Installation

Download latest HDF5 ImageJ plugin from here.

Go into the ImageJ installation folder and extract the downloaded zip.

cd <IMAGEJ_HOME>
unzip <path of downloaded zip>

Prerequisites

This plugin requires ImageJ to be run with a Java 7 or greater JVM.

Usage

Mac OS X

java -Djava.library.path=./lib/mac64 -Xmx3048m -jar ImageJ64.app/Contents/Resources/Java/ij.jar

Linux

java -Djava.library.path=./lib/linux64 -Xmx3048m -jar ij.jar

The Xmx setting is quite random it depends on how big hdf5 files you are planning to open.

Fiji

Fiji currently comes with Java 6 bundled. As the HDF5 Plugin requires Java 7 or higher we have to instruct Fiji to use an alternative Java. This can be done as follows:

cd <FIJI_HOME>
<fiji> --java-home /usr/lib/jvm/jre-1.7.0-openjdk.x86_64 -Djava.library.path=lib/linux64

Development

To create an all in one zip file for installation in a ImageJ installation use: mvn clean compile assembly:assembly

The zip file contains an all in one jar as well as the required native libraries for Windows, Linux and Mac OS X.

References

This project started from and is inspired by: ImageJ HDF Plugin of Matthias Schlachter Chair of Pattern Recognition and Image Processing, University of Freiburg, Germany. https://code.google.com/p/imagej-hdf/