I am working with a Hitachi FESEM and would like to automate the collection of images. So I can collect and image, move the stage some step size, refocus, collect image, repeat...
Do you know if HITACHI does provide an API (advanced programming interface) for their SEMs ? In order to automate any SEM function, including stage control for navigation and image acquisition controls, my guess is you'll either need HITACHI to provide an additional application tailored to your needs or you will have to code it yourself. Hence the need for access to the SEM software libraries and controles.
Fyi, Zeiss is allowing full control of their SEMs through an API (SmartSEM API), that allows you to develop your own applications using VB.NET or C++ (should evolve towards Python).
Alternatively, they also provide an additional piece of software called MultiScan that would do exactly what you're contemplating : define global area, choose shape, mag, autofocus through three point plane focus definition...
To be honest, this was the main reason we decided to buy from Zeiss some years ago as they were the only one to allow access to SEM programming then : we're into a lot of image analysis and this took care of the "non-productive" part of our methods, freed a technician to do something else while the SEM randomly aquired 10,20,50 or 100 pictures of a sample before sending it to MatLab or ImageJ for IA.
As with Hitachi or others, I don't know how they evolved on this : I thus suggest you get back to HITACHI first and ask them about an API or additional software they might have developed.
An alternative would be to use a "click programming" software to design a macro that runs a sequence of "mouse clicks" on your scan, X&Y stage, freeze and save buttons. Used to do that years ago but you better pray that the buttons do not move and that nobody messes up with your SEM software layout...
in this article, the author used "... an external freeware macro program was used to control the mouse and keyboard to streamline and automate the SEM stage tilt, stage rotation and image acquisition (“Mini mouse Macro, n.d.)..."