GUI arduino serial communication

Hello, I have created a GUI where I am going to capture an image and perform some operations only after I get an interrupt from arduino. Arduino gives interrupt after every 60 sec(It can be anything). So after the first interrupt, I want the camera to take snapshot (meanwhile the timer should be ON at background counting 60 sec). This is what is expected but when I tried to do this either I can access the camera or I can do the serial communication but not both. This is my code:

%Start Your Timer

 p1='';

 while 1

     set(r, 'Timeout',5);
     p= fgets(r);

   if ~strcmp(p,p1)

   if strcmp(p,'N') %Comes after 60 sec
     vid= videoinput('winvideo', 1);
                axes(handles.axes2);
                hImage=image(zeros(640,480,3),'Parent',handles.axes2);
                preview(vid,hImage)

   end

   if strcmp(p,'C') %Comes after 60 sec
     %Do something else
   end

    end
 end

How can I do it simultaneously? Any help? Thank you