as @Danielle_Z mentioned, your question is quite broad and it is not totally clear what is needed. Do you need to use the existing Matlab functions or existing software packages to analyse images or you need to develop your own procedure?
The analysis depends on type of imaging that you are aiming to analyse. In some cases, you can use automatic methods to segment the areas of interest and quantify them (for example, their area, diameter, intensity of underlying image); in many others, you have to stick (stuck) with doing all the same manually.
In any case, Matlab has many useful functions and good examples on how to use them, so please check the Image Processing and Computer Vision section (https://se.mathworks.com/help/index.html). The good starting point is Image Processing toolbox (https://se.mathworks.com/help/images/index.html).
In addition, Mathworks in the recent releases started to include ready made solutions for various image processing tasks. You can also check the source code of MIB (http://mib.helsinki.fi/downloads.html), which is utilizing many of these and other functions for image processing in Matlab.
I recommend you to find a local bio-image analyst, he/she will be able to guide you.