DOI: 10.7554/elife.70506. A modular platform for automated cryo-FIB workflows

A modular platform for automated cryo-FIB workflows

10.7554/elife.70506

Crossref journal-article

eLife Sciences Publications, Ltd

eLife (4374)

Abstract

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.

Bibliography

Klumpe, S., Fung, H. K., Goetz, S. K., Zagoriy, I., Hampoelz, B., Zhang, X., Erdmann, P. S., Baumbach, J., MÃ¼ller, C. W., Beck, M., Plitzko, J. M., & Mahamid, J. (2021). A modular platform for automated cryo-FIB workflows. ELife, 10. CLOCKSS.

Authors 12

Sven Klumpe (first)
Herman KH Fung (first)
Sara K Goetz (first)
Ievgeniia Zagoriy (additional)
Bernhard Hampoelz (additional)
Xiaojie Zhang (additional)
Philipp S Erdmann (additional)
Janina Baumbach (additional)
Christoph W Müller (additional)
Martin Beck (additional)
Jürgen M Plitzko (additional)
Julia Mahamid (additional)

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Dates

Type	When
Created	3 years, 7 months ago (Dec. 24, 2021, 8 a.m.)
Deposited	1 year, 10 months ago (Oct. 11, 2023, 9:19 p.m.)
Indexed	12 hours, 2 minutes ago (Aug. 20, 2025, 9:15 a.m.)
Issued	3 years, 7 months ago (Dec. 24, 2021)
Published	3 years, 7 months ago (Dec. 24, 2021)
Published Online	3 years, 7 months ago (Dec. 24, 2021)

Funders 5

European Research Council 10.13039/501100000781
Region: Europe
gov (National government)
Labels1
1. ERC
Awards1
1. 760067
European Research Council 10.13039/501100000781
Region: Europe
gov (National government)
Labels1
1. ERC
Awards1
1. 871037
European Molecular Biology Laboratory 10.13039/100013060
Region: Europe
gov (Research institutes and centers)
Labels2
1. EMBL Heidelberg
2. EMBL
Awards1
1. Interdisciplinary Postdoctoral Program COFUND 664726
Max Planck Institute Magdeburg 10.13039/501100012319 Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg
Region: Europe
pri (Research institutes and centers)
Labels3
1. Max Planck Institute Magdeburg
2. Max Planck Institute for Dynamics of Complex Technical Systems
3. Max-Planck-Institut für Dynamik komplexer technischer Systeme Magdeburg
Marie Sklodowska-Curie Actions 10.13039/100018694 HORIZON EUROPE Marie Sklodowska-Curie Actions
Region: Europe
gov (National government)
Labels5
1. Marie Sklodowska-Curie Actions
2. Horizon Europe - Marie Skłodowska-Curie Actions
3. Marie Skłodowska-Curie Actions
4. HORIZON EUROPE Marie Skłodowska-Curie Actions
5. MSCA
Awards1
1. Interdisciplinary Postdoctoral Program COFUND 664726

BibTeX

@article{Klumpe_2021, title={A modular platform for automated cryo-FIB workflows}, volume={10}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.70506}, DOI={10.7554/elife.70506}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Klumpe, Sven and Fung, Herman KH and Goetz, Sara K and Zagoriy, Ievgeniia and Hampoelz, Bernhard and Zhang, Xiaojie and Erdmann, Philipp S and Baumbach, Janina and Müller, Christoph W and Beck, Martin and Plitzko, Jürgen M and Mahamid, Julia}, year={2021}, month=dec }

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