David Mastronarde and co-workers develop and distribute software for acquisition, processing, and analysis of image data, primarily from electron microscopes. This work was originally done in the former Boulder Laboratory for 3-D Electron Microscopy of Cells, a national research center funded by the NIH. Efforts continue on the first three packages described below. Mastronarde develops SerialEM and IMOD. The co-workers currently include Sue Held, who primarily works on the eTomo user interface in IMOD, and John Heumann, who works on PEET. The group is not part of the Boulder EM Service.


SerialEM is a program that can acquire a variety of data from FEI and JEOL electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods. The main focus of the program is automated tilt series acquisition. For this, it uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. With this method, it achieves both robustness and speed. The program also provides tools for locating and navigating to areas of interest on the specimen.


IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package includes a graphical user interface for tomographic reconstruction that provides access to various tools for solving problems that arise in these reconstructions, particularly with very large data sets. There are also programs for assembling and aligning images from serial sections viewing 3-D data from any orientation, and modeling and displaying the image files.


Particle Estimation for Electron Tomography (PEET) is a package for aligning and averaging 3-D volumes extracted from tomograms and containing a particle of interest. The programs can conpensate for the wedge of missing data characteristic of tomographic volumes during both the alignment and the averaging. The operations can be run in parallel on multiple computers and there is a graphical user interface available in IMOD.


Shape is a program developed by Kristian Sandberg for automated modeling of membranes and other extended structures in tomographic volumes. It provides a user interface for adjusting several size and threshold parameters on a test portion of the volume. Once parameters are found, it can be run on the whole volume and a model exported for viewing and correction in IMOD. Shape interfaces with IMOD to automate segmentation of membranes.

YouTube Tutorials

These tutorials show you how to build dual axis tomograms using IMOD, how to use PEET for sub volume averaging, and how to use SerialEM for tilt series acquisition.

Last updated: 2014-10-14