imagej/ch.psi.imagej.hdf5
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ebner dfa00c8dc4 updated readme
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Overview

ImageJ plugin for reading and writing HDF5 files.

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

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 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.

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