BF-(S)TEM Tomography Software


While Bright Field-Electron Tomography (BF-ET) is very popular in the biological sciences, its use in the physical sciences is limited because the measurements are affected by Bragg scatter (and other anomalies) leading to contrast reversals. In this work, we propose a model that takes into account the occurrence of these anomalies in the MBIR framework. We then develop an efficient algorithm based on functional substitution/majorization/surrogate functions to minimize the MBIR cost. The algorithm works well with both crystalline and amorphous samples and can be very useful for low-dose imaging.

For more details see

S. V. Venkatakrishnan, L. F. Drummy, M. Jackson, M. De Graef, J. Simmons and C. A. Bouman, "Model-Based Iterative Reconstruction for Bright-Field Electron Tomography," in IEEE Transactions on Computational Imaging, vol. 1, no. 1, pp. 1-15, March 2015. (pdf)

C++ Based Software (with GUI)

Main features

Software Download (Version 2.3.5)

YouTube application tutorials: Basic and Advanced

Software supports aligned input files stored in FEI mrc format
New [4/20/2014] : Added support for non-FEI MRC. See this very short video tutorial.

Software Source Code

All code is available from the Git Repository server. (Master branch)