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:
Three-dimensional anisotropic noise reduction with automated parameter tuning. Application to electron cryotomography.
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.