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cellbaseImageJPlugin

ImageJ Applet 1.2.17 compilation documentation

written by Ruben Gomez

Compilation documentation for ImageJ Applet 1.45l

cellBASE comes with a modified version of ImageJ Applet 1.45l. This document explains how to compile it and install it. The following procedure needs to be done upon modification of the applet code.

Requirements

The only requirement to compile the applet and run it is to have the Sun (or Oracle) Java Development Kit Version 5 or higher installed. It has been tested to work on Mac OS X and other *NIX systems were the command 'jar' and 'jarsigner' is available.

Location of the required software

In a cellBASE installation, the ImageJ Applet code is located within the src folder, more concretely in the subfolder src/ImageJA.

Compiling the applet

If you are in the indicated folder and using a *NIX system you simply need to type.

./compile.sh

In order to start the script that will create 'ij.jar'. To make the script work it is necessary that the command 'jar' provided with JDK5 is included in your PATH (e.g. the $PATH variable includes the folder with JDK5 binaries, tipically $JAVA_HOME/bin or $JDK_HOME/bin).

Signing the applet

The applet doesn't strictly need to be signed but it was signed in order to make it compatible with older browsers. In concrete there were problems with previous versions of Firefox for Mac.

Creating a valid keychain

In order to sign the applet, one needs to generate a valid keychain in the system that will do the signature. The following commands expects you to replace by your favourite key name. keytool -genkey -alias -keyalg RSA -keystore .keystore

Then you will be asked for a number of questions about the emissor of the certificate that you are generating, and also for a keychain password and a key password. The key passwords is necessary to sign the applet afterwards.

Signing the applet

Once the keychain has been created, the applet can be signed by starting the *NIX script with the key name as an argument in the directory

NOTE: In order the script to work, it is necessary that the command 'jar' provided with JDK5 is included in your PATH (e.g. the $PATH variable includes the folder with JDK5 binaries, tipically $JAVA_HOME/bin or $JDK_HOME/bin). src/ImageJA ./make-signed-applet.sh

That will generate the file signed-ij.jar that once copied to the correct directory, will install the applet in cellBASE.

Installing the applet

To install the applet, it is enough to copy the file signed-ij.jar to the directory www/imagej. That will permit cellBASE to find the file the next time on that the Plate View is opened.

Important considerations

The applet is cached by most of the browsers. Once the applet is recompiled and installed, it might be neccesary to clear the browser cache and/or the Java runtime cache, found under Java Internet settings.