I recently tested the Matlab/ImageJ connection via mij/ij utility provided by http://bigwww.epfl.ch/sage/soft/mij/
MIJ.createImage(image3D); to pass the 3D image matrix from Matlab to ImageJ. and
xyPointsM = MIJ.getRoi(0); to get the x,y ROI points out of ImageJ. However, I am having trouble creating an ROI on multiple slices and then passing the ROI coordinates on multiple slices back to Matlab.
Any help is much appreciated.