Visium
Human intestine
ZEN38
silver Interactive viewer H&E colon adenocarcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'ZEN38_full_image': DataTree[cyx] (3, 16804, 16954), (3, 8402, 8477), (3, 4201, 4238), (3, 2100, 2119)
├── Shapes
│ └── 'ZEN38_spots': GeoDataFrame shape: (387, 2) (2D shapes)
└── Tables
└── 'table': AnnData (387, 36601)
with coordinate systems:
▸ 'global', with elements:
ZEN38_full_image (Images), ZEN38_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("WlpixsZ1jpJGnWn9") # 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/WlpixsZ1jpJGnWn9
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WlpixsZ1jpJGnWn9 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["WlpixsZ1jpJGnWn90000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Charting the Heterogeneity of Colorectal Cancer Consensus Molecular Subtypes using Spatial Transcriptomics: datasets→ 14 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- intestine
- Condition
- colon adenocarcinoma
- Modality
- RNA
- Observations
- 387
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 16,954 × 16,804 px
- mpp
- 0.460 µm/px
- Size
- 451 MB
- Sample ID
- ZEN38
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jan 19, 2023
Cite this dataset
doi.org/10.1101/2023.01.23.525135 ↗ BibTeX
@article{Valdeolivas_2023,
title = {Charting the Heterogeneity of Colorectal Cancer Consensus Molecular Subtypes using Spatial Transcriptomics},
url = {http://dx.doi.org/10.1101/2023.01.23.525135},
DOI = {10.1101/2023.01.23.525135},
publisher = {openRxiv},
author = {Valdeolivas, Alberto and Amberg, Bettina and Giroud, Nicolas and Richardson, Marion and Gálvez, Eric J.C. and Badillo, Solveig and Julien-Laferrière, Alice and Turos, Demeter and von Voithenberg, Lena Voith and Wells, Isabelle and Lo, Amy A. and Yángüez, Emilio and Das Thakur, Meghna and Bscheider, Michael and Sultan, Marc and Kumpesa, Nadine and Jacobsen, Björn and Bergauer, Tobias and Saez-Rodriguez, Julio and Rottenberg, Sven and Schwalie, Petra C. and Hahn, Kerstin},
year = {2023},
month = Jan
}Source: biorxiv.org ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB