If I understand your question correctly, all you need to do is have a call to imwrite inside the loop that writes the video frame with the markers for visible points and bounding box to a file.
So something like this:
Before the while loop:
nFrame = 1;
In the loop right at the end,
imwrite(videoFrame,['image_' double2str(nFrame)],'png');
n = n + 1;
