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 simple set of scripts for reading image files:

bfopen.m

bfCheckJavaPath.m

bfGetFileExtensions.m

bfGetPlane.m

bfGetReader.m

bfUpgradeCheck.m

We are not MATLAB experts—any comments on improving the script are welcome.

Performance

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.

Installation

To use the script, download bfopen.m, bfGetPlane.m, and bfGetReader.m (above) and loci_tools.jar and place them in your MATLAB work directory.

Upgrading

To use a newer version of Bio-Formats, overwrite loci_tools.jar with the newer version and restart MATLAB.

More information

For further instructions on working with Bio-Formats from MATLAB, see the Bio-Formats MATLAB Guide.