This project originated 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/

Usage

To open a HDF5 file use:

File > Import > HDF5...

To save to an HDF5 file use:

File > SaveAs > HDF5

Installation

To be able to install this plugin ImageJ need to be run with a Java 7 or greater JVM.

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>

Configuration (Optional)

If you want to configure the HDF5 Reader as a standard file reader you need to register the reader within the HandleExtraFileTypes.java file. This can be done as follows (details on this can be found on: http://albert.rierol.net/imagej_programming_tutorials.html):

Add HandleExtraFileTypes.java

if (name.endsWith(".h5") || name.endsWith(".hdf5")) {
    return tryPlugIn("ch.psi.imagej.hdf5.HDF5Reader", path);
}

Recompile HandleExtraFileTypes.java

javac -classpath ij.jar ./plugins/Input-Output/HandleExtraFileTypes.java

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

Starting with Java 8 just the LD_LIBRARY_PATH variable need to be set. For MacOSX it is export DYLD_LIBRARY_PATH=lib/mac64/:$DYLD_LIBRARY_PATH.

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.