This program takes a sub block from the ISH database of the Ivy Glioblastoma Atlas Project and loads the different regions into the R library spatstat. It downloads the images using the API, detects the different boundaries within the images, detects the cells within the images, and finally saves the result in a spatstat ppp object in a seperate .Rdata file for each gene.
To run the program follow these steps (Note: the application has only been tested for Windows devices) Installation:
- Download this GitHub repository
- Download QuPath https://github.com/qupath/qupath/releases/tag/v0.4.3 Make sure to download the .zip version and extract the contents
- Run the following commands in the command prompt (or any terminal) in the same directory as this repository to install the necessary dependencies pip install -r requirements.txt pip install lxml
- Download R https://cran.r-project.org/bin/windows/base/
- Run the following R commands install.packages("spatstat") install.packages("rlist")
Running the application:
- Update the tissueSubBlock, QuPathAbsPath, RscriptAbsPath, and currentDirectory variables in the top of the main.py file to the desired values.
- Run the main.py file. Make sure to run main.py in the same working directory as the repository