The SerialEM Script Repository

Welcome to the SerialEM Script Repository

SerialEM (Mastronarde, 2005) is a software developed at the The Boulder Laboratory for 3D Electron Microscopy that can acquire a variety of data from transmission electron microscopes: tilt series for electron tomography, large image areas for 3D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods. It interfaces with the FEI Tecnai, Titan, and Talos platforms, JEOL TEM with the TEMCON or TEMCENTER user interface, and the Hitachi HT-7700, as well as detectors from numerous manufacturers.

SerialEM also features a powerful scripting language (until version 3.6.0 in 2016/17: "macros") allowing to control various microscope parameters, acquire, process and save images, and call higher level functions of SerialEM such as autofocus, alignment to reference images, or automatic adjustment of intensity. For tasks of higher complexity, SerialEM scripts can include control structures such as conditional expressions, loops, and functions.

This website was set up in collaboration with the developer of SerialEM to serve as a central sharing point for scripts/macros, to make them easily accessible in a well organised and documented way, and to stimulate exchange between SerialEM users. To access the scripts available via the repository, starting at a categorised list, no registration is required. To upload new scripts or to edit your own existing scripts, login or register.

The SerialEM Script Repository is operated by Nexperion – Solutions for Electron Microscopy, a solutions provider in the field of EM located in Vienna, Austria, who also provides SerialEM installations, calibrations, and trainings worldwide as a service.