I’m brand new to ImageJ and, after two weeks of trying to figure this out on my own, I’ve decided to ask for help.
I’m doing a mutagenesis screen in worms with fluorescence as my reporter. This means that when I have a hit, the worm stops fluorescing. This is looking for a dark needle in a dark haystack, and I was hoping ImageJ could help me automate the load.
Essentially, I take two images of many worms in the same field, a brightfield and a fluorescent image, in quick succession. Then, I want to automate ImageJ to locate and outline/select the worms in the brightfield image, and then run(“measure”) on each of the worms in the fluorescent image. Thus, a worm is detected in the brightfield image and, should it measure at nearly the same brightness as it’s background in the fluorescent image, it’s a hit!
So far, I’m opening images as a stack, running subtract background and threshold on the brightfield and getting selections, but I can’t seem to figure out how to identify each worm, and then analyze it in the other image. Can anyone please help me?? I have this feeling that the answer is obnoxiously obvious and that I’m missing it due to inexperience with this program…
Thanks in advance!