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Electron Microscopy Software

AUTO3DEM (including RobEM)

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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 and visualization. AUTO3DEM is free to use for educational, research and non-profit purposes (see LICENSE file).

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 User's guide (PDF) (HTML)

RobEM User's Guide (PDF) (HTML)

Software Modification History (PDF) (HTML)

AUTO3DEM Test Problem and Tutorial: Documentation and all necessary image data required to go from digitized micrographs to a 3D reconstruction. (Requires auto3dem_v4.03 or later)

Documentation for parallel programs called by AUTO3DEM (PDFs)
P3DR 3D image reconstruction
PCUT Cutting spherical annulus from map
POR Local refinement of image origins and orientations
PPFT Local refinement of image origins and orientations
PSF Structure factor determination and FSC calculation

IHRSR++ v 1.5 January 27, 2014

IHRSR++ is a user-friendly extension to 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.
IHRSR++ Tutorial (PDF) January 27, 2014
IHRSR++ Test Problem (~5 GB Tar file) September 28, 2010

IHRSR++ v 1.3 February 5, 2010

Other Old Programs
Date Modified: March 13, 2014