To create a custom application, you need the tools and knowledge to modify and build source code. In particular, you need a compiler supported by MATLAB®.
To exchange custom data with MATLAB data, use a MAT-file, a MATLAB format binary file. You do not need the MAT-file format specifications because the MAT-File Interface Library provides the API to the data. You need to know the details of your data to map it into MATLAB data. Get this information from your product documentation, then use the mxArray type in the Matrix Library to declare the data in your program.
In your custom program, use functions in the MATLAB C/C++ and Fortran API:
MAT-File Interface Library
To build the application, use the mex build script with the -client engine option.