ImageJ

Platforms
Windows
MacOS
Linux
Raspberry Pi
Android

Learn programming through fun, practical projects!

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.

Installation

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. Open the terminal.
2. Install Java 8 on your Pi (sudo apt-get install openjdk-8-jre).
3. Choose Java 8 (sudo update-alternatives --config java).
4. Verify it works using java -version.
5. Download and install the platform-independent "no JRE" distribution of Fiji.
6. Download the ImageJ.sh shell script
7. Move the ImageJ.sh file to the Fiji.app folder
8. Set the executable bit (chmod +x ImageJ.sh)
9. Run it (./ImageJ.sh) to launch ImageJ.

You may also need to disable (comment out) assistive_technologies=org.GNOME.Accessibility.AtkWrapper in /etc/java-8-openjdk/accessibility.properties.

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.

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

1. Download the Fiji icon image: Fiji icon link
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 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

• Topics tagged raspberry-pi on the Image.sc Forum.
• The Linux page, for general information about ImageJ on Linux systems.