IJP ImageJ Launcher

IJP ImageJ Launcher is a native launcher that starts ImageJ 2 or Fiji. It is intended to be a general drop-in replacement for the original ImageJ Launcher. IJP ImageJ Launcher is a clean implementation on the core function of starting ImageJ 2 or Fiji.

Contents

• Why Another ImageJ Launcher
• Features [work in progress]
  • Full list of command line options
• Installation
• Developer Setup

Why Another ImageJ Launcher

I needed to use Fji with the current versions of Java, version 11 and newer. The original ImageJ Launcher works with Java 8, but not that well with the current versions, in particular not well on Mac with Arm64 processors (Apple Silicon). I attempted to fix the original ImageJ Launcher source. The source is burdened by technical debt, the logic flow is too complex to correct without a significant rewrite.

Features

• Uses similar options to the original ImageJ Launcher, si IJP Launcher can be drop-in replacement
• Provides native executable for various OS/Hardware systems
  • Windows
  • Mac OS X Arm64 (Apple Silicon)
  • Mac OS X Intel
  • Linux
• Selects location of the ImageJ directory
  • Startup directory or
  • Directory specified by --ij-dir command line option
• Locates Java Virtual Machine for ImageJ:
  • Use Java VM requested by the user (--java-home)
  • Use JAVA_HOME environment variable
  • Search ImageJ directory for available Java executables
• Determines the amount of memory used by JVM based on total system memory use 75% of the max
• Determines available imagej-launcher*.jar
• Performs updates pending after the last time ImageJ was closed

Full list of command line options

  -h, --help          prints this usage text
  --version           prints version
  --dry-run           show the command line, but do not run anything
  --info              informational output
  --debug             verbose output
  --java-home <path>  specify JAVA_HOME explicitly
  --ij-dir <path>     set the ImageJ directory to <path> (used to find jars/, plugins/ and macros/)

Installation

The IJP ImageJ Launcher executables will be available on the [Releases] page.

Example of Installing Fiji with the IJP ImageJ Launcher on Mac OS X Arm64

1. Download FIJI without JRE

Go to https://fiji.sc/ and select "Download the no-JRE version". That should het you file called fiji-nojre.zip

2. Unzip the fiji-nojre.zip in the directory of choice

In Mac OS X, if you double-click on the file fiji-nojre.zip You should get Fiji.app click and select "show Content"

3. Create place for Java (JRE)

Inside Fiji.app create directory java. Next to directories that are already there, like Contents, images, jars, ...

4. Download Java JRE or JDK,

In browser open https://adoptium.net/temurin/releases/ Select:

• operating system: macOS
• architecture: aarch64 also know as Apple Silicon or Arm64
• package: jre (jdk is fine too, is larger supports Java compilation)
• version: 11 (17 will work too, but you will not have JavaScript available, if you use it)

Click on tar.gz button and download to the java directory you created earlier. You should have file like OpenJDK11U-jre_x64_windows_hotspot_11.0.19_7.tar.gz.

5. Uncompress into the java directory

That will create directory like jdk-11.0.19+7-jre

6. Download IJP ImageJ Launcher to Fiji.app directory

Go to [Releases] and download ??? and ???.???

7. Start ImageJ

In Fiji.app double-click on ???.??? (note the extension ???) that should start FIJI.

You can also create an alis on the desktop to avoid navigating to Fiji.app directory each time. Press ??? and ??? and drag ???.??? to the Desktop. It will create an alias. Now you can double-click on the alias ???.??? on the Desktop to start Fiji.

If you have problems installing, please report in [Discussions]

Troubleshooting

1. Open command prompt (terminal).
2. Navigate to Fiji.app directory
3. Run IJP ImageJ Launch typing: ./ijp-imagej-launcher --debug

You should see diagnostic information about how ijp-imagej-launcher is attempting to start Fiji. The error messages shoudl help you to address the issue. Please use [Discussions] if you have additional questions

Developer Setup

Information here is only applicable if you want to rebuild from sources.

Setup Scala Native dependencies following instructions at:https://scala-native.org/en/v0.4.12/user/setup.html In brief, you will need the following installed: JDK, SBT, and LLVM/CLang. Details depend on OS. On Windows you will also need Visual Studio 2019 (the Community Editions is sufficient). Alternatively on Windows, you can build using WSL Linux prompt, in that case, follow Linux installation instructions.

This should work with JDK 8 or newer, including the latest JDK 20.

After requirements are installed, you should be able to build and run the launcher using command:

sbt run

You can pass additional command line arguments, for instance --help:

sbt "run --help"

Notice the use of quotes.