Merging a Matlab m application with GUI from App Designer

I have a matlab program that reads in a series of DICOM files and displays them in video format. So far so go. I would like to add GUI widgets to allow the user to control the display speed, CLUT and constrast, an query about the displayed images. I can see the ease of creating the tools/interface using appdesigner, but I am having conceptual difficulty with where and how to put my code in merging the two.

I would like to see an example of this being done, and/or an explaination of how to do this. So far everything I have seen is building simple GUIs from the ground up.

Thanks