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.
C++ Based Software (with GUI)
- Automatic initialization of parameters
- Reconstruct the volume at various voxels sizes
- Can be used for reconstructing amorphous as well as crystalline samples
- Multi-threaded code using Intel TBB
Software Download (Version 2.3.5)
YouTube application tutorials:
Software supports aligned input files stored in
FEI mrc format
New [4/20/2014] : Added support for non-FEI MRC. See this very short
Software Source Code
All code is available from the Git Repository server. (Master branch)