Software
IMOD
This 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.
SerialEM
Is a program to acquire tilt series for electron tomography on Tecnai and JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. It assesses the quality of a prediction before relying on it. With this method, it achieves both the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the speed of the newer approaches that take advantage of well-behaved specimen stages. The program also provides tools for locating and navigating to areas of interest on the specimen.
PEET
Particle Estimation for Electron Tomography 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
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.
