Create a standalone executable program in C++/Java or similar language using existing libraries such as OpenCV / OpenGL to perform the following -
Compute the average of ~20 images to use as a reference.
During execution, capture a test image and compare it to the reference to create a difference image. (simple subtraction, or variance, etc)
Visualize the difference image as a 3D rotatable topographical mesh. (similar to what is available in Excel - probably OpenGL will be the easiest way to do this)
The program would also need a GUI that would let the user mark regions of interest (ROIs). For each ROI, compute the mean and compare with the reference mean and display it in the ROI as text.