Upon opening an HDF5 file, an import dialog lists the available image data sets contained in the file and allows the selection of one or multiple data sets to be opened:

Note that the Fiji distribution of ImageJ comes with an hdf5 plugin already installed out of the box. This packaged hdf5 plugin (HDF5_Vibez) has some great features, and may be all you need. However, it does not allow one to load large image arrays as virtual stacks or to select only sliced subsets of the data, and thus often results in "out of memory" errors when working with large data sets. In those cases, the PSI plugin for reading and writing HDF5 files described here might be your preferred choice to work with HDF5 files.

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

All you need is to download the latest HDF5 ImageJ plugin from releases and copy the jar into the plugins directory of ImageJ. After this you should be able to simply start ImageJ and use the Plugin.

Troubleshooting

Prerequisites

To be able to run this plugin, ImageJ needs to be run with a Java 8 or greater JVM.

At the time of writing, the latest Fiji distribution of ImageJ comes bundled with Java 8 by default, while older versions of ImageJ and Fiji are still using Java 6. ImageJ itself (or more precisely the current ImageJ2 flavor of ImageJ) seems to still be in a transitionary phase from Java 6 to Java 8 and does not yet provide the full Java 8 functionality by default. The simplest option is therefore to use a newer Fiji version which comes bundled with Java 8 for the installation of this hdf5 plugin.

The one caveat about using Fiji is that one needs to disable the pre-packaged hdf5 plugin included in the distribution before installing this plugin.

In the following, the installation procedure is detailed for a Fiji installation with Java 8 included and also for older installations based on Java 6.

Checking the Java version

You can check whether Java-8 is included with Fiji as follows:

Open the update dialog from the menu via Fiji > Help > Update....
Wait for the application to finish checking for new updates.
In the ImageJ Updater Window, click on "Advanced Mode"
Type java-8 into the "Search" field.
If you see an entry lib/Java-8 in the results box below, then Java 8 is ready to be used on your system (see screenshots below).

Installation for Fiji with Java 8

Deactivate the distributed hdf5 plugin

As mentioned previously, unfortunately the standard hdf5 plugin (HDF5_Vibez) of Fiji interferes with the PSI plugin. You will be able to tell which plugin is currently active when trying to import an hdf5 file (Fiji > File > Import > HDF5...). Once you have selected an hdf5 file, the standard plugin opens an import dialog that looks as follows:

To disable the standard hdf5 plugin, follow these steps.

Open the update dialog from the menu via Fiji > Help > Update....
Wait for the application to finish checking for new updates.
In the ImageJ Updater Window, click on "Advanced Mode".
Type hdf5 into the "Search" field.
The results box below should now list the plugins/HDF5_Vibez entry.
Select that plugins/HDF5_Vibez entry and click "Uninstall" below, then hit "Apply Changes".
The "Status/Action" column of the plugins/HDF5_Vibez entry should now say
Not installed.
Restart Fiji.

Install the PSI hdf5 plugin

The installation of the plugin essentially only requires one to add the downloaded jar into the plugins directory inside the Fiji installation directory. Follow these steps:

Locate the installation directory of the Fiji application (FIJI_DIR).
Copy the downloaded jar file file into FIJI_DIR/plugins
Close any running instances of the Fiji applications, then reopen Fiji.
Try to import an hdf5 file: Fiji > File > Import > HDF5....
- If the installation of the pluging was sucessful, the file import dialog should look like in the screenshot below once you have selected an hdf5 file.
- If there is no HDF5... loader available in the Fiji > File > Import menu, the installation did not succeed. Check that all the files downloaded for the new plugin are actually present in the correct locations, i.e. in <FIJI_DIR>/plugins and <FIJI_DIR>/lib.
The new hdf5 plugin is now ready to be used!

Installation for older versions of ImageJ/Fiji with Java 6

The following steps assume that no other hdf5 plugin is already installed with ImageJ/Fiji (see above).

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

cd <IMAGEJ_HOME>
unzip <path of downloaded source zip>

The plugin is now available in ImageJ/Fiji, but you may want to configure it further for easier use (see below).

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

Older Fiji versions

For older versions of Fiji, we have to instruct Fiji to use an alternative Java (which has to be installed on the systems separately, of course). This can be done as follows:

cd <FIJI_HOME>
<fiji> --java-home /usr/lib/jvm/jre-1.8.0-openjdk.x86_64

Usage

For normal usage, you should just be able to open Fiji/ImageJ as usual and start using the hdf5 plugin. Below are some hints for advanced usage, specifying the amount of memory to be used, etc.

java -Xmx3048m -jar ij.jar

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

Development

To create an all in one jar file for installation in a ImageJ installation use: ./gradlew clean fatJar

The jar file is an all in one jar including all required native libraries for Windows, Linux and Mac OS X.

Dependencies

The java HDF5 libary as well as the precompiled code we downloaded and copied from: https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page All the necessary jars where copied from there into the /lib directory.

The files in the package hdf.objects in this repository were copied from the hdfviewer source code. We were not able to find a jar that contained them.

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