Chapter 5 Instructions - From Start to Finish

This section describes how to use the script from start to finish, without too much extra detail. Find here a YouTube video with step by step instructions for running the pipeline with the sample data.

5.1 Download the Repository

  1. Download the github repo and save the folder on your device. Find the CoMarker Github page here.
  2. The main folder must include the ‘Functions’ and ‘HTML Reports’ folders. This naming is crucial for the R script to run.

5.2 Run ImageJ

  1. Download Fiji ImageJ here if it is not already installed on your device.
  2. Open the script named ‘CoMarker_Macro.ijm’ on ImageJ, and click run.
  3. Input your parameters in the dialog box, referring to the ImageJ Walkthrough section of this site for additional details.
  4. Once all three parameter boxes have been completed, the script will run automatically. The time taken to run the script will depend on the number of images used. It typically takes 1 to 8 seconds to analyse all of the images for each replicate.
  5. Once the script has finished running, ImageJ may be closed.

5.3 Run R Studio

  1. Open R and run or source the wrapper function, which is situated in the functions folder of the repository.
  2. Input the parameters, as explained in the R Walkthrough section of this site.
  3. Run the script. A HTML document will be produced in the results directory, summarising your results.