CLIJ2-Assistant installation instructions

For installing clij2 and the clij2-assistant, please follow the instructions on the clij website.

Optional: Extensions

There are extensions available, e.g. for BoneJ, ImageJ, ImageJ2, ImageJ 3D Suite, Imglib2, MorphoLibJ and SimpleITK. To make use of them, please also activate these update sites:

Installation in MicroManager 2

Download and install MicroManager 2 and some jar files:

Please put these jar files in the plugins\Micro-Manager sub-directory of MicroManager: Image

Start MicroManager and check if the installation worked as in the ImageJ section above. During multi-dimenionsal acquisition, just Start CLIJx-Assistant and use the right click menu to setup a workflow: Image


In case of any issues, please refer to the more detailed installation instructions of CLIJ2 and the trouble shooting section.

Windows specific installation

Windows users may have to install graphics cards drivers downloaded from the vendors website (AMD, NVidia). The driver delivered by Windows Update is not sufficient.

MacOS specific installation

When using an AMD graphics card in recent Macs, you may want to turn OFF the option “Automatic graphics switching” under System Preferences / Energy Saver. Thanks to Tanner Fadero for finding this out.

Linux specific installation

Also under linux, installation of drivers from the vendors website is necessary (AMD, NVidia). Furthermore, when working with Intel graphics, it might be necessary to install packages such as “ocl-icd-devel” to make Fiji / CLIJ discover the right GPU devices.

Optional: ImageJ Macro Markdown Installation

If you want to export your workflows notebook style with ImageJ Macro Markdown, please also activate the “IJMMD” update site in Fiji.

Optional: Plugin generator Installation

In order to build Fiji plugins, please install Java Development kit, version 8 or higher, e.g. OpenJDK. Furthermore, please download and install git and maven. For technical reasons, the /bin/ folder of the git installation must be added to the PATH of the operating system. Furthermore, it is recommended to add maven to the path as well.
(How to: Windows Linux MacOS ).

After installing git, maven and the JDK, please enter appropriate paths under Plugins > ImageJ on GPU (CLIJx-Assistant) > Options > Build and Run options


The above mentioned tools allow you to compile Fiji plugins. In order to edit the code conveniently, it is recommended to install an Integrated Development Environment (IDE) such as IntelliJ or Eclipse.

Optional: C++ compilation (CLIc / clEsperanto)

If you want to implement workflows using CLIc in C++, please follow the installation instructions here.

Optional: Icy Protocol bridge

For exporting workflows to Icy Protocols, it might be handy to start Icy from ImageJ. Therefore, download and install Icy and enter its location under Plugins > ImageJ on GPU (CLIJ2-Assistant) > Options > Build and Run options.

Optional: Te Oki / Python Installation

If you want to run Python and/or Napari from Fiji, please install a conda environment, e.g. via mini-conda.

Using conda, create a conda environment e.g. named te_oki:

conda create --name te_oki 

Activate the environment:

conda activate te_oki 

Install dependencies, either via conda install or

pip install pyopencl napari ipython matplotlib numpy pyclesperanto_prototype scikit-image jupyter

Within this environment you can run generated clEsperanto python scripts.

If the name of your conda environment differs, please configure it under Plugins > ImageJ on GPU (CLIJx-Assistant) > Options > Build and Run options

Optional: CLIJPY / PyImageJ / Python Installation

For running pyimagej python code, please follow the installation instructions on the pyimagej github page.

Hardware requirements

CLIJx-Assistant uses modern graphics cards to ensure real-time image processing experience. Therefore, it is recommended to utilize state-of-the art graphics computing units (GPUs). When considering purchasing modern GPUs, please take into account:

You can check the capabilities of your graphics processing units by selecting a device using the menu Plugins > ImageJ on GPU (CLIJx) > Change default CL device``


The menu Plugins > ImageJ on GPU (CLIJx) > Memory Display allows you to overview available memory and memory consumption while building your workflow.


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