MinIJPlugin

An ImageJ plugin (with a GUI) that allows users to select a square ROI with specified coordinates

View the Project on GitHub CreLox/MinIJPlugin

Minimal ImageJ GUI Plugin

This is an ImageJ plugin (with a GUI) that allows users to select a square ROI with specified coordinates. More importantly, this is a template of a (really) minimal ImageJ plugin.

Below is a step-by-step instruction to make a functional plugin without the tedium of configuring an IDE - a text editor will do the job as long as you know how to code in java [to learn the source codes of ImageJ utilities, use Plugins > Utilities > Find Commands... > (choose a specific command) > Source]. Note that these steps are for Unix-like OS’s (macOS/Linux distributions/…); use Command Prompt/PowerShell on Windows.

  1. Download this repository entirely and edit the source code (SelectSquareROI.java) and the configuration file (plugins.config - do not change this filename) accordingly.

  2. Prepare dependency package(s) (here ij.jar is needed, which could be downloaded from here) in the same folder as our source code.

  3. Install JDK. On Windows, add the folder containing all executables to the PATH environment variable; otherwise, you need to provide the full path of the executable (if the path contains special characters, you may find this helpful).

  4. Go to Terminal and compile our source code into a java class file: javac -classpath ij.jar SelectSquareROI.java (Note: edit the filename accordingly). If you want to check the version of a java class file and determine its compatibility, you might find this thread helpful.

  5. Compress the configuration file and the compiled java class file into one java archive file (Select_Square_ROI.jar): jar -cfe Select_Square_ROI.jar SelectSquareROI SelectSquareROI.class plugins.config (Note: edit the filenames and the class name(s) accordingly; include an underscore in the filename of the java archive file).

  6. Move our java archive file into the plugins subfolder of ImageJ (or open ImageJ and run “Plugins > Install Plugin...”).

  7. Restart ImageJ and test the plugin. There should now be a corresponding option in the menu if the configuration file is written correctly.

  8. (Optional) set a shortcut for our plugin by running the ImageJ command: “Plugins > Shortcuts > Add Shortcut...”.