Most source code control providers have built-in diff and merge capabilities for text-based files, but they also typically allow users to override the default utilities for specific file-types. The binary nature of LabVIEW file-types requires the use of custom utilities for diff and merge, which are available in the professional version of LabVIEW 2009 or later.
Calling graphical merge from an external application requires the ability to pass parameters to the command line. In windows, the executable to be run for Graphical Diff is available at the following location: C:\Program Files\National Instruments\Shared\LabVIEW Compare\LVCompare.exe. The analogous executable for Graphical Merge is available at C:\Program Files\National Instruments\Shared\LabVIEW Merge\LVMerge.exe.
Both executables offer a variety of command-line parameters that can be used to customize the behavior and results of the utility. As an example, these settings can be used to exclude changes that are purely cosmetic and do not affect the behavior of code.
Example code from the Example Code Exchange in the NI Community is licensed with the MIT license.