TomoEED 1.0
Fast Edge-Enhancing Denoising of Tomographic Volumes
J.J. Fernandez (1), S. Li (2), V. Lucic (3),
J.J. Moreno (4), A. Martinez-Sanchez (5), J.A. Martinez (4), E.M. Garzon (4)
(1) Spanish National Research Council (CSIC). Oviedo. Spain.
(2) Dept. Biochemistry and Biophysics. UCSF. USA.
(3) Dept. Structural Biology, MPI Biochemistry, Martinsried, Germany.
(4) Dept. Informatics. University of Almeria. Almeria. Spain.
(5) University of Murcia. Murcia. Spain.
Contact: jjfernandez.software @ gmail.com
Description
TomoEED is an optimized software tool for fast feature-preserving noise filtering of large three-dimensional (3D) tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers.
A detailed description of the procedure implemented in the package can be found in the following articles:
Primary publications to cite:
An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms.
J.J. Fernandez, S. Li.
Journal of Structural Biology 144:152-161, 2003.
TomoEED: Fast Edge-Enhancing Denoising of Tomographic Volumes.
J.J. Moreno, A. Martinez-Sanchez, J.A. Martinez, E.M. Garzon, J.J. Fernandez.
Bioinformatics 34:3776-3778, 2018.
Additional references:
J.J. Fernandez, S. Li, V. Lucic
Lecture Notes in Computer Science 4788:60-69, 2007.
Please, cite any of these articles if you use TomoEED in your works.
Download
Current version: March 2018
Available material:
Documentation in PDF: tomoeed.pdf
Binaries for x86-based platforms under Linux and OSX (64 bits) and NVIDIA GPUs.
The development of TomoEED has been supported by AEI/FEDER and Fundación Ramón Areces.
Copyright by the authors.