Open-source acquisition software for scanning electron microscopy with a focus on serial block-face imaging.

SBEMimage is designed for complex, challenging acquisition tasks, such as large-scale volume imaging of neuronal tissue or other 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. It includes a user-friendly Viewport to visually set up acquisitions and monitor them.

SBEMimage is customizable and extensible, which allows for fast prototyping and permits adaptation to a wide range of SEM/SBEM systems, auxiliary devices and applications.

For more background and details read the paper.

Please read the user guide: https://sbemimage.readthedocs.io. It currently contains installation instructions, a short introduction to the software (to be expanded) and information for developers. For users who are not familiar with Python, it is recommended to download the Windows 7/10 installer. For support and discussion, please use the Image.sc forum and post to the forum with the tag 'sbemimage'.

The development of SBEMimage at the Friedrich Miescher Institute in Basel has been 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: EPFL, Lausanne, Switzerland (CIME/BioEM); Francis Crick Institute, London, UK.

Current development team: Benjamin Titze (btitze; lead developer); Thomas Templier, Janelia Research Campus; Joost de Folter, Francis Crick Institute; Philipp Schubert, Max Planck Institute of Neurobiology; and others: https://github.com/SBEMimage/SBEMimage/graphs/contributors

Contact btitze 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 btitze 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.