This documentation is for a legacy ScanImage version. The current documentation is ScanImage 2019.

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There is no Command Window in compiled MATLAB (along with any other UI commonly found within the MATLAB workspace).  However, using ScanImage's own Status Window should allow for running MATLAB-specific commands (e.g. no local MATLAB scripts, see User Functions).  There are also limitations on which built-in MATLAB commands are available in compiled MATLAB.  A full listing of non-compilable unsupported functions can be found here.