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A Modular Platform for Streamlining Automated Cryo-FIB Workflows

By Sven Klumpe, Herman K H Fung, Sara K Goetz, Ievgeniia Zagoriy, Bernhard Hampoelz, Xiaojie Zhang, Philipp S Erdmann, Janina Baumbach, Christoph W Mueller, Martin Beck, Juergen M Plitzko, Julia Mahamid

Posted 20 May 2021
bioRxiv DOI: 10.1101/2021.05.19.444745

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, current 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 3-dimensional correlative light and electron microscopy (CLEM) tools. The software enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM guided 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.

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