Welcome to the Forum!
So... just to get you started on what you'd need to do to measure the intensity of your signal - take a look at the Segmentation page of the ImageJ wiki. There are also some nice step-by-step explanations in this Fiji-Segmentation workshop.
But just looking at your images... you have areas within the image that are out-of-focus. This will disrupt your measurements - as those areas will presumably vary from image-to-image - so you need to keep that in mind, knowing your measurements may not be as robust as you need in the end. Would it be possible to take stacks of these samples?
I hope this can at least get you started.