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Raspberry Pi

Learn programming through fun, practical projects!

The Raspberry Pi is an inexpensive single-board computer system which runs Raspberry Pi OS, a flavor of Debian Linux. This page provides advice and guidance for running ImageJ, ImageJ2, and Fiji on Raspberry Pi systems.

Installation

You might notice there is as an imagej package available from your package manager. Please be aware that this provides the original ImageJ only, packaged by a third party. 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 Fiji on a Raspberry Pi:

Fiji-Latest

  1. Download and extract the Linux arm64 distribution of Fiji
  2. Launch Fiji using the executable fiji-linux-arm64

Fiji-Stable

  1. Open the terminal
  2. Install SDKMAN!

  3. Verify it works:

    sdk version

  4. Install Java 8:

    sdk install java 8.0.402-tem

  5. Verify it works:

    java -version
  6. Download and extract the portable “no bundled Java” distribution of Fiji
  7. Download the ImageJ.sh shell script
  8. Move the ImageJ.sh file to the Fiji.app folder

  9. Set the executable bit:

    chmod +x ImageJ.sh

  10. Launch Fiji:

    ./ImageJ.sh

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.

Desktop Icon

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

  1. Download the Fiji icon
  2. Press ⌃ Ctrl + ⌥ Alt + T to open the terminal window
  3. Type nano Fiji.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 fiji-linux-arm64 or ImageJ.sh file and the Fiji icon:
[Desktop Entry] Name=Fiji Version=1.0 Comment=Launches Fiji Exec=/path/to/ImageJ.sh Icon=/path/to/48px-Fiji-icon.png Terminal=false Type=Application Categories=Education
  1. Press ⌃ Ctrl + X and then press Y to exit and save the new desktop icon.
  2. Enter your desired file name, such as Fiji.desktop and press return. Once complete, an icon should be visible on the desktop.
  3. Press ⌃ Ctrl + X to return to the terminal window
  4. In the terminal window, type the following to navigate to the Desktop cd ~/Desktop
  5. Then type the following to make the new icon executable chmod +x Fiji.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 Image.sc Forum!

Troubleshooting

See the Troubleshooting page.

Frequently Asked Questions

See the Frequently Asked Questions page.

See also

ImageJ Docs