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OpenFIBSEM: A universal API for FIBSEM control.

Patrick Cleeve1, David Dierickx1, Lucile Naegele1

  • 1Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia.

Journal of Structural Biology
|April 27, 2023
PubMed
Summary
This summary is machine-generated.

OpenFIBSEM is a new, open-source API that enhances automation for Focused Ion Beam Scanning Electron Microscopes (FIBSEM). This tool improves programmability for structural biology research, offering cross-platform compatibility and core microscopy functions.

Keywords:
APIAutomationControllerFocused Ion Beam microscopyMicroscopyPython

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Area of Science:

  • Microscopy and Imaging
  • Structural Biology
  • Software Engineering

Background:

  • Focused Ion Beam Scanning Electron Microscopes (FIBSEM) are crucial for high-resolution imaging in structural biology.
  • Current FIBSEM systems often lack universal programmability and automation, hindering complex research workflows.
  • Developing integrated software solutions for FIBSEM is challenging due to hardware diversity.

Purpose of the Study:

  • To introduce OpenFIBSEM, a universal, cross-platform API for controlling FIBSEM instruments.
  • To enhance the automation and programmability of FIBSEM workflows, particularly in structural biology.
  • To provide a foundation for a unified development ecosystem for FIBSEM systems.

Main Methods:

  • Development of a core API with functionalities for imaging, movement, milling, and manipulator control.
  • Integration of system calibration, alignment, and image analysis modules.
  • Provision of reusable user interface components compatible with napari for application development.
  • Support for multiple hardware manufacturers (ThermoFisher, TESCAN) with plans for expansion.

Main Results:

  • OpenFIBSEM offers a composable and extendable software solution for FIBSEM control.
  • Demonstrated improved automation capabilities through example applications compatible with diverse hardware.
  • Successful integration with napari for streamlined application development.
  • Open-source availability fosters community development and broader adoption.

Conclusions:

  • OpenFIBSEM establishes a foundation for a cross-platform operating system and development ecosystem for FIBSEM.
  • The API significantly enhances the automation and programmability of FIBSEM instruments for research.
  • Open-source accessibility promotes wider adoption and collaborative advancement in FIBSEM applications.