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Using Netbeans

The following instructions for debugging Micro-Manager’s Java code with NetBeans are intended to work on Windows or Mac. Updated for 2.0.0

(See also: Writing plugins for Micro-Manager)

  1. Download and install a recent Micro-Manager nightly build. We will refer to the installed Micro-Manager directory as $INSTALLDIR below.

  2. Download a copy of the latest Micro-Manager source.
    • Clone the main repository:
      git clone https://github.com/micro-manager/micro-manager
    • Initialize all submodules:
      cd micro-manager
      git submodule update –init –recursive

    • We’ll refer to the root source directory as $SRCDIR below.
  3. Download, install and run NetBeans. The Java SE Bundle is sufficient if you already have the JDK (Java Development Kit) installed on your computer. Otherwise, download a JDK from AdoptOpenJDK . Micro-Manager is currently developed with JDK 8.

  4. Choose File > New Project… > [Categories] Java > [Projects] Java Project with Existing Sources. Press Next.

  5. Give your project a name. The Project Folder is best saved outside of the Micro-Manager source directory. Press Next.
  6. Under Source Package Folders, click Add Folder at right and browse to $SRCDIR/mmstudio/src/main/java, as well as $SRCDIR/mmstudio/src/main/resources. If you want to develop a plugin, you can also add $SRCDIR/plugins/*/src/main/java at this time. You can also add plugins later. Press Next.

  7. Include all files (**). Press Finish.

  8. Right-click your project in the Projects tab (probably at left) and select Properties.

  9. Select Libraries under Categories. Make sure the Java Platform matches the version of Micro-Manager you are using (e.g., 64-bit JDK 1.8 - but using a newer Java Platform in NetBeans than the one shipped with Micro-Manager is usually okay).

  10. Under Compile > Compile-time Libraries, click Add Jar/Folder and add $INSTALLDIR/ij.jar, as well as all jars in $INSTALLDIR/plugins/Micro-Manager except for MMJ_.jar.

  11. Select Run under Categories. For the <default config>, set the following parameters:
    • Main Class: type in ij.ImageJ
    • Working Directory: type in your $INSTALLDIR
    • VM options: for 64 bit systems, type in -Xmx3000M, otherwise use -Xmx600M. This sets the maximum memory (megabytes) used by Java.
      If running Micro-Manager 2.0, you also need to supply -Dforce.annotation.index=true.
  12. Click OK, and then right-click your project and choose Debug. If all is well, then Micro-Manager should launch inside ImageJ.

The components from the installed Micro-Manager can get out of sync with the source. If you encounter unexpected errors, update to the latest nightly build and the latest source revision.