Visium

Human intestine

ZEN36

silver Interactive viewer H&E rectum adenocarcinoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'ZEN36_full_image': DataTree[cyx] (3, 16804, 16954), (3, 8402, 8477), (3, 4201, 4238), (3, 2100, 2119)
├── Shapes
│     └── 'ZEN36_spots': GeoDataFrame shape: (1691, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1691, 36601)
with coordinate systems:
    ▸ 'global', with elements:
        ZEN36_full_image (Images), ZEN36_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("sY8sJhrva5EhZ5iX0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("sY8sJhrva5EhZ5iX")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download sY8sJhrva5EhZ5iX0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/sY8sJhrva5EhZ5iX

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid sY8sJhrva5EhZ5iX

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part 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: rectum adenocarcinoma
Modality: RNA
Observations (spots): 1,691
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 16,954 × 16,804 px
mpp: 0.459 µm/px
Size: 609 MB
Sample ID: ZEN36
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