ImageJ is probably one of the most widely used open source image processing frameworks in the biomedical community. We strongly encourage the use of it.

Key features are:

  • opens most of the microscopy formats thanks to the Bio-Formats plugin. This allows to skip an exportation step after image acquisition and also allows to conserve the meta-data of the image acquisition.
  • cutting edge: There is an increasing number of cutting edge image processing techniques published and implemented in ImageJ.
  • flexibility: The user is free to come up with any workflow and can automate it with the image macros.
  • extensibility: the architecture of ImageJ allows easy addition of functionality. In case some particular functionality is missing, it can be implemented using scripts/macro or java to create a proper plugin.



On windows machines ImageJ can be installed with the Baramundi Kiosk. You can use the direct link or go via the icon in the task bar (see screenshot).

Of course there is the official web-site of ImageJ where you can find the binary dirstributions for Windows, OsX and Linux.


Update Sites

The updater of ImageJ is a feature that we like to point out specifically here and it stands for the extensibility of ImageJ. There are many third party plugins available via update sites. You can find a list of update sites  as well as the instructions on how to use a particular update site are to be found on the ImageJ wiki.



Please contact us if you have request  regarding image processing pipelines or custom functionality of ImageJ.