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We present a software module MIJ1 that allows to combine the powerful numerical computation of Matlab2 and the image-analysis capabilities of ImageJ3. Since both ImageJ and Matlab run on multiple operating systems, MIJ is platformindependent. MIJ uses the Java Virtual Machine (JVM) of Matlab to call ImageJ methods from the Matlab console or scripts. In such way, we could bring the richness of ImageJ and of their plugins to the Matlab world.

MIJ contains a collection of static methods to exchange data bidirectionally between Matlab and ImageJ. MIJ has methods to convert and transpose images of ImageJ to 2D matrices and stacks of images to 3D arrays into Matlab. MIJ tries to avoid loss of accuracy by converting the image data to the closest numerical type of Matlab. The only drawback of this interoperability model is the current limitation of the heap memory in Matlab. Depending of the architecture and of …