In order to use Doxygen Integrator inside Atmel Studio we must configure Doxygen inside Atmel Studio. In Doxygen Integrator VSIX package already contains Doxygen Executable with latest update. And if you choose to use that executable the path is preconfigured. If you want to use your own installed Doxygen executable then, Go to Tools -> Option -> Documentation. In that select Doxygen Setting tab, Set the Doxygen Executable Path by selecting Doxygen executable inside the computer. After that press OK. Refer the screenshot below.