SerialEM
SerialEM is a software developed by Dr. David Mastronarde (at the University of Colorado and formerly part of The Boulder Lab for 3D Electron Microscopy of Cells) enabling cutting-edge automated acquisition of a variety of data from transmission electron microscopes: tilt series for (cryo-)electron tomography, large image areas for 3D reconstruction from serial sections, images for reconstruction of macromolecules by single-particle methods, and many more.
SerialEM is compatible with devices from major manufacturers:
- Thermo Scientific/FEI Tecnai, Titan, Spectra, and Talos microscopes with TEM scripting adapter
- JEOL TEMs with TEMCON or TEMCENTER interface
- Hitachi HT7700/7800 systems
- Cameras and detectors from all major brands
- STEM scan generators, including Digiscan, JEOL STEM (selected models), Thermo Scientific/FEI STEM, and TVIPS USG
In close collaboration with SerialEM's author, Nexperion provides comprehensive support and resources for this essential tool, whilst managing the financial resources for ongoing software development. For prompt assistance with any issues or feature requests, please reach out to
A community meeting about technical aspects in SerialEM is being organized by Nexperion in April 2026 in hybrid format.
The installation and calibration of SerialEM is available as a service by Nexperion for all supported platforms, both on-site as well as remotely.
A series of video tutorials, aiming to make important features of SerialEM more accessible and easy to learn.
Nexperion provides on-site and remote training on SerialEM, typically in conjunction with an installation or as a part of a bigger event.
A repository for sharing SerialEM scripts (both native and Python) allowing automation of TEM data acquisition is being operated by Nexperion.
A web app to generate customised "basic mode" files, allowing to reduce the complexity of the SerialEM 4.x user interface.
Register here for a Nexperion Service to receive automatic email notifications once a SerialEM version is published.
To enable user support and future development of SerialEM, Nexperion is managing a fund of support payments on behalf of the developer.