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.

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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

will start a Fiji inside MATLAB.

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• 1Getting started

Using MATLAB as processing core and sending results to Fiji

An example how to work with MIJ is provided here:

If you get an error saying that some Plugin related classes cannot be found, please update your Fiji with Help › Update Fiji!

Running ImageJ commands

In ImageJ, you can record macros, one of the most powerful ways to use the program. Most of the recorded statements will look like this:

The first parameter to the run() method is the menu item's label which identifies the plugin to run (in this example, the label would read: Command).

The second parameter is a String containing values the user specified via an ImageJ dialog. Every value is identified by a label, and except for checkboxes (such as key2 in the example above), they have values. If the values contain spaces, you need to enclose the value in square brackets (such as key3 in the example above).

Note that the backslash is a so-called escape character, i.e. it can be used to insert special characters such as line breaks or tabs. To insert a plain backslash, it has to be repeated therefore (as in the key3 value: C:Documents and Settings becomes 'C:Documents and Settings').

You can use those recorded statements in a slightly modified form via MIJ:

1. replace the double quotes by single quotes
2. prefix the run name with MIJ.

The above example would read like this:

Note: in MATLAB, it is not strictly necessary to end the MIJ.run() statement with a semicolon, because it does not return anything. However, it is good practice with MIJ to end all statements in semicolons: some functions return images, cluttering the output and taking a very long time to print if the statement does not end in a semicolon.

Opening images

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Normally, the best way to use MIJ is to use ImageJ's macro recorder. However, this procedure does not work when opening images because ImageJ records simply: open('/path/to/image.png');

Instead, one needs to keep in mind how run() statements are constructed and imitate it for the Open... command:

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.

To get a quick help on the available functions, call

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).

If you want to use the functions without starting Fiji's graphical interface, just call

A related project is MatlabControl which allows you to start MATLAB conveniently from within Java.

Matlab On Mac

The function get_google_map.m uses the Google Maps API (https://developers.google.com/maps/documentation/static-maps/) to retrieve a google map image from Google given coordinates of the center of the image and the desired zoom level (default 15). The image is returned as a raster array and a color map.
In addition, an estimate of the X and Y coordinate vectors are returned in UTM coordinates to facilitate easy plotting of additional information on the map from within MATLAB.
The desired height and width of the image (in pixels) may be specified as well as the 'MapType' (one of roadmap, mobile, satellite, terrain, hybrid, mapmaker-roadmap, mapmaker-hybrid) and up to 50 Google Map markers. For each marker one may specify the location, size, color and optional label.
Default values: Zoom 15, MapType = 'satellite', Height = 640, Width = 640
One may utilize the Google Maps API without a key for a limited number of queries per day. To utilize the Google Maps API up to 25,000 queries per day, one must obtain a Google Maps API Key, freely available from Google. The key may be obtained here: https://developers.google.com/maps/documentation/static-maps/ (click 'Get a Key')

Note, the key requirement places limitations on the portability of this function, as the key, and therefore the function is necessarily tied to a domain name and therefore (usually) a physical location. None-the-less it remains a very handy function for quickly plotting data on a map.

The following code produce the attached screenshot:

[xx yy M Mcolor] = get_google_map(43.06374,-70.703993);
imagesc(XX,YY,M); shading flat; colormap(Mcolor)
xlabel('Eastings UTM')
ylabel('Northings UTM')
title('Entrance to Portsmouth Harbor')

Known Issues:
1) The estimate of the X and Y coordinate vectors are just that, a guess at an algorithm for determining these values from the images size and zoom level. The algorithm was determined by trial and error (as the API provides no way to query for the spacial bounds of an image), and therefore will likely produce poor results for some locations. In the vicinity of Portsmouth Harbor, NH the resulting image is geo-referenced to about +/- 3m.

2) Because of MATLAB's poor rendering performance on the Mac platform, my experience has been that maps plotted as in the example above produce white gaps whose cause and resolution are unknown.