[3dem] Open-Source Software Development for Cryo-FIB-SEMs

[Klumpe,Sven Dominik]

TL;DR: open-source FIBSEM control software fibsemOS kickoff meeting January 29th at 9:30 am and 6 pm CET via Zoom, if interested in contributing please write contact at fibsemos.org<mailto:contact at fibsemos.org> for a Slack invite and Zoom link.


Stronger Together: A Case for Community-Driven, Open-Source Software Development for Cryo-FIB-SEMs


Dear FIB-SEM Community,

As operators and managers of FIB-SEM instruments, you know firsthand how important reliable automation software will be in maximizing the value of limited microscope time. Open-source software packages are essential for ensuring long-term instrument support and enabling the continuous development and rapid implementation of novel workflows and tools.

Our community has seen numerous parallel software developments in many different areas, e.g. SBEMImage, CLEMsite, CorRelator, 3DCT, openFIBSEM, SerialFIB, and many others. While these have all been instrumental to many of the biological discoveries that (cryo-)FIBSEM has delivered, they all had to integrate basic functionality from scratch using vendor-specific APIs. We believe that in the open-source software stratosphere of research institutes, we should aim at an open-source, vendor-agnostic software platform to enable the integration and rapid dissemination of new developments across the community.

Out of this motivation, we are launching the fibsemOS<https://urldefense.com/v3/__http://www.fibsemos.org/__;!!Mih3wA!FUWehofoly2EB7VhbronYsSbqsJLMPIybg4t8RHkPwanDcGiDfXnk-lsP2MQWk1t7kW5hXSdU5lYcSXDNSqmLqlZ2w$ > initiative to consolidate our efforts in developing microscope control software for FIB-SEM instruments, and we are extremely excited that the Chan Zuckerberg Initiative is financially supporting us in this effort. To coordinate this project, we've created a Slack channel where interested community members can collaborate on development, testing, and implementation. There, you will also find information on our two kick-off meeting in an attempt to cater to most time zones, happening on January 29th at 9:30 am and 6 pm CET.

If you're using or developing tools for FIBSEM and are interested in shaping and participating in this open-source software package - whether through development, testing, or feedback - please get in touch with us (contact at fibsemos.org<mailto:contact at fibsemos.org>) for an invitation to the Slack channel. There, you will also find the Zoom link for the kick-off meeting. We envision this platform as truly community-driven: from the community, for the community.

We are excited to work with you together on this!

Sincerely,

Patrick Cleeve, Georg Ramm and Sven Klumpe

on behalf of the fibsemOS team


P.S.: The impetus and initiative for this effort was formulated at the 2025 3DEM GRC in a meeting where the following representatives of the cryoET community all enthusiastically endorsed the idea of supporting a single community-driven open-source software package:


Bridget Carragher (Biohub), Patrick Cleeve (Remote and represented by Sven Klumpe), Maud Dumoux (Rosalind Franklin Institute), Sven Klumpe (IMP/IMBA, Vienna BioCenter), Julia Mahamid (EMBL Heidelberg), Alex de Marco (New York Structural Biology Center), Jürgen Plitzko (MPI of Biochemistry), Georg Ramm (Monash University)




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Sven Klumpe, PhD

Principal Investigator – In Situ Structural Biology Group

Research Institute of Molecular Pathology, IMP &

Institute of Molecular Biotechnology, IMBA

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Campus-Vienna-Biocenter 1, 1030 Vienna, Austria

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