Hello! I am a humble bioengineer with 0 life experience in coding, and this rep is for keeping my ugly scripts to get some easy ImageJ stuff automated.
This script was written for ImageJ 1.54d. If the output of your microscope is a grayscale image and you'd like it to be coloured in red, green or blue, this script will enable you to batch-process a folder of images and create an output folder containing the result.
After live/dead imaging of spheroids on the confocal, I got a Z-stack series of images from two channels. I exported images as greyscale, and eventually in the folder I had tiff files with the names ending by ch00 (for green) and ch01 (for red). I wanted to calculate the total area of green (live) and red (dead) cells in each layer of my z-stack to calculate the ratio afterwards. This script enables me to do so.