸ 'global', with elements:
MEND40_full_image (Images), MEND40_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("lYMZtFpcJbilQiqS") # 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/lYMZtFpcJbilQiqS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lYMZtFpcJbilQiqS Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["lYMZtFpcJbilQiqS0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST]→ 16 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- skin squamous cell carcinoma
- Modality
- RNA
- Observations
- 2,793
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 48,640 × 47,104 px
- mpp
- 0.172 µm/px
- Size
- 3.1 GB
- Sample ID
- MEND40
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Aug 20, 2021
Cite this dataset
doi.org/10.1016/j.cell.2020.05.039 ↗ BibTeX
@article{Ji_2020,
title = {Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma},
volume = {182},
ISSN = {0092-8674},
url = {http://dx.doi.org/10.1016/j.cell.2020.05.039},
DOI = {10.1016/j.cell.2020.05.039},
number = {2},
journal = {Cell},
publisher = {Elsevier BV},
author = {Ji, Andrew L. and Rubin, Adam J. and Thrane, Kim and Jiang, Sizun and Reynolds, David L. and Meyers, Robin M. and Guo, Margaret G. and George, Benson M. and Mollbrink, Annelie and Bergenstråhle, Joseph and Larsson, Ludvig and Bai, Yunhao and Zhu, Bokai and Bhaduri, Aparna and Meyers, Jordan M. and Rovira-Clavé, Xavier and Hollmig, S. Tyler and Aasi, Sumaira Z. and Nolan, Garry P. and Lundeberg, Joakim and Khavari, Paul A.},
year = {2020},
month = July,
pages = {497–514.e22}
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB