TomoAND/TomoEED 2.0

Fast 3D Denoising with Anisotropic Nonlinear Diffusion

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

TomoAND (also known as TomoEED) is an optimized program for denoising tomographic volumes with the Anisotropic Nonlinear Diffusion (AND) method, using the EED (Edge-Enhancing Diffusion) mode. This mode manages to reduce noise in the volume with good abilites to preserve and enhance the structures.

This version is equipped with mechanisms to automated parameter tuning and is optimized in terms of memory requirements and processing time. It also includes CTF deconvolution using D. Tegunov's filter, which substantially improves the contrast of tomograms from cryoET.

A detailed description of the procedures implemented in TomoAND 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 TomoAND in your works.

Request the package

Current version: 2.0 (May 2023)

Available material:

Documentation in PDF: tomoand.pdf
Binaries for x86-based platforms under Linux (64 bits) and Windows WSL.
Binaries for Macs based on Intel and Apple Silicon processors under OSX/macOS.

The development of tomoand has been supported by the Medical Research Council, the Spanish MEC and MCI, J.Andalucia, Human Frontier Science Program, European Molecular Biology Organization and the 3DEM Network of Excellence.