Java, already installed.

here is the procedure to install ImageJ:

• ImageJ is contained in a JAR archive, all ready to execute via a script called run found in the folder created after decompressing the Zip archive.

% wget http://rsbweb.nih.gov/ij/download/zips/ij143.zip
% unzip ij143.zip
% cd ImageJ && ./run&

• ImageJ has always been a fast-evolving program… A consequence of this is that the archive you just downloaded is rarely the latest available version. The last command of the preciding block of commands will start ImageJ to allow you to update to the latest In the menu, yo ushould be able to see a Help menu. In thuis menu, select Update ImageJ…. A window will pop up and you only have to click Ok to do the update to the latest version!

• The whole ImageJ folder has to be moved to /opt/bio/sources. This folder should belong to root and its permissions set to 755.

% sudo chown -R root:root /opt/bio/sources/ImageJ
% sudo chmod 755 /opt/bio/sources/ImageJ

• Once you are in /opt/bio/sources/ImageJ, you need to edit the run script so that it looks like this:

#!/bin/bash
export IJ_HOME=/opt/bio/sources/ImageJ
java -Xmx512m -jar $IJ_HOME/ij.jar

• You need to make this script available to all:

% sudo ln -s /opt/bio/sources/ImageJ/run /usr/local/bin/runImageJ

• To add ImageJ to the Impilo application menu, you need to edit the Xfce4 configuration file:
  • More to come…

• To have access to ImageJ from the command line:

% runImageJ