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
• Full List of Command Line Options
• Installation
  • Installing Fiji on Mac OS X Arm64
  • Installing Fiji on Windows x64
  • Troubleshooting
    • Start-up log ~/.ijp_imagej_launcher.log
    • Starting from command prompt
• 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

Here are the futures that are already implemented (see release notes for futures ofa specific release):

• Uses similar options to the original ImageJ Launcher, so IJP Launcher can be used as a drop-in replacement
• Intended to be used with Java 11 or newer (the original launcher can be used for Java 8)
• 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.

Installing Fiji on Mac OS X Arm64

This example will show how to:

• Download FIJI and unzip installation.
• Download and install JVM for it.
• Download the IJP ImageJ Launcher and use it to start Fiji

1. Download FIJI without JRE

Go to https://imagej.net/software/fiji/downloads and download the "No JRE" version (not specific to any OS). That should get file called fiji-nojre.zip

2. Unzip the fiji-nojre.zip in a folder of choice

You should get new app folder called Fiji.app. "Right-click" to show a popup menu and select "Show Package Contents" to see what is inside the Fiji.app folder. Inside you should see folders and files like "Contents", "db.xml.gz", "ImageJ-linux64", ...

3. Create place for Java (JRE)

Inside the Fiji.app folder create a new folder called java.

4. Download Java JRE or JDK

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

• Operating System: macOS
• Architecture: aarch64 also known as Apple Silicon or Arm64
• Package Type: JRE (JDK is fine too, is larger and supports Java compilation)
• Version: 11-LTS (17-LTS will work too, but you will not have JavaScript available, if you want to use it)

Click on tar.gz button to download and save to the java folder you created earlier. You should have file like OpenJDK11U-jre_aarch64_mac_hotspot_11.0.20_8.tar.gz.

5. Uncompress into the Fiji.app/java folder

That will create folder like jdk-11.0.20+8-jre. This is the Java VM that IJP ImageJ Launcher will use to start Fiji.

6. Download the IJP ImageJ Launcher and uncompress

Go to Releases, download "IJP-ImageJ-Launcher-0.2.0-macosx-arm64.zip"

Uncompress "IJP-ImageJ-Launcher-0.2.0-macosx-arm64.zip". Inside you will get ImageJ-macosx.

7. Add to Fiji.app

Inside Fiji.app locate folder Contents/MacOS.

Copy ImageJ-macosx to the Contents/MacOS folder, replacing ImageJ-macosx that was there.

8. Move Fiji.app to the Application folder

At this point you can move the Fiji.app folder to the Applications folder and use is as a regular msOS application.

9. Troubleshooting

When you attempt to run Fiji with the new Launcher you may get a warning dialog

Possible work-around

1. Delete Fuji.app folder
2. Uncompressed fiji-nojre.zip to recreate Fuji.app folder, but do not make any changes to it yet. You may need to do it is different folder than before.
3. Control-clock on Fuji.app and select "Open". You will see dialog saying "macOS cannot verify the developer of “Fiji”. Are you sure you want to open it?"
4. Click on "Open". You will see Fiji logo, but the application will close since it is not setup yet
5. Now you can repeat steps "3. Create place for Java (JRE)" to "7. Add to Fiji.app" above

If you have problems installing, please report in Discussions or Image.sc Forum

Installing Fiji on Windows x64

This example will show how to:

• Download FIJI and unzip installation.
• Download and install JVM for it.
• Download the IJP ImageJ Launcher and use it to start Fiji

1. Download FIJI without JRE

Go to https://imagej.net/software/fiji/downloads and download the "No JRE" version (not specific to any OS). That should get file called fiji-nojre.zip

2. Unzip the fiji-nojre.zip in a folder of choice

You should get new app folder called Fiji.app. Inside you should see folders and files like "Contents", "db.xml.gz", "ImageJ-linux64", ...

3. Create place for Java (JRE)

Inside the Fiji.app folder create a new folder called java.

4. Download Java JRE or JDK

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

• Operating System: Windows
• Architecture: x64 also known as Apple Silicon or Arm64
• Package Type: JRE (JDK is fine too, is larger and supports Java compilation)
• Version: 11-LTS (17-LTS will work too, but you will not have JavaScript available, if you want to use it)

Click on .zip button to download and save to the java folder you created earlier. You should have file like OpenJDK11U-jre_x64_windows_hotspot_11.0.20_8.zip.

5. Uncompress into the Fiji.app/java folder

That will create folder like jdk-11.0.20+8-jre. This is the Java VM that IJP ImageJ Launcher will use to start Fiji.

6. Download the IJP ImageJ Launcher to the Fiji.app directory

Go to Releases, download "IJP-ImageJ-Launcher-0.2.0-windows_x64.exe", save it to the Fiji.app folder.

7. Start ImageJ

In the Fiji.app folder double-click on IJP-ImageJ-Launcher-0.2.0-windows_x64.exe. That should start Fiji.

You can also create a shortcut on the Desktop to avoid navigating to the Fiji.app folder each time.

Left-click on the IJP-ImageJ-Launcher-0.2.0-windows_x64.exe and drag it to the Desktop. Once you release mouse button, a pop-up manu will open, select "Create shortcut here". Now you can double-click on the new shortcut on the Desktop to start Fiji.

You can rename the Desktop alias to whatever you like, for instance, Fiji.

If you have problems installing, please report in Discussions or Image.sc Forum

Troubleshooting

Start-up log ~/.ijp_imagej_launcher.log

The IJP-ImageJ-Launcher writes diagnostic info to a file .ijp_imagej_launcher.log in the users home directory. The information recorded is some as using --debug on command line.

Starting from command prompt

You can start the IJP Image Launcher from the terminal and see diagnostic printouts that may help troubleshoot potential issues.

1. Open the terminal (command prompt).
2. Navigate to Fiji.app directory, for instance cd ~/Download/Fiji.app
3. Run IJP ImageJ Launch typing: ./IJP-ImageJ-Launcher-0.1.0-macosx-arm64 --debug

You should see diagnostic information about how the IJP ImageJ Launcher is attempting to start Fiji. The error messages should help you to address the issue. Please use Discussions or Image.sc Forum if you have additional questions.

Developer Setup

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

The IJP ImageJ Launcher is written mostly in Scala. With about 10 lines of C code. Native binaries are created with help from Scala Native.

To rebuild the IJP ImageJ Launcher from sources, you need to setup Scala Native dependencies following instructions at Scala Native. In brief, you will need to install the following: JDK, SBT, and LLVM/CLang. Details depend on OS. On Windows you will also need Visual Studio 2019 (the Community Editions is sufficient). 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.