yes ImageJ/Fiji is thought to measure and analyse and visualize images;)
I think you can start from here:
and in particulare for what you are asking, you can refer to the ROI Manager:
Essentially you can draw a line with line tool then add to the ROI Manager (Analyse->Tools->ROI Manager then with Add you can add your line) and you can also save it (under the More menu of the ROI Manager.
To save the Image with line overlaid you can use the Flatten command (just look that now your new flattened image is an RGB and you can save it in your fav format).
Hoping to be helpful,
have a nice day