Model based iterative reconstruction for Bright Field electron tomography

Singanallur V. Venkatakrishnan; Lawrence F. Drummy; Marc De Graef; Jeff P. Simmons; Charles A. Bouman

doi:10.1117/12.2013228

14 February 2013 Model based iterative reconstruction for Bright Field electron tomography

Singanallur V. Venkatakrishnan, Lawrence F. Drummy, Marc De Graef, Jeff P. Simmons, Charles A. Bouman

Proceedings Volume 8657, Computational Imaging XI; 86570A (2013) https://doi.org/10.1117/12.2013228
Event: IS&T/SPIE Electronic Imaging, 2013, Burlingame, California, United States

Abstract

Bright Field (BF) electron tomography (ET) has been widely used in the life sciences to characterize biological specimens in 3D. While BF-ET is the dominant modality in the life sciences it has been generally avoided in the physical sciences due to anomalous measurements in the data due to a phenomenon called “Bragg scatter” - visible when crystalline samples are imaged. These measurements cause undesirable artifacts in the reconstruction when the typical algorithms such as Filtered Back Projection (FBP) and Simultaneous Iterative Reconstruction Technique (SIRT) are applied to the data. Model based iterative reconstruction (MBIR) provides a powerful framework for tomographic reconstruction that incorporates a model for data acquisition, noise in the measurement and a model for the object to obtain reconstructions that are qualitatively superior and quantitatively accurate. In this paper we present a novel MBIR algorithm for BF-ET which accounts for the presence of anomalous measurements from Bragg scatter in the data during the iterative reconstruction. Our method accounts for the anomalies by formulating the reconstruction as minimizing a cost function which rejects measurements that deviate significantly from the typical Beer’s law model widely assumed for BF-ET. Results on simulated as well as real data show that our method can dramatically improve the reconstructions compared to FBP and MBIR without anomaly rejection, suppressing the artifacts due to the Bragg anomalies.

Citation Download Citation

Singanallur V. Venkatakrishnan, Lawrence F. Drummy, Marc De Graef, Jeff P. Simmons, and Charles A. Bouman "Model based iterative reconstruction for Bright Field electron tomography", Proc. SPIE 8657, Computational Imaging XI, 86570A (14 February 2013); https://doi.org/10.1117/12.2013228

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