MIA-MATLAB is a MIA plugin, which adds additional modules that rely on MATLAB. The latest release includes the following modules:
- "Fit alpha shape" will create an alpha shape for each object in a specified object collection.
- "Sort stack" will order slices of an image stack such that the difference in normalised cross-correlation between adjacent slices is minimised.
- Download the version of MIA-MATLAB, corresponding to your copy of MIA, from the Releases page.
- Place this .jar file into the /plugins directory of the your Fiji installation
- Install the relevant version of MATLAB (or the MATLAB Runtime). Filenames for MIA-MATLAB indicate the version of MATLAB to use (e.g. 2018b).
- Copy the javabuilder.jar file from the installed MATLAB directory to your Fiji's /jars directory. The javabuilder.jar file can typically be found at the following locations:
- Linux: /usr/local/MATLAB/MATLAB_Runtime/v95/runtime/toolbox/javabuilder/jar
- Mac: /Applications/MATLAB/MATLAB_Runtime/v95/runtime/toolbox/javabuilder/jar
- Windows: C:\Program Files\MATLAB\MATLAB Runtime\v95\toolbox\javabuilder\jar
- (Linux and Mac only) Add the MATLAB Runtime to the relevant system path. Details of this can be found here.
MIA-MATLAB will add various modules to MIA (e.g. the ability to create alpha surfaces for objects). These can be accessed in the same way as other modules.
This plugin relies on the MATLAB Runtime or a full copy of MATLAB if available.
This plugin is still in development and test coverage is currently incomplete. Please keep an eye on results and add an issue if any problems are encountered.