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Enable Java

Java is a free piece of software that other programs use to run parts of their code. It has nothing to do with JavaScript used on web pages and does not need to be started or updated by hand, MIB uses it in the background.

Starting from MATLAB R2026b, Java is no longer included with MATLAB or with the MATLAB Runtime used by the standalone version of MIB. MIB starts and works without Java, but the following features need it:

  • Bio-Formats: opening microscope formats such as CZI (Zeiss), LIF (Leica), ND2 (Nikon), ZVI, OIB, VSI and many others, and saving OME-TIFF
  • connections to Fiji, Imaris and OMERO
  • on macOS and Linux, copying images to and from the system clipboard

Do I need Java?

If you only work with TIF, PNG, JPG, AM, MRC, HDF5/XML, OME-Zarr or MIB's own formats, you can skip this page. You can always come back to it later: MIB tells you when a feature needs Java.

When Java is missing, MIB shows a Java is missing dialog at startup. Setting up Java takes about five minutes and has to be done once per computer.

Step 1: Download Java

MIB recommends Eclipse Temurin 21, a free Java distribution.

  1. Press Configure Java in the Java is missing dialog and then Download Java, or open the Eclipse Temurin download page in a web browser.
  2. Make sure the page shows Version 21 - LTS, Package Type: JRE and your operating system (for example Windows, x64).

  3. Download one file:

    Your computer Download
    Windows, you can install programs (administrator rights) the .msi file
    Windows, you cannot install programs (typical for computers managed by the IT department) the .zip file
    macOS the .pkg file; on Apple silicon (M1, M2, ...) choose aarch64
    Linux see Linux below
Can I use another Java version?

MATLAB R2026b works with Java versions 8, 11, 17, 21 and 25, from Eclipse Temurin (Adoptium) or Amazon Corretto. MIB warns you when the selected Java is not one of those versions. If you do not have a reason to choose another one, use Temurin 21.

Step 2: Install Java

Windows with administrator rights (.msi file)

Double-click the downloaded .msi file and press Next until the installation finishes. Keep the default settings. Java is installed to a folder like C:\Program Files\Eclipse Adoptium\jre-21.0.12.101-hotspot.

Windows without administrator rights (.zip file)

  1. Open your user folder in File Explorer, for example C:\Users\your-name, and create a new folder called Java.
  2. Right-click the downloaded .zip file, choose Extract All..., select the new Java folder and press Extract.

You now have a folder like C:\Users\your-name\Java\jdk-21.0.12+101-jre. MIB looks for Java in your user folder, in Documents and in Java automatically.

Note

Do not delete or move this folder later: MIB uses Java from where it is.

macOS (.pkg file)

Double-click the downloaded .pkg file and follow the installer.

Step 3: Restart and check

  • MIB for MATLAB: close MIB and MATLAB, then start MATLAB and MIB again.
  • Standalone MIB: close MIB and start it again.

After an installation with the .msi or .pkg file, MATLAB usually finds the new Java by itself. If the Java is missing dialog no longer appears, Java works and you are done. Otherwise, continue with Step 4. After an installation from the .zip file, Step 4 is always needed.

Step 4: Connect MIB to Java

  1. Open Ribbon → Home → Preferences → External directories, or press Configure Java in the Java is missing dialog, which does steps 2 and 3 for you.
  2. In the Java path row press Find Java... and choose your Java from the list.
    • If you have just installed Java and the list is empty, press Search to look again.
    • If your Java is not in the list, choose Select the Java folder manually... and select the Java folder: the folder that contains the bin folder (for example C:\Users\your-name\Java\jdk-21.0.12+101-jre).
  3. Press Configure Java....
    • Standalone MIB asks whether to set Java Only for me or For all users of the computer. Choose Only for me; choose For all users when you set up a computer that several people use, or when Java is still missing after the restart. Windows then asks for an administrator password.
  4. Press OK and restart as in Step 3.

Java now works: the Java is missing dialog no longer appears. Open one of your microscope files to check.

After installing a new version of MATLAB

A new MATLAB version, or a new MATLAB Runtime for standalone MIB, may not know about the Java that you set up before. MIB remembers the Java folder and offers to connect it again with one click in the Java is missing dialog.

Troubleshooting

The Java is missing dialog appears again after the restart

  • Make sure MATLAB was closed completely, not only MIB.
  • Open Preferences → External directories and check that the Java path folder still exists, then press Configure Java... again.
  • Standalone MIB: press Configure Java... again and choose For all users.

"This is not a Java folder"

The selected folder is not the Java folder itself. Select the folder that contains bin, lib and a file called release.

No administrator rights and no .zip file allowed

Ask your IT department to install Eclipse Temurin JRE 21 and to connect it to MATLAB as described in the box below.

For IT administrators

Install Eclipse Temurin JRE 21 (or another OpenJDK version supported by MATLAB R2026b: 8, 11, 17, 21, 25). With the default MSI options (Java added to PATH), MATLAB R2026b found Temurin 21 without further configuration. To set the folder explicitly for all users, run from an elevated command prompt:

  • MATLAB: "<MATLAB folder>\bin\matlab_jenv" -allusers "<Java folder>"
  • MATLAB Runtime (standalone MIB): "<MATLAB Runtime folder>\R2026b\bin\matlab_jenv" -allusers "<Java folder>"

Run matlab_jenv without arguments to see the current setting. In MATLAB the same for the current user is jenv("<Java folder>") in the Command Window, followed by a MATLAB restart. More details: MATLAB Support for OpenJDK and Use JRE with MATLAB Runtime.

Linux

Install Java 17 with the package manager of your distribution, for example sudo apt install openjdk-17-jre on Ubuntu, and connect it in Step 4 (Java installations in /usr/lib/jvm are found automatically). Java 17 is recommended on Linux because MATLAB R2026b on Linux supports Java 21 only up to version 21.0.2, older than what the package managers install.

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