Calling ImageJ plugins directly in MATLAB

Posted by ddickinson on
URL: http://imagej.273.s1.nabble.com/Calling-ImageJ-plugins-directly-in-MATLAB-tp5002621.html

Hi everyone,

I'm using Michael Schmid's "Find Maxima" plugin to locate peaks in some images.  This is part of a complicated image processing pipeline that runs in MATLAB, so I've been calling the command using

MIJ.run('Find Maxima...')

This works, but the problem is that MIJ seems to require that the image is displayed in order for the "Find Maxima" command to work (if I change to non-displaying mode, I can see that the ImagePlus object is there - i.e. the image is open - but the command returns error "No Images Open").  I think it should be possible to use the Java functionality of MATLAB to call functions directly, without using MIJ (or using MIJ only to generate the ImagePlus object, not to run the command), but I can't seem to find any documentation on this.  Does anyone know how to do it?  

Thanks,
Dan Dickinson
University of North Carolina