Three-dimensional feature-preserving noise reduction for real-time electron tomography
Section snippets
Jose-Jesus Fernández received the M.Sc. and Ph.D. degrees in computer science from the University of Granada, Spain, in 1992 and 1997, respectively. From 2002 to 2006 he was a postdoctoral scientist at the Laboratory of Molecular Biology (Medical Research Council, Cambridge, UK). In the last few years he was a professor of computer science at the University of Almeria, Almeria, Spain. In 2009 he got a position as a scientist at the National Center for Biotechnology (CNB) of the Spanish National
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Analysis of controversies in the formulation and evaluation of restoration algorithms for MR Images
2019, Expert Systems with ApplicationsCitation Excerpt :There is no reliable guidance available in the literature so far for the selection of a suitable technique for denoising Magnetic Resonance (MR) images. The performance evaluation of edge-preserving denoising schemes like Nonlocal Means filter (NLM) (Singh & Bala, 2019), Bilateral Filter (BF) (Akar, 2016), Total Variation (TV) (Kang, Jung, & Kang, 2018), Anisotropic Diffusion (AD) (Tong, Sun, Payet, & Ong, 2012), Kuwahara (Bartyzel, 2016; Djurović, 2017), wavelet denoising (Khatami, Khosravi, Nguyen, Lim, & Nahavandi, 2017), Linear Minimum Mean Square Error (LMMSE) (Golshan & Hasanzadeh, 2015), Smallest Univalue Segment Assimilating Nucleus (SUSAN) (Smith & Brady, 1997), and Beltrami (Fernández, & Martínez, 2010) filters are done in this study. Among the edge-preserving filters listed above, except the wavelet denoising, all other filters belong to the class of ‘edge-preserving spatial filters’.
Local regularization of tilt projections reduces artifacts in electron tomography
2014, Journal of Structural BiologyCitation Excerpt :The final 3D sample volume is obtained using volumetric reconstruction techniques (Herman, 2009) and processed using different segmentation tools to identify specific features (Ali et al., 2012; Kremer et al., 1996; Mumcuoglu et al., 2012; Nguyen and Ji, 2008). The requirement for low electron doses leading to short exposure times means that noise-related artifacts are an important issue in ET and can severely degrade the quality of the reconstruction (Arslan et al., 2006; Baumeister et al., 1999; Cao et al., 2010; Fernández and Martínez, 2010; Frangakis and Hegerl, 2001; van der Heide et al., 2007). The development of filtering algorithms can help to improve the quality of the reconstructed images and if coupled with further processing such as segmentation and rendering can help to identify important biological structures.
Computational methods for electron tomography
2012, MicronCitation Excerpt :Essentially, the volume is decomposed into overlapping subvolumes to be filtered and, at each iteration, the overlapping areas are updated with data from neighbor processors or nodes. Based on similar ideas, there have been proposals for other methods to exploit multicore computers (Beltrami flow (Fernandez and Martinez, 2010), mean-shift (Bilbao-Castro et al., 2010), non-local means (Darbon et al., 2008)). Simpler filtering techniques, such as the median or bilateral, have been implemented for GPUs, obtaining very good acceleration factors, in the range 10–70× (Castano-Diez et al., 2008).
Performance evaluation of 67 denoising filters in ultrasound images: A systematic comparison analysis
2023, International Journal of Imaging Systems and TechnologyHPC enables efficient 3D membrane segmentation in electron tomography
2022, Journal of SupercomputingHyperspectral Image Classification Method Combined Beltrami Flow and Recursive Filter
2018, Nongye Jixie Xuebao/Transactions of the Chinese Society for Agricultural Machinery
Jose-Jesus Fernández received the M.Sc. and Ph.D. degrees in computer science from the University of Granada, Spain, in 1992 and 1997, respectively. From 2002 to 2006 he was a postdoctoral scientist at the Laboratory of Molecular Biology (Medical Research Council, Cambridge, UK). In the last few years he was a professor of computer science at the University of Almeria, Almeria, Spain. In 2009 he got a position as a scientist at the National Center for Biotechnology (CNB) of the Spanish National Research Council (CSIC). His current research interests include high performance computing, image processing and tomographic reconstruction for molecular and cellular biology.
Jose-Antonio Martínez received the M.Sc. and Ph.D. degrees in computer science from the University of Granada, Spain, in 1992 and from the University of Almeria, Spain, in 2007, respectively. He is an associate professor of computer science at the University of Almeria, Almeria, Spain. He has long expertise in parallel computing, computer architecture and networking. His current research interests include high performance computing paradigms, including message passing, multithreading, GPU computing and hybrid techniques for heterogeneous platforms, as well as applications for optimization and image processing.