Thresholded Constrained cross-correlation Print

In the past few years, three-dimenional (3D) subtomogram classification and averaging has become an important tool in cryo-electron tomography (CET). This technique allows to resolve higher resolution structures of targets that can not be reconstructed by single-particle methods. Based on previous approaches, we present a new dissimilarity measure between subtomograms named Thresholded Constrained Cross-Correlation (TCCC). TCCC has shown to improve results for Signal-to-Noise Ratios (SNR) lower than 0.1. This allows to analyze macromolecules in thicker samples like whole cell or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). TCCC uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation. The thresholding has two main advantages in the cross-correlation score: first, reduces the influence of the noise; second, avoids the missing wedge normalization problem since we consider the same amount of coefficients for all possible pairs of subtomograms. You can download the code to test TCCC here:

· Parallel TCCC for Linux

The code also incorporates the possibility to use Constratined Cross-Correlation (Forster et al. JSB 2008) and the dissimilarity score from (Bartesaghi et al. JSB 2008). The code has been compiled for linux machines for 32 or 64 bit machines.  It is completely written in C++ and it only needs the FFTW libraries compiled for floating point precision. The tar file also includes a README file with instructions on how to use and compile the code from command line. It also includes an example folder to show how to use the code. Finally, it you are brave you can test the code in MacOS. There is no reason why it should not compile, so if it does, please let me know and I update MacOS to supported platforms.

This software is intended for research purposes. Any commercial application that intends to use TCCC should contact the authors first. Please, if you use TCCC in your research cite the following paper:

[1] F. Amat, L. R. Comolli, F. Moussavi, J. Smit, K. H. Downing, and M. Horowitz, “Subtomogram alignment by adaptive Fourier coefficient thresholding,” Journal of Structural Biology, vol. 171, no. 3, pp. 332-344, Sep. 2010.
Last Updated on Friday, 22 November 2013 14:26