I am trying to automate the procedure of comparing the colocalization in two images using the headless mode in Fiji.
A brief procedure of what I am trying to do:
- Open an image, split channels, and close the blue and green channels.
- Open a second image and again split channels, and close the blue and green channels.
- Analyze the two red channel images using coloc 2 and save the log file.
I have added the imagej source folder to the path.
Here is the batch code I have so far:
imagej-win64 --ij2 --headless MZ_104.0263.png -run "Split Channels" -run "Close" -run "Close" MZ_108.0951.png -run "Split Channels" -run "Close" -run "Close" -run "Coloc 2"
How do I proceed after this? Manipulating the various options that coloc 2 offers, then running it and then saving the report and the log files (using a naming scheme of my choice)?
Also, I need to do this for multiple pairs of images, if there is a way to do that efficiently.
This bat file would be created as a part of a larger python script and the log text file saved from it would be used for further analysis. Mentioning this just in case there is a python based solution to this problem. I am using python 3.7
Any help will be much appreciated. I have attached the images I am using.