ImageJ is an image processing software, very popular in the Life-Science field. If you are a master student, a PhD or a postdoc in Biology, there is a very good chance that ImageJ is installed on your computer.
ImageJ is developed mainly by Wayne Rasband, and is written in Java (see http://rsb.info.nih.gov/ij/index.html). It has a clever plugin system that allows users to extend it with new functionalities.
Fiji (Fiji is Just ImageJ, http://fiji.sc/) is a distribution of ImageJ, that includes (amongst other things) a lot of plugins, some useful libraries and an updater to keep everything up to date.
Amongst other things, it is made to facilitate inter-operability with other softwares. For instance, it offers scripting facilities using popular languages such as Python, Ruby, Clojure, Beanshell, Javascript, etc. It also ships with Miji, a set of utilities made to ease its interaction with MATLAB. Since ImageJ is written in Java, it can be called directly from within MATLAB, and be used as a supporting image visualization, processing or analysis tool.
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In this demo bundle, we demonstrate how to use Fiji to get a very nice, hardware accelerated, 3D viewer in MATLAB.
This is not a totally trivial example, as it requires to have the Java libraries for accelerated 3D rendering installed for the MATLAB Java Virtual Machine. Fortunately, Fiji comes with a script that automates the process.
But you still have to install Fiji. Best film planning apps mac free.
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Installing Fiji
Simply go to http://fiji.sc/Downloads and download the binaries for your OS. You will not find an installer; you just have to unzip the Fiji folder to somewhere convenient for you.
For demonstration purposes, let us assume you have a PC machine that runs a 64-bit version of Windows. You then have downloaded the matching Fiji version (fiji-win64-something.zip), and unzipped it in C:Program Files and now have a folder called C:Program FilesFiji.app.
Before launching MATLAB, launch Fiji itself. You will find an executable in the Fiji folder that you just need to run. At startup, Fiji should offer you to go to the updater. Do that and run the update. If you are not proposed this, you can find the updater in the Help > Update Fiji menu item.
Close Fiji when the update is done.
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A side note: ImageJ and its plugin are very useful if you are interested in scientific Image Processing. There are a zillion things you can do with it. If you are interested in using Fiji as a standalone application, check some of the tutorials there: http://fiji.sc/Documentation.
Making MATLAB aware of Fiji
Legit app that cleans mac of deleted apps. The utilities for interaction with MATLAB can all be accessed by adding a single folder to the MATLAB path. They are all located in the scripts folder of the Fiji folder.
So, if you have installed Fiji in C:Program FilesFiji.app, you just have to add C:Program FilesFiji.appscripts to the MATLAB path, and that's all.
By the way, it is in this folder that you will find all the m-files of this demo bundle. So you can launch the demos listed below simply by typing their name in MATLAB command window; they will be found since they are on the path.
Installing the Java3D libraries
You are done with the main installation part. You just have to do it once, and if some updates are made to Fiji, you just have to launch its updater to get them.
You still have to install the Java3D libraries. Fortunately, this is done automatically with a Fiji script:
If you get a message stating that the function cannot be performed, this is because you did not add the Fiji scripts folder to the MATLAB path. in that case, go back to the previous paragraph.
The InstallJava3D will tell you what it does verbosely. It will check whether your Java Virtual Machine already has Java3D installed, and if the version requirement is met. If not, it will automatically download Java 3D and install it to the right folder.
There might be some issues if you do not have write permission to the target folder. In that case, the script will tell you what folder to make writable. Then you can simply re-launch the script.
Once you are done, you have to restart MATLAB, so that the new libraries are sourced.
What now?
You are all set.
You can now play with the 2 demo files Matlab3DViewerDemo_1.m and Matlab3DViewerDemo_2.m, that are heavily annotated and published in the same folder as this file.
Fiji.app For Mac Catalina
MIJ is the low level Java class that contains static methods to exchange data between MATLAB and ImageJ. You can find its documentation there: http://bigwww.epfl.ch/sage/soft/mij/
Miji is the glue that facilitates the use of all these components. It is described in the aforementioned demo files.
AuthorsFiji.app For Macbook
It's all open source, feel free to modify, distribute, comment or whatever you feel like.
Version history
Jean-Yves Tinevez <jeanyves.tinevez at gmail.com> - July 2011
Fiji.app For Mac ProPublished with MATLAB® 7.12 Comments are closed.
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