MATLAB ====== `MATLAB `_ is a high-level language and interactive environment that facilitates rapid development of algorithms for performing computationally intensive tasks. Calling Bio-Formats from MATLAB is fairly straightforward, since MATLAB has built-in interoperability with Java. We have created a :sourcedir:`toolbox ` for reading and writing image files. Note the minimum recommended MATLAB version is R2017b. .. note:: It is possible to run Bio-Formats 6 on earlier MATLAB versions using a JVM version 8 or greater although using a different JVM than the one shipped with MATLAB can affect other functionalities. Please refer to the `MATLAB Answers `__ for more information. Installation ------------ Download the MATLAB toolbox from the Bio-Formats `downloads page `_. Unzip :file:`bfmatlab.zip` and add the unzipped :file:`bfmatlab` folder to your MATLAB path. Usage ----- Please see :doc:`/developers/matlab-dev` for usage instructions. If you intend to extend the existing .m files, please also see the :doc:`developer page ` for more information on how to use Bio-Formats in general. Performance ----------- In our tests (MATLAB R14 vs. java 1.6.0\_20), the script executes at approximately half the speed of our :doc:`showinf command line tool `, due to overhead from copying arrays. Troubleshooting --------------- If you encounter an error trying to open JPEG-2000 data in MATLAB but the file will open e.g. in Fiji using Bio-Formats, it may be due to conflicting versions of JAI ImageIO in different JARs. As discussed on the component page, :ref:`JAI ImageIO ` is no longer maintained and you will likely need to remove the conflicting JAR(s) as a workaround. Upgrading --------- To use a newer version of Bio-Formats, overwrite the content of the :file:`bfmatlab` folder with the `newer version `_ of the toolbox and restart MATLAB. Alternative scripts ------------------- Several other groups have developed their own MATLAB scripts that use Bio-Formats, including the following: - ``_ - `imread for multiple life science image file formats `_