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• 3d Image Processing and Analysis with ImageJ
• Tutorial for 3DRoiManager

Author: Vital (Vital.Gutierrez_Fernandez@onera.fr)

This tutorial consists in a set of instructions to use Eclipse to write plugins for ImageJ. Furthermore, a set simple plugins is provided to familiarize the reader to plugins functions going from the opening of images to modify the data in the results table. The author appreciates any email with requests of simple codes or suggestions. The readers are encouraged to become acquaintance with the book of Burger and Burge to learn about the Image Processing Science. As the author becomes more confident with the ImageJ Wiki, the format of the tutorials will be improved with images and videos.

In the How-Tos section http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howto, as well as in the tutorial of David Edenberg http://rsbweb.nih.gov/ij/docs/eclipse-tutorial/index.html it has been described several possible aproaches to use Eclipse and ImageJ together. Novel users, however, may find the extra capabilities in these installations not worth the extra complexity involved. The proposed solution consists in saving the plugins written with eclipse directly in the plugins folder of ImageJ. Furthermore, by adding the ImageJ jar file as a library to ImageJ, it is possible to have the coding facilities of Eclipse, while writting plugins for ImageJ. We shall start by the installation of eclipse and its configuration. This tutorial assumes you are using windows and that you already have installed ImageJ

1. Download Eclipse from: http://www.eclipse.org/downloads/. The classic version should be good enough. Even if you are using windows Vista or 7 in their 64bits versions, there should not be any combatibility issues.
2. Eclipse does not need to “be installed” as normal software does, rather it must be extracted from the zip file into a suitable folder (for example an eclipse folder created in C:\Program Files)
3. Click twice on the eclipse.exe file (the one with the eclipse symbol)
4. As this is the first time the software is launched it will ask for a location for the workspace. This is the folder where our codes are saved. In our case it is important to remember where this folder is located, as if there is any problem with our ImageJ installation (see later) our work will be also saved there. Appart from this, any location is equally valid (mine is C:\Users\Vital\workspace)
5. At this point Eclipse window is open and there is a default workspace (which eventually can be changed at any point). If running the .exe did not create a desktop shortcut, it can be useful to create it right now.
6. Before going to Eclipse, we shall move all the subfolders in “C:\Program Files\ImageJ\plugins” to a temporary folder as we want to distinguish between our own Plugins and the “default plugins” ImageJ provides.

Eclipse is a powerful text editor, which is well known for its application in Java coding. Nowadays, it can be use to write in C or fortran. Users should be aware that eclipse is extremely flexible and each person has a different design. The reader should not get discouraged by these extreme capacities. Instead, he/she is incouraged to use the inbuilt tutorials to get familiar with its properties. Although, this is not required for this tutorial. As we perform more complex tasks, the reader will become more familiar to this text editor. To start, we shall only use the Package explorer tag (where we see our plugins tree) and the central window (where we write our plugins). At this point we shall configure eclipse to use it in combination with ImageJ. This will be accomplished by saving our plugins directly in the ImageJ plugins folder and importing ImageJ into eclipse as a library.

1. Create a new Java Project, where we shall save our plugins. This can be done in several ways (as anything else in eclipse): File –> New –> Java Project
2. This opens the New Java Project window. In the Project layout options choose: Use project folder as root for sources and class files
3. Set a Project Name. I named mine “ImageJPlugins_ExternalCompilation” though any name is valid (the reason behind the ExternalCompilation notation will become clear later when we create an Internal compilation Java Project)
4. Click on Next
5. Now you are on the New Java Project window, at the Java Settings ing the Source tab
6. To change the Default output folder: click on Browse…
7. In the Folder Selection window click on Create New Folder…
8. Now the New Folder window should be active. Click on Advanced»
9. Activate the Link to folder in the file system option this will make available the Browse… icon
10. Click on Browse… and link to the ImageJ plugins folder (mine is in “C:\Program Files\ImageJ\plugins”)
11. Click on OK to accept the changes in the New Folder window and the Folder Selection window
12. Click on Finish

At this point, we have configured Eclipse to work with ImageJ. Soon we shall create a plugin to check how this works. But first we shall add the ImageJ library to eclipse.

1. Download the ImageJ source file from http://rsbweb.nih.gov/ij/download/src/. In most cases you want to download the latest version.
2. Return to eclipse and over our Java Project name, in the Package Explorer tag, righ-click
3. A menu opens, click on the last option Properties
4. This opens the Properties for our project window. On the left, click on the Java Build Path
5. In this Java Build Path menu (very similar to the New Java Project window seen before) click on the Libraries tag.
6. Here you can find all the libraries employed in a given project. To add the one of ImageJ click on Add External JARs…
7. Link to the file ij.jar file in the ImageJ folder (mine is located in “C:\Program Files\ImageJ”)
8. Click on OK

At the bottom of your Java Project, in the Package explorer tag you might see the ij.jar file and its location as a reference library (left click on the small arrow of Referennced libraries):

1. Right click on this ij.jar library to open a menu. Left click on the last option Properties
2. This opens the window Properties for the C:\Program Files\ImageJ\ij.jar
3. Click on External file… in the Java Source Attachment menu.
4. Link to the source file you downloaded previously.

