Miji
short URLFrom Fiji
MIJ is a java package to exchange images between Matlab and ImageJ. It is written by Daniel Sage (Biomedical Image Group (BIG), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland) and Dimiter Prodanov (Department of Physiology and Pharmacology, Université Catholique de Louvain (UCL), Brussels, Belgium). It allows to start a instance of ImageJ inside Matlab and exchange images back and forth with it. It takes advantage of the fact that the user interface of Matlab is written in Java.
For your convenience, Jacques Pecreaux & Johannes Schindelin wrote Miji.m, which makes it super-easy to use Fiji and the libraries and functions provided by Fiji's components from within Matlab. Simply make sure that the scripts/ directory of your Fiji.app/ is in Matlab's search patch, via File>Set Path... (on Mac, the file chooser doesn't let you choose directories within .app packages, so you have to use the Matlab command addpath('/Applications/Fiji.app/scripts') ). Then a simple
Miji;
will start a Fiji inside Matlab.
Contents |
Getting started
Using MATLAB as processing core and sending results to Fiji
An example how to work with MIJ is provided here:
MIJ.run('Embryos (42K)');
I = MIJ.getCurrentImage;
E = imadjust(wiener2(im2double(I(:,:,1))));
imshow(E);
MIJ.createImage('result', E, true);
If you get an error saying that some Plugin related classes cannot be found, please update your Fiji with Help>Update Fiji!
Using Fiji as a 3D viewer for MATLAB
A set of demos made for MATLAB users, and introducing how to install and use Fiji as a visualization tool for MATLAB is published on the fex.
Getting help
To get a quick help on the available functions, call
MIJ.help
Further descriptions and example code can be found on the home page for MIJ. Eventually, detailed documentation about the class MIJ can be found here (suitable if you have a bit of experience with Java).
Alternative: do not start the Fiji GUI
If you want to use the functions without starting Fiji's graphical interface, just call
Miji(false);
Links
A related project is MatlabControl which allows you to start Matlab conveniently from within Java.
