MIJ

A Java package for running ImageJ and Fiji within Matlab

Daniel Sage, Biomedical Image Group, EPFL, Switzerland

Dimiter Prodanov, Bio-Nano Electronics Department, Imec, Leuven, Belgium

Carlos Ortiz, Department of Physics, North Carolina State University, Raleigh, NC, USA

Jean-Yves Tinevez, Imagopole, Institut Pasteur, Paris, France

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.

Reference

Daniel Sage, Dimiter Prodanov, Jean-Yves Tinevez and Johannes Schindelin, MIJ: Making Interoperability Between ImageJ and Matlab Possible ImageJ User & Developer Conference, 24-26 October 2012, Luxembourg. Poster [PDF, 1.9 Mb]

splash image

Software

Some interesting features

Run ImageJ in the Java Virtual machine (JVM) of Matlab. It is required a JVM version > 1.6
Export/Import a 2D Matlab variable as ImageJ's image: the image can be displayed or not
Export/Import a 3D Matlab variable as ImageJ's stack: the image stack can be displayed or not
ImagePlus references can be converted to Matlab matrices for further processings using the Java interpreter of Matlab
Enables to run plugins (setup path)
Enables to run macros (setup path)
Additional information from ImageJ: can be transferred to Matlab: histogram, table of results, column of results, and region-of-interests

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 (e.g for Window Machine '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 1.3.9

Method	Description
MIJ.closeAllWindows	Close all windows
MIJ.createColor	exports RGB image
MIJ.createImage	exports other images
MIJ.error	display a error message in a dialog box
MIJ.exit	exists MIJ
MIJ.getCurrentImage	returns a 2D array representing the current image
MIJ.getImage	returns a 2D array representing the image specified by the title
MIJ.getColumn	imports column of the ResultsTable
MIJ.getCurrentTitle	imports the title of the current image
MIJ.getHistogram	imports the histogram of the current image
MIJ.getLog	returns the contents of the window log of ImageJ
MIJ.getListImages	returns the list of opened images
MIJ.getListColumns	returns the list of columns currently used in the ResultsTable
MIJ.getResultsTable	imports the ResultsTable
MIJ.getRoi	imports the current ROI
MIJ.help	gives a brief description of the MIJ methods
MIJ.log	print a message in the window console of ImageJ
MIJ.selectWindow	select a window
MIJ.setRoi	exports the current ROI
MIJ.setColumn	exports contents to a column in the ResultsTable
MIJ.setSlice	set the slice of a stack of image
MIJ.setThreshold	sets the threshods of the image
MIJ.setupExt	points to the folder containing ij.jar and plugins and macros folder
MIJ.showStatus	display a message in the status bar of ImageJ
MIJ.start	starts MIJ
MIJ.run	runs command or macro
MIJ.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

Using fast Matlab routines and display resulting images on ImageJ

screenshot

Reading image files using Bio-Formats on Matlab

screenshot

Image-analysis on ImageJ, statistics on Matlab

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 • 09.11.2018