Figure 1. Software architecture, modules, and use cases of SerialFIB.

Developments presented in this work are highlighted in green. The graphical user interface (GUI) is largely decoupled from instrument operations, which are controlled by the developed SerialFIB driver. Modules (right) enable design of protocols for different use cases (bottom, 1–4), and a scripting interface that offers flexibility for new developments (bottom, N).

Figure 1—figure supplement 1. Graphical user interface (GUI) for automated cryo-focused ion beam (cryo-FIB) protocols.

(A) The GUI displays buttons for the main functions (imaging and several FIB milling procedures; left), the image buffer where reference images are selected and displayed in the alignment window to prepare and adjust milling patterns (top right, red rectangles). Specialized applications (volume imaging, custom milling procedures, and fluorescence overlay) are available below the image buffer. In the coordinate navigator (bottom), milling sites are connected with alignment images and corresponding patterns. From the Tools tab, Lamella Designer, Pattern Designer, Volume Designer, and Script Editor can be selected. (B) The Lamella Designer allows for stepwise construction of user-defined patterns and milling procedures. (C) The Pattern Designer enables creation of customized patterns, for example, for lift-out site preparation.

Figure 1—figure supplement 2. SerialFIB interface for volume imaging and Script Editor.

(A) In the Volume Designer, FIB-SEM volume imaging workflows can be constructed with user-definable FIB milling and SEM imaging parameters. (B) The Script Editor offers a scriptable interface for customized milling protocols, which can be saved as independent scripts or within libraries.