Model-Based Iterative Reconstruction (MBIR) for Electron Tomography

Latest source code versions can be downloaded from github.
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Bright Field Electron Tomography (BF-ET)

While 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 occurance 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.
Free C++ Based Software

Main features
Download MBIR-BF

Youtube application tutorials: Basic and Advanced

High Angle Annular Dark Field Scanning Transmission Electron Microscope (HAADF-STEM) Tomography

HAADF-STEM tomography is a widely used in the physical sciences for 3-D reconstructions because it is not effected by the dynamical diffraction effects seen in BF-ET. Since the data comes from a limited-tilt acquistion, analytical methods like FBP and iterative method like SIRT can results in reconstructions with noise and streak artifacts. In this work, we propose an MBIR method for HAADF-STEM tomography that can result in significant improvements in reconstruction quality. Further, it can also account for missing calibration parameters that are associated with the measurement.
Free C++ Based Software (with GUI)

Main features

Youtube application tutorials: Basic and Advanced