SBEMimage is a free and open-source acquisition software for scanning electron microscopy with a focus on serial block-face imaging. It has been designed for complex, challenging acquisition tasks, such as large-scale volume imaging of biological ultrastructure. Advanced monitoring, process control, and error handling capabilities improve reliability, speed, and quality of acquisitions. Debris detection, autofocus, real-time image inspection, and various other quality control features minimize the risk of data loss. Adaptive tile selection allows for efficient imaging of large volumes of arbitrary shape. The software’s graphical user interface is optimized for remote operation with visual setup and monitoring capabilities.
SBEMimage is customizable and extensible, which allows for fast prototyping and permits adaptation to a wide range of SEM/SBEM systems and applications.
For more background and details read the paper.
SBEMimage is currently deployed as open-source software at research institutions worldwide, including:
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Friedrich Miescher Institute in Basel, Switzerland |
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European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany |
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Francis Crick Institute in London, UK |
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Stellenbosch University in Stellenbosch, South Africa |
It is being used for a variety of applications, including:
- CZI-funded Democratising Volumetric Visual Proteomics project, together with a napari annotation plugin for Targeted Array EM Imaging at the Francis Crick Institute (UK) and Stellenbosch University (South Africa)
- MRC-funded multi-modal project, together with a napari registration plugin for Targeted Array EM Imaging at EMBL Heidelberg (Germany)
A user guide containing installation instructions and a short introduction to the software is available here: sbemimage.github.io/SBEMimage.
For users who are not familiar with Python, it is recommended to download the Windows 10+ installer.
Detailed generated information can be found here deepwiki.com/SBEMimage/SBEMimage
For support and discussion, please use the Image.sc forum and post to the forum with the tag 'sbemimage'.
SBEMimage was originally developed at the Friedrich Miescher Institute in Basel, supported by the Novartis Research Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 742576). Other institutes that have substantially contributed to SBEMimage development, testing and bug fixing include the Francis Crick Institute, London, UK, and EPFL, Lausanne, Switzerland (CIME/BioEM). See https://github.com/SBEMimage/SBEMimage/graphs/contributors for the list of individual contributors.
Contact benjamin.titze ÄT protonmail.ch if you are interested in contributing to the development of SBEMimage. All ongoing development takes place in the 'dev' branch. Pull requests to that branch are welcome. For more information, see the section 'For developers' in the user guide.
Please use GitHub Issues (https://github.com/SBEMimage/SBEMimage/issues) for bug reports. For general feedback or feature suggestions, post to the Image.sc forum with the tag 'sbemimage', or send an email to benjamin.titze ÄT protonmail.ch.
Please cite the following paper if you use SBEMimage:
Titze B, Genoud C and Friedrich RW (2018) SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy. Front. Neural Circuits 12:54. doi: 10.3389/fncir.2018.00054
This software is licensed under the MIT License - see the LICENSE file for details.