Klumpe, Sven / Fung, Herman Kh / Goetz, Sara K. / Zagoriy, Ievgeniia / Hampoelz, Bernhard / Zhang, Xiaojie / Erdmann, Philipp S. / Baumbach, Janina / Müller, Christoph W. / Beck, Martin / Plitzko, Jürgen M. / Mahamid, Julia. A modular platform for automated cryo-FIB workflows. 2021-12, eLife, Vol. 10
Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.