Image-guided tracking and autofocus corrections are handled by the freely-available microscope-control software SerialEM, in conjunction with a high angle annular dark field (HAADF) image acquired simultaneously. 
SerialEM
The open source SavvyScan system offers a versatile set of scanning patterns, operated by commercially available multi-channel acquisition and signal generator computer cards (Spectrum Instrumentation GmbH). 
SavvyScan