Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system

Garcı́a, Inmaculada; Roca, Javier García; Sanjurjo, Jorge; Carazo, José Marı́a; Zapata, Emilio L.

doi:10.1016/0165-1684(96)00032-1

Cited by 7 publications

(3 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The first parallelizations of reconstruction algorithms for electron microscopy date back to early-mid 1990s, where weighted backprojection (WBP) and iterative methods were implemented by fine-grain strategies for shared-memory and distributed-memory computers (Zapata et al, 1990Garcia et al, 1996). The parallelization of WBP, a common method in cryoEM, is straightforward.…”

Section: D Reconstructionmentioning

confidence: 99%

High performance computing in structural determination by electron cryomicroscopy

Fernández

2008

Journal of Structural Biology

View full text Add to dashboard Cite

Section: D Reconstructionmentioning

confidence: 99%

High performance computing in structural determination by electron cryomicroscopy

Fernández

2008

Journal of Structural Biology

View full text Add to dashboard Cite

“…[ 64 ]). Given a collection of convex sets representing our a priori knowledge about the reconstructed particle, C 1 , C 2 ,…, C K , we may try to find a feasible volume at the intersection

This problem has been extensively explored in the EM community under the name Projection Onto Convex Sets (POCS) and the interested reader is referred to Carazo and Carrascosa [ 115 , 116 ], Carazo [ 117 ], García et al [ 31 ], Sorzano et al [ 64 ], and Deng et al [ 118 ]. The idea is to alternate between projections onto the subspaces defined by the experimental measurements ( H i ) and projections onto the convex sets (the projector onto the set of nonnegative volumes simply sets all negative values to 0; the projector onto the set of volumes defined within a mask applies that mask to the current solution; the projector onto the set of symmetric volumes symmetrizes the current solution; the projector onto the set of bandlimited volumes applies a low-pass filter to the current solution; etc.).…”

Section: Constrained 3d Reconstructionmentioning

confidence: 99%

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

Sorzano

Vargas

Otón

et al. 2017

BioMed Research International

View full text Add to dashboard Cite

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

show abstract

“…CT Brush could have been implemented by considering all of the rays through the central point at once as in SIRT/SART (Simultaneous Iterative/Algebraic Reconstruction Techniques) and its variants [ 70 , 92 - 97 ], or with variants on the ART algorithm itself [ 39 , 89 , 90 , 98 - 101 ], including parallel computing versions [ 91 , 102 , 103 ].…”

Section: Introductionmentioning

confidence: 99%

CT brush and CancerZap!: two video games for computed tomography dose minimization

Alvare

Gordon

2015

Theor Biol Med Model

View full text Add to dashboard Cite

BackgroundX-ray dose from computed tomography (CT) scanners has become a significant public health concern. All CT scanners spray x-ray photons across a patient, including those using compressive sensing algorithms. New technologies make it possible to aim x-ray beams where they are most needed to form a diagnostic or screening image. We have designed a computer game, CT Brush, that takes advantage of this new flexibility. It uses a standard MART algorithm (Multiplicative Algebraic Reconstruction Technique), but with a user defined dynamically selected subset of the rays. The image appears as the player moves the CT brush over an initially blank scene, with dose accumulating with every “mouse down” move. The goal is to find the “tumor” with as few moves (least dose) as possible.ResultsWe have successfully implemented CT Brush in Java and made it available publicly, requesting crowdsourced feedback on improving the open source code. With this experience, we also outline a “shoot ‘em up game” CancerZap! for photon limited CT.ConclusionsWe anticipate that human computing games like these, analyzed by methods similar to those used to understand eye tracking, will lead to new object dependent CT algorithms that will require significantly less dose than object independent nonlinear and compressive sensing algorithms that depend on sprayed photons. Preliminary results suggest substantial dose reduction is achievable.Electronic supplementary materialThe online version of this article (doi:10.1186/s12976-015-0003-4) contains supplementary material, which is available to authorized users.

show abstract

Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system

Cited by 7 publications

References 10 publications

High performance computing in structural determination by electron cryomicroscopy

High performance computing in structural determination by electron cryomicroscopy

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

CT brush and CancerZap!: two video games for computed tomography dose minimization

Contact Info

Product

Resources

About