MIJ

A Java package for bi-directional communication and data exchange from Matlab to ImageJ/Fiji

Daniel Sage, Biomedical Image Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland

Dimiter Prodanov, Department of Physiology and Pharmacology, Université Catholique de Louvain (UCL), Brussels, Belgium

Carlos Ortiz, North Carolina State University, USA

Jean-Yves Tivenez, France

splash image

Outline

MIJ offers the missing link between two imaging software: ImageJ/Fiji and Matlab. The goal of the package mij.jar is to provide static methods to exchange images and volumes. MIJ allows also to access to all built-in functions of ImageJ and to third-part plugins of ImageJ. MIJ is integrated in Fiji with a super-easy script to use it.

Thanks to the Fiji team, MIJ is now super-easy to use using a Matlab script Miji.m which is integrated in Fiji. ImageJ/Fiji becomes a image-processing librairie of Matlab.

Software

Matlab prerequirements

The package requires a proper installation of ImageJ and Matlab. The package was tested since Matlab 7.9.0 (R2009b) on different plateforms a Windows XP, Mac OSX 10.6, and Linux Ubuntu.

Download and install

Download mij.jar and place it into the java directory of Matlab (typically 'C:\Program Files\MATLAB\R2009b\java\'). Copy also the ij.jar of ImageJ in the java directory of Matlab.

Set up the path (with a ImageJ already installed and configured):

Extend the java classpath to mij.jar, e.g using the Matlab command: javaaddpath 'C:\Program Files\MATLAB\R2009b\java\mij.jar'.
Start MIJ/ImageJ by running the Matlab command: MIJ.start("imagej-path"); e.g. MIJ.start('/Applications/ImageJ'

Set up the paths (without any ImageJ yet installed):

Download ij.jar
Extend the java classpath to mij.jar, e.g using the Matlab command: javaaddpath 'C:\Program Files\MATLAB\R2009b\java\mij.jar'.
Extend the java classpath to ij.jar, e.g using the Matlab command: javaaddpath 'C:\Program Files\MATLAB\R2009b\java\ij.jar'.
Start MIJ, e.g. MIJ.start;

Set up the memory:

Edit the java.opts file to increase the JVM memory. Check the Matlab page.
With the more recent versions of Matlab, you can increase the memory by using File > Preferences > General > Java Heap Memory.

Source Code and Documentation

Java Source Code of MIJ: MIJ.java
Documentation of MIJ: API of MIJ

Supported methods in the version 1.3.7

Method	Description
createColor	exports RGB image
createImage	exports other images
exit	exists MIJ
getCurrentImage	returns a 2D array representing the current image
getImage	returns a 2D array representing the image specified by the title
getColumn	imports column of the ResultsTable
getCurrentTitle	imports the title of the current image
getHistogram	imports the histogram of the current image
getListImages	returns the list of opened images
getResultsTable	imports the ResultsTable
getRoi	imports the current ROI
setRoi	exports the current ROI
setColumn	exports contents to a column in the ResultsTable
setThreshold	sets the threshods of the image
start	starts MIJ
run	runs command or macro
version	return the MIJ version

Mapping the Matlab numeric type to ImageJ type

Matlab	ImageJ image type
uint8	Grayscale 8-bit
int8	Grayscale 8-bit
uint16	Grayscale 16-bit
int16	Grayscale 16-bit
uint32	Grayscale 16-bit (Possible loss of precision)
int32	Grayscale 16-bit (Possible loss of precision)
uint64	Not allowed
int64	Not allowed
single	Grayscale 32-bit
double	Grayscale 32-bit (Possible loss of precision)

Script examples

Comparison of the Matlab watershed and the ImageJ watershed: compare_watershed.m
Read an image (from a file or a URL) using the Image reader: mijread.m
Create a dialog box: dialogdemo.m

Screenshot

Enlarge the screenshot

Conditions of use

You'll be free to use this software for research purposes, but you must not transmit and distribute it without our consent. In addition, you undertake to include a citation whenever you present or publish results that are based on it. EPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology.

daniel.sage@epfl.ch • 23.09.2011