help ginput
That function will get the coordinates of the pixel the user clicks. You could have the user press a pushbutton to enable the pixel selection, then put your ginput call in the pushbutton callback.
Then, you can store these values by saving them to the handles structure:
[x,y] = ginput(N) %where N is the number of points desired
handles.X = x;
handles.Y = y;
guidata(handles.my_pushbutton,handles)
