If you have a MATLAB license it is recommended to use MIB for MATLAB distribution of MIB suitable for Windows, MacOS and Linux. Otherwise use the standalone versions of MIB compiled for your operating system. As they are compiled with our academic MATLAB license, the standalone versions are for non-commercial academic research only (see license).

Installation instructions for MIB3 MATLAB
• Requires MATLAB R2025a or newer (R2026a is recommended). For older MATLAB releases use MIB 2
• Download MATLAB distribution of the program (MIB3_Matlab.zip), or get the source code from GitHub
• Unzip the archive to a folder of your choice. For example, c:\MATLAB\MIB3\
• Start MATLAB
• Make the mib subfolder (for example, c:\MATLAB\MIB3\mib\) the current folder in MATLAB, for example by browsing to it in the Current Folder panel or by typing cd('c:\MATLAB\MIB3\mib') in the MATLAB command window.
  Alternatively, add the mib subfolder to the MATLAB path (MATLAB->Home tab->Set Path...->Add Folder...->Save, or use the pathtool function from the MATLAB command window); MIB can then be started from any folder
• Type mib3 in the MATLAB command window and hit the enter button to start MIB
• Check System Requirements for further details about optional steps, such as use of Fiji or OMERO
• Read the Starting MIB section of the MIB 3 user guide. If MIB does not start, see Configuration files

• The first start takes a few extra seconds while MATLAB initializes the required libraries
• MIB may show a few dialogs: where to keep your statistics (asked once on each computer), how to enable Java (MATLAB R2026b and newer) and whether to download a newer version. They are explained in First start of MIB 3

Java and MATLAB R2026b or newer

MATLAB R2026b and newer no longer include Java. MIB works without it, but Bio-Formats, Fiji, Imaris and OMERO need Java: how to enable Java

If you plan to modify MIB or develop your own plugins, open MIB 3 as a MATLAB project. The complete project, with the project file MIB3.prj in its top folder, is available from the GitHub repository. The MATLAB distribution from this website (MIB3_Matlab.zip) is optimized for size and does not contain the complete project.

• Get the source code from GitHub, for example to c:\MATLAB\MIB3\, using one of these options:
  • clone the repository with git clone https://github.com/Ajaxels/MIB3.git
  • download it as a ZIP archive from the repository page (Code->Download ZIP) and unzip it
• Start MATLAB
• Add the Project button to the MATLAB sidebar, if it is not there yet
• Press the Project button, choose Open project and select MIB3.prj (for example, c:\MATLAB\MIB3\MIB3.prj). Alternatively, double-click MIB3.prj in the Files panel or type openProject('c:\MATLAB\MIB3\MIB3.prj') in the MATLAB command window
• The project automatically initializes the MIB directories: all source folders, including the plugins, are added to the MATLAB path, so there is no need to use Set Path. The folders are removed from the path again when the project is closed, so they do not interfere with other code, such as an installation of MIB 2
• Type mib3 in the MATLAB command window and hit the enter button to start MIB
• The classes and functions of MIB are described in the MIB 3 API reference

---