This descibed an old version of the HDF5 plugin. Pleae look at the Current Version of the HDF5 plugin

HDF5 is a data format for storing extremely large and complex data collections. For more information see the official website http://hdf.ncsa.uiuc.edu/HDF5/. The plugin uses the HDF5 Java Library for reading and writing HDF5 files.


The HDF5 plugin for ImageJ provides The following features:

  • Reading 2D/3D/4D datasets
  • Writing 2D/3D/4D datasets
  • Reading and writing 2D/3D rgb datasets

Change Log

  • Version 2011-11-25:
    • No automatic brightness/contrast adjustment for 8bit data
  • Version 2011-06-22:
    • Now also available for Windows 64bit
    • Easier installation (no more editing of configuration files, no unpacking of zip-archives)
    • Automatic Adjustment of Brightness/Contrast when loading 16bit and float data sets
    • Updated to latest HDF5 Java Library (V2.7 from February,2011)


  • ImageJ, plugins tested with Version 1.38 and newer.
  • Linux, Mac OS X, or Windows, 32bit or 64bit

Download and Install

Download:The plugin uses a platform specific library for accessing the HDF5 files. So you have to download the plugin and the appropriate library for your system. ATTENTION: the 32/64bit must match your JAVA Installation. This is not necessarily identical with your Operation System. E.g. if you installed a 32bit Java on a 64bit Windows, you have to download the 32bit libraries. If unsure, check "Help--About ImageJ..."


  • Copy the plugin into the "plugins" folder of your ImageJ-installation.
  • Copy the platform-specific libraries into the main folder of your ImageJ-installation
    (this is the folder, where the "run"-script (Linux) or the "ImageJ.exe" (Windows) is located).

Update from older Versions: Ensure, that you delete the files from the old versions, before installing the new one

Other versions

See here for older versions of this plugin. Matthias distributes the source code on http://imagej-hdf.googlecode.com

Example Data Set

  • pollen.h5 (3D confocal data, 8 bit gray, approx. 16MB)


Here you can download a short manual in PDF format.

Developed by

Matthias Schlachter, bug fixes and small improvements by Kun Liu and Olaf Ronneberger

Contact, Bug reports and Questions

We are always interested in bug reports and feedback. Please contact us via email to Olaf Ronneberger.

Olaf Ronneberger 22.6.2011