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 set of scripts for reading image files. Note the minimum supported MATLAB version is R2007b (7.5).
Download the MATLAB toolbox from the Bio-Formats downloads page. Unzip bfmatlab.zip and add the unzipped bfmatlab folder to your MATLAB path.
Note
As of Bio-Formats 5.0.0, this zip now contains the bundled jar and you no longer need to download loci_tools.jar or the new bioformats_package.jar separately.
Please see Using Bio-Formats in MATLAB for usage instructions. If you intend to extend the existing .m files, please also see the developer page for more information on how to use Bio-Formats in general.
In our tests (MATLAB R14 vs. java 1.6.0_20), the script executes at approximately half the speed of our showinf command line tool, due to overhead from copying arrays.
To use a newer version of Bio-Formats, overwrite the content of the bfmatlab folder with the newer version of the toolbox and restart MATLAB.
Several other groups have developed their own MATLAB scripts that use Bio-Formats, including the following: