title: Local regularization of tilt projections reduces artifacts in electron tomography.
abstract: Electron tomography produces very high resolution 3D image volumes useful for investigating the structure and function of cellular components. Unfortunately, unavoidable discontinuities and physical constraints in the acquisition geometry lead to a range of artifacts that can affect the reconstructed image. In particular, highly electron dense regions, such as gold nanoparticles, can hide proximal biological structures and degrade the overall quality of the reconstructed tomograms. In this work we introduce a pre-reconstruction non-conservative non-linear isotropic diffusion (NID) filter that automatically identifies and reduces local irregularities in the tilt projections. We illustrate the improvement in quality obtained using this approach for reconstructed tomograms generated from samples of malaria parasite-infected red blood cells. A quantitative and qualitative evaluation for our approach on both simulated and real data is provided.
authors.affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Vic. 3010, Australia; Australian Research Council Centre of Excellence for Coherent X-ray Science, Australia. Electronic address: mauromaiorca@gmail.com.
authors.forename: Mauro
authors.initials: M
authors.lastname: Maiorca
authors.affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Vic. 3010, Australia; Australian Research Council Centre of Excellence for Coherent X-ray Science, Australia.
authors.forename: Coralie
authors.initials: C
authors.lastname: Millet
authors.affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Vic. 3010, Australia; Australian Research Council Centre of Excellence for Coherent X-ray Science, Australia; Electron Microscopy Unit, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic. 3010, Australia.
authors.forename: Eric
authors.initials: E
authors.lastname: Hanssen
authors.affiliation: Australian Research Council Centre of Excellence for Coherent X-ray Science, Australia; Department of Physics, La Trobe University, Vic. 3071, Australia.
authors.forename: Brian
authors.initials: B
authors.lastname: Abbey
authors.affiliation: Department of Computer Science and Software Engineering, The University of Melbourne, Vic. 3010, Australia.
authors.forename: Edmund
authors.initials: E
authors.lastname: Kazmierczak
authors.affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Vic. 3010, Australia; Australian Research Council Centre of Excellence for Coherent X-ray Science, Australia. Electronic address: ltilley@unimelb.edu.au.
authors.forename: Leann
authors.initials: L
authors.lastname: Tilley
mesh_terms: D000465:Algorithms; D016477:Artifacts; D002478:Cells, Cultured; D003198:Computer Simulation; D055032:Electron Microscope Tomography / Q000379:methods* / Q000592:standards; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008870:Microtubules; D010963:Plasmodium falciparum / Q000648:ultrastructure; D058996:Quality Improvement
keywords: Electron tomography; Gold artifact reduction; Image reconstruction; Non-linear diffusion; Plasmodium