For 3D datasets an individual slice can be selected for visualization. Also, especially for very big datasets only every x-th slice can be selected for visualization. This can be done by either specifying a number, e.g. 10 (for the slice 10) or a number with a preceding %, e.g. %10 (for every 10th image). Indexing starts at 0.

Usage

To open a HDF5 file use:

File > Import > HDF5...

To save to an HDF5 file use:

File > SaveAs > HDF5

Scripting

To use this plugin from the ImageJs' (python) scripting interface these lines can be used to open a dataset:

from ch.psi.imagej.hdf5 import HDF5Reader
reader = HDF5Reader()
stack = reader.open("",False, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchange/data_dark", True)

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 releases.
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 be able to run the tests and plugin from within the following arguments need to be passed:

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.

Note: to be able to build the package you need to have access to the PSI artifact server. Therefore this only works within the PSI networks and if you have a certain maven configuration. An example Maven settings.xml that you can copy to ~/.m2/settings.xml is located here.

Acknowledgements

This project was inspired by the ImageJ HDF Plugin of Matthias Schlachter Chair of Pattern Recognition and Image Processing, University of Freiburg, Germany ( https://code.google.com/p/imagej-hdf ) . It is a complete rewrite of the code with the focus on efficiency and maintainability