title: High-performance electron tomography of complex biological specimens.
abstract: We have evaluated reconstruction methods using smooth basis functions in the electron tomography of complex biological specimens. In particular, we have investigated series expansion methods, with special emphasis on parallel computation. Among the methods investigated, the component averaging techniques have proven to be most efficient and have generally shown fast convergence rates. The use of smooth basis functions provides the reconstruction algorithms with an implicit regularization mechanism, very appropriate for noisy conditions. Furthermore, we have applied high-performance computing (HPC) techniques to address the computational requirements demanded by the reconstruction of large volumes. One of the standard techniques in parallel computing, domain decomposition, has yielded an effective computational algorithm which hides the latencies due to interprocessor communication. We present comparisons with weighted back-projection (WBP), one of the standard reconstruction methods in the areas of computational demand and reconstruction quality under noisy conditions. These techniques yield better results, according to objective measures of quality, than the weighted backprojection techniques after a very few iterations. As a consequence, the combination of efficient iterative algorithms and HPC techniques has proven to be well suited to the reconstruction of large biological specimens in electron tomography, yielding solutions in reasonable computation times.
authors.affiliation: Departamento de Arquitectura de Computadores, Universidad de Almería, 04120 Almería, Spain.
authors.forename: José-Jesús
authors.initials: JJ
authors.lastname: Fernández
authors.forename: Albert F
authors.initials: AF
authors.lastname: Lawrence
authors.forename: Javier
authors.initials: J
authors.lastname: Roca
authors.forename: Inmaculada
authors.initials: I
authors.lastname: García
authors.forename: Mark H
authors.initials: MH
authors.lastname: Ellisman
authors.forename: José-María
authors.initials: JM
authors.lastname: Carazo
mesh_terms: D000465:Algorithms; D000818:Animals; D022082:Cellular Structures / Q000648:ultrastructure*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional / Q000295:instrumentation / Q000379:methods; D008122:Local Area Networks; D008854:Microscopy, Electron / Q000295:instrumentation / Q000379:methods*; D008928:Mitochondria / Q000648:ultrastructure; D019047:Phantoms, Imaging; D014057:Tomography, X-Ray Computed / Q000295:instrumentation / Q000379:methods*