Make a GUI with pushbutton and axis
Display the image on that axis
The button callback will be something like this
This will allow you to get the coordinates of the pixels, x is a vector with the vertical positions and y is a vector with the horizontal positions, number is the number of points you let the user mark on the picture.
If you want the user to decide how many points he wants do something like this
xx=[xx x];yy=[yy y];
This will save the points the user selected into xx and yy vectors until the user presses another button than 1 (left mouse button on my system)