I am completely new to ImageJ but I would love to learn more and understand better if it suits to my analysis.
In summary, I have two pictures of bacteria cells and I want to measure the intensity of their reflection with two different wavelengths.
My desire is to select the bacterial cells, measure the intensity of the light and apply the same selection with the same outlines (the two pictures are the same but different light exposure) in the second picture, in order to have the same selected cells and automatically record the intensity of the light. Is it something I can do with this software?
Yes, absolutely. I would suggest familiarizing yourself with the ROIManager. You may also want to familiarize yourself with the Measurements feature and the various ways to create selections (and this for basic-shape selections).
One you have made a selection, you should be able to save it to the ROIManager. You can then select the other image and use the saved ROI to select the same region in your second image.
Please let us know if you need any more help.