title: Image registration in imageJ or matlab
body: <p>I am looking for advice on how to automatically register image stacks acquired at different magnifications. Specially we need to align a small z-stack (~100um) taken of several brain cells in the live brain to a large z stack(~2mm) taken of the fixed brain. We want to be able to find back the cells that were previously imaged and take high resolution images of the staining to identify pre-synaptic inputs. Both the difference in magnification and rotation need to be taken into account as well as possible shrinkage or swelling. We would like an advice on the best way to do this using ImageJ or matlab.</p>