Overview

ImageJ plugin for reading and writing HDF5 files.

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:

Import dialog to select datasets 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

Prerequisites

This plugin requireds ImageJ/Fiji to be run with a Java 8 or greater. To check with wich version your installation is running please refer to the Troubleshooting section below.

ImageJ

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.

Fiji

Fiji already comes with an HDF5 plugin (HDF5_Vibez) installed. However, as mentioned above it has certain limitations. Before installing this plugin, HDF5_Vibez need to be deinstalled.

To disable the standard hdf5 plugin, follow these steps.

Close any running instances of the Fiji applications
Locate the installation directory of the Fiji application (FIJI_DIR).
Remove the HDF5_Vibez jar from the plugins directory: rm $FIJI_DIR/plugins/HDF5_Vibez*.jar
Remove the provided HDF5 binary jar from the jar directory: rm $FIJI_DIR/jars/jhdf5-*.jar

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:

Download the latest HDF5 ImageJ plugin from releases and copy the jar into the $FIJI_DIR/plugins directory
Restart Fiji.

To verify the correct installation:

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.

Import dialog to select datasets to be opened

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

Troubleshooting

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).

ImageJ Updater Advanced Mode ImageJ Updater Search Java 8

Check Which Plugin is Installed

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 HDF5_Vibez plugin opens an import dialog that looks as follows:

Import dialog of packaged HDF5_Vibez plugin

Running Older Fiji Versions with Java 8 or Greater

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

Adjust Memory Settings

For normal usage, you should just be able to open Fiji/ImageJ as usual and start using the hdf5 plugin. If you experience out of memory problems while opening very large datasets try to increaste the initial amount of memory to be used as follows:

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

paulscherrerinstitute / ch.psi.imagej.hdf5

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