Background Removal and Object Tracking - Track Fish Jumping Out of the Water 0 down vote favorite

I am totally new to Image processing. I just started my Master thesis in the area of Computer vision and Machine learning. My background is Informatics. Now, my first task is to register the images of some fishes(Image registration) as they come out of water. I have got stream of images and I want to come up with a model of the fish by aligning the temporally different images of a fish. As, I can understand, I will have to fist of all remove the background and water from the images to work on just fishes, am I right?

Can anyone give me a brief idea of how I should go forward or the things I should read first before I can understand the things. For example, should I read the basics of Image Processing, Feature detection, Image segmentation....? and regarding the programming language I can use - one where I can find good libraries, forums, other help.

I would be really grateful, if anyone can help. Thanks
I`d recommend you to go through any of this courses (they include lectures, references and task for labs)


https://cw.felk.cvut.cz/wiki/courses/ae4m33mpv/start - course from Czech Technical University 
http://cs.brown.edu/courses/cs143/ from Brown University