Raspberry Pi

Revision as of 18:08, 7 December 2018 by Llamero (talk | contribs) (Added clarification about where to put the ImageJ.sh file, as well as a guide on how to make an executable desktop icon for Fiji)
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The Raspberry Pi is an inexpensive single-board computer system which runs the Raspbian operating system, a flavor of Debian Linux. This page provides advice and guidance for running ImageJ and Fiji on Raspberry Pi systems.


You might notice there is as an imagej package available from your package manager. Please be aware that this provides ImageJ 1.x only, packaged by a third party, without cooperation from the core ImageJ development team. You will not have access to any ImageJ2-specific features such as parameterized scripts, and you will likely have permissions errors because it is a system-wide ImageJ installation.

The following steps describe how to install ImageJ on a Raspberry Pi:

  1. Install Java 8 on your Pi. Verify it works using java -version from the command line.
  2. Download and install the platform-independent "no JRE" distribution of Fiji.
  3. Download the ImageJ.sh shell script, set its executable bit (chmod +x ImageJ.sh) and run it to launch ImageJ. Note that the shell script supports only a subset of the functionality of the native ImageJ Launcher, but it should be able to run ImageJ successfully.
  4. Move the ImageJ.sh file to the Fiji.app folder

The following steps describe how to create a desktop icon to launch FIJI on a Raspberry Pi:

  1. Dowload the Fiji icon image: Fiji icon link
  2. Press ctrl + alt + t to open the terminal window
  3. Type: nano FIJI launcher.desktop and press return. This will load Nano which will allow you to create a desktop icon.
  4. Type the following code, replacing "/path/to" with the paths to the ImageJ.sh file and the Fiji icon:
[Desktop Entry]
Name=Fiji launcher
Comment=Launches Fiji
  1. Press Ctrl + x and then press Y to exit and save the new desktop icon. #Enter you desired file name, such as "Fiji Launcher.desktop" and press return. Once complete, an icon should be visible on the desktop.
  2. Press Ctrl + x to return to the terminal window
  3. In the terminal window, type the following to navigate to the Desktop: cd ~/Desktop <code>
  4. Then type the following to make the new icon executable: <code>chmod +x "Fiji Launcher.desktop"

3D Visualization

It is supposedly possible to run Java 3D on the Pi; see this StackOverflow thread. However, there have been no official reported successes on ImageJ community channels yet. If you get it working, please edit this section to describe the steps you used!

Even better, if you get ClearVolume and/or SciView working on the Pi, please update this page, and announce it on the ImageJ Forum!


See the Troubleshooting page.

Frequently Asked Questions

See the Frequently Asked Questions page.

See also