High-performance electron tomography of complex biological specimens Jos  e-Jes us Fern andez, a Albert F. Lawrence, b Javier Roca, a Inmaculada Garc  ıa, a Mark H. Ellisman, b and Jos  e-Mar  ıa Carazo c, * a Departamento de Arquitectura de Computadores, Universidad de Almer  ıa, 04120 Almer  ıa, Spain b National Center for Microscopy and Imaging, University of California, San Diego, La Jolla, CA 92093-0608, USA c Biocomputing Unit, Centro Nacional de Biotecnolog  ıa, Universidad Aut onoma, 28049 Madrid, Spain Received 10 December 2001; and in revised form 15 February 2002 Abstract We have evaluated reconstruction methods using smooth basis functions in the electron tomography of complex biological specimens.Inparticular,wehaveinvestigatedseriesexpansionmethods,withspecialemphasisonparallelcomputation.Amongthe methods investigated, the component averaging techniques have proven to be most efficient and have generally shown fast conver- gencerates.Theuseofsmoothbasisfunctionsprovidesthereconstructionalgorithmswithanimplicitregularizationmechanism,very appropriate for noisy conditions. Furthermore, we have applied high-performance computing (HPC) techniques to address the computationalrequirementsdemandedbythereconstructionoflargevolumes.Oneofthestandardtechniquesinparallelcomputing, domain decomposition, has yielded an effective computational algorithm which hides the latencies due to interprocessor communi- cation. We present comparisons with weighted back-projection (WBP), one of the standard reconstruction methods in the areas of computationaldemandandreconstructionqualityundernoisyconditions.Thesetechniquesyieldbetterresults,accordingtoobjective measuresofquality,thantheweightedbackprojectiontechniquesafteraveryfewiterations.Asaconsequence,thecombinationof efficientiterativealgorithmsandHPCtechniqueshasproventobewellsuitedtothereconstructionoflargebiologicalspecimensin electron tomography, yielding solutions in reasonable computation times. Ó 2002ElsevierScience(USA).Allrightsreserved. Keywords: Electron tomography; High-performance computing; Iterative reconstruction algorithms; Parallel computing 1. Introduction Electron microscopy is central to the study of many structural problems in modern biology, biotechnology, biomedicine, and other related fields. Electron micro- scopy together with sophisticated image processing and three-dimensional (3D) reconstruction techniques yields quantitative structural information about the 3D struc- ture of biological specimens (Frank, 1992; Koster et al., 1997; McEwen and Marko, 2001; Perkins et al., 1997). Knowledge of three-dimensional structure is critical to understanding biological function at all levels of detail. In contrast to earlier instruments, high-voltage elec- tron microscopes (HVEMs) are able to image relatively thick specimens that contain complex 3D structure. Electron tomography simplifies determination of com- plex 3D structures and their subsequent analysis. This method requires a set of HVEM images acquired at different orientations, via tilting the specimen around one or more axes (Mastronarde, 1997; Penczek et al., 1995; Perkins et al., 1997). Rigorous structural analyses require that image ac- quisitionandreconstructionintroduceaslittlenoiseand artifact as possible at the spatial scales of interest, for a properinterpretationandmeasurementofthestructural features. As a consequence of the need for structural information over a relatively wide range of spatial scales, electron tomography of complex biological specimens requires large projection HVEM images (typically 1024  1024 pixels or larger). Electron tom- ography on this scale yields large reconstruction files and requires an extensive use of computational re- sources and considerable processing time. Journal of Structural Biology 138 (2002) 6–20 www.academicpress.com Journal of Structural Biology * Corresponding author. Fax: +34-915-854-506. E-mail address: carazo@cnb.uam.es (J.-M. Carazo). 1047-8477/02/$ - see front matter Ó 2002 Elsevier Science (USA). All rights reserved. PII:S1047-8477(02)00017-5