This source file contains the description of the ImageJ functions and algorithms. From now on as you move your mouse above an ImageJ class in eclipse it will provide you with a small description. As you will learn this is extremly usefull while writting plugins.

If the installation of Eclipse-ImageJ has been succesful, any new class in a package should be visible in the ImageJ plugins menu. Two things should be remember while creating a new plugin:

1. A class name is only recognized if it includes an underscore“ _ “
2. To see a new plugin in ImageJ, save the class in eclipse and update the menus in ImageJ (in the help tab)(check the tips and trick section to do this in fast way)

1) Creation of a New Pluging

To create a new package and a new class in Eclipse follow the following steps:

1. Right click on the Java project which holds your ImageJ library
2. In the displayed menu click on New
3. In the displayed menu select Package
4. In the New Java Package window write a name for the package, for example “testing”
5. Right click in the Package you want to create the new class
6. In the displayed menu click on New
7. In the displayed menu select Class
8. In the New Java Class window write any name for the class for example “my_first_Plugin”. If you put another name just remember to include an underscore ” _ ”

If you need to create a new class, but not a package, you just need to do steps 5 to 8. To see if the package and the plugin were rightly exported:

• Save the class. For every modification to take effect on your plugin, the class must be saved. Just click on the symbol with the floopy disk.
• If ImageJ is open click Update Menus in the Help menu. Otherwise start ImageJ
• Left click on the Plugins menu. Below the option Compile and Run… you should see your package name (It may be “testing”)
• Left click on the menu “testing”, you should see your plugin name (It may be “my_first_Plugin”).

2) Importing a Plugin

In other cases, however, you may need to download a plugin from the ImageJ website and modify it. Moreover, The examples provided below can be modified and combined to produce more complex tasks. The first step in this coding process, consists in importing the java files into your Eclipse-ImageJ compilation.

1. Download a plugin. For example the java file from this tutorial: i_create_duplicates_image.java
2. We may want to create a new Package for these plugins, repeat the previous 1-4 steps with a different name. For example “downloads”
3. Right click on your “downloads” package
4. In the displayed menu, left click on Import…
5. The Import window opens, you need to open the General folder icon
6. Select as import source the File System option
7. Left click on Next >
8. In this new Import window left click on the superior Browse… icon
9. Select the folder where you downloaded the java files are located
10. On the right whiteboard select the files you want to import into the package
11. Left Click on Finish

You may observe on the right page on the package explorer that the i_create_duplicates_image.java has been included in the “downloads” package. However, you may also notice a small red square with a white cross in your class, package and java project. This illustrates how Eclipse shows you that there is an error in the code.

The reason for this error in the code is fairly common: you gave a name to your package that does not agree with the one of the class creator. To solve this problem follow these steps, using the quick fix solutions of eclipse:

1. If the main eclipse window is not already displaying the class code, double click on its name (i_create_duplicates_image.java) in the Package Explorer, to display it.
2. At the top of the window you will see the package declaration: package imagej_plugins_ward;. The first word should be in purple (this means “fix” parts of the code, the second is black (this means user-chosen code)
3. You will see at the left part of the window that there are two lightbulbs with the cross symbols. These are the lines that are suspected to have code errors. In most cases the earlier errors should be solved first.
4. Right click on the first one, at the package declaration: package imagej_plugins_ward;
5. Left click on Quick Fix
6. A small menu opens which displays the possible solutions: 1) Create a new package named “imagej_plugins_ward” 2) Change the name of the declaration by “downloads” (or the name of the package to which you imported the class) 3) Move to another workspace.
7. The simpler option for us is the second: Change the declaration of the package

Once ImageJ menus are updated or ImageJ reopened, you will see the new plugins in your Plugins menu in the “downloads” submenu.

3) Coping a plugin

Assuming you have two packages, you can simply copy a plugin by several ways including:

1. Right click on desired class in the source package. For example “my_first_Plugin” in the “testing” package.
2. In the displayed menu click on Copy
3. Right click target package. For example the “downloads” package.
4. In the displayed menu click on Paste

Unlike in the case of importing a class, Eclipse changes automatically the package declaration to the one of the current package.

The following codes consist in simple examples of ImageJ plugins. By their own, they have little use by any user. However, these functions are commonly used while writting any plugin. The aim of this work is to allow the reader to become familiar with the Java-ImageJ programing. For any doubt or problem please do not doubt to contanct (Vital.Gutierrez_Fernandez@onera.fr).

i_create_duplicates_imagev1.java

ii_modify_active_imagev2.java

iii_modify_roi_imagev1.java

iv_modify_pixeloperation_image.java

v_modify_anyroi_imagev1.java

vi_opensave_imagev1.java

vii_batchopesave_imagev1.java

viii_modify_stackv1.java

x_createstack_imagev1.java

xi_loadrois_stackv1.java

xii_particleanalyzer_imagev1.java