Dr. Timothy S. Baker - Electron Microscopy Software

Electron Microscopy Software

AUTO3DEM (including RobEM) v 3.14 February 4, 2010

AUTO3DEM is an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, and PSF. The archives for v3.0 and later also include the complete source code for building RobEM, a GUI driven program used both for image preprocessing (particle boxing, blemish removal, apodization, normalization, gradient correction) and visualization.

To reference this program, please cite: Yan X., R.S. Sinkovits, and T.S. Baker (2007) AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Bio. 157:73-82. (PDF)

AUTO3DEM is free software, licensed under the BSD License .

AUTO3DEM, © 2006-2010, Regents of the University of California

Documentation (PDFs)

P3DR Parallel 3D image reconstruction program: October 29, 2004

PCUT Parallel code for cutting spherical annulus from map: November 10, 2004
POR Parallel code for determining particle image origins and orientations in refine mode

PPFT Parallel code for determining particle image origins and orientations in search mode (PFTSearch.pdf)

PSF Parallel structure factor determination code

AUTO3DEM Keywords: Description of keywords for automated image reconstruction system: February 4, 2010

AUTO3DEM Test Problem Documentation: This document describes how to run the test problem that is distributed with AUTO3DEM. The data set is derived from nine micrographs of frozen-hydrated reovirus. The necessary files are below.

AUTO3DEM Test Problem (600 MB)

AUTO3DEM Modification History: February 4, 2010

AUTO3DEM - Older Versions

IHRSR++ v 1.3 February 5, 2010

IHRSR++ is a user-friendly extension to the Ed Egelman’s Iterative Helical Real Space Reconstruction (IHRSR) software. It includes all of the original IHRSR functionality plus the capabilities to determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data.

IHRSR++ also contains a number of Perl and Spider scripts for performing common preprocessing and data manipulation tasks such as power spectra calculations, application of CTF corrections, image stack generation, image centering, and tube diameter determination.

IHRSR++ is free software, licensed under the BSD license. Although we have successfully used it for a number of reconstructions, it should be considered a work in progress. Owing to time constraints, neither the Egelman nor Baker labs are able to provide support. The software is provided purely as a convenience to those attempting helical reconstructions.

Other Old Programs