Published May 31, 2024
| Version v2
Dataset
Open
Visium HD Human Colorectal Cancer (FFPE) data release pathologist annotation
Authors/Creators
-
1.
RWTH Aachen University
-
2.
Graz University Hospital
- 3. Berlin Institute of Health at Charité – Universitätsmedizin Berlin
Description
10X Genomics released a spatial transcriptomic dataset of human colorectal cancer collected on the Visium HD platform.
The dataset was divided into different spatial domains based on the accompanying HE stain and the expression of characteristic marker genes.
The pathologist's annotation was added with the help of Napari and the Spatialdata python package.
Every .csv file contains the Visium HD bin barcode and annotation for the respective level of binning.
In addition the HE image was segmented and bins were assigned to Nuclei for a pseudo single cell resolution, as described here.
This work was carried out for the SpaceHack2023 project and the data shared here is licensed CC0.