Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
Ievgeniia Zagoriy
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Bernhard Hampoelz
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Xiaojie Zhang
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Philipp S Erdmann
Department Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
Janina Baumbach
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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.
