LungJ README

What is this repository for?

providing a Plug-In for Fiji / ImageJ for segmenting images, too large to process in RAM at once as well as several other tools for image segmentation & processing.

Requirements

• ImageJ 1.49s or later
• Trainable Weka Segmentation Plugin
• Flood Fill (3D) Plugin
• 3D Viewer Plugin
• FeatureJ (http://imagej.net/FeatureJ)
• Fiji (advised as it provides many extra tools including the Trainable Weka Segmentation and Flood Fill (3D))

How do I get set up?

Automatic

• Add http://sites.imagej.net/LungJ/ to your download pages

Easy

• The main directory includes the latest build
• copy the .jar file into the Fiji ./plugins/LungJ directory
• restart Fiji

Detailed

• download LungJ_.jar from the main directory
• place LungJ_.jar file into the Fiji ./plugins/LungJ directory of your Fiji installation
• if there are problems, try creating a subfolder so that the file is placed in ./plugins/LungJ_/LungJ_.jar
• restart Fiji
• the new functions should be available under Plugins>LungJ>

For Developers

• Java sourcecode is in the src folder
• Fiji configuration file (for menu creation) is under config
• run javac (comes with Fiji) on the src folder to create compiled java classes in the class folder
• run jar (comes with Java JDK) to combine the classes and config files into a .jar
• copy the .jar file into the Fiji ./plugins directory
• restart Fiji

Who do I talk to?

• Repo owner: Lasse Wollatz (l.wollatz@soton.ac.uk)
• More info: http://imagej.net/LungJ