Tomographic reconstruction techniques optimized for velocity-map imaging applications.

Convergence rate calculation of simultaneous iterative reconstruction technique algorithm for diffuse optical tomography image reconstruction: A feasibility study

Optical projection tomography (OPT) is an advanced three-dimensional (3D) imaging technology, which uses the filtered backprojection (FBP) algorithm to recover the 3D volume with sufficient number of projections. As to in vivo imaging, it is urgent to reduce the number of projections because the acquisition time could be minimized. However, reconstructing from undersampled OPT data can lead to artifacts and the decline in image quality. The simultaneous iterative reconstruction technique (SIRT) is introduced to remove artifacts and improve the image quality. The image qualities reconstructed from FBP and SIRT separately are compared, and the structural similarity and peak signal-to-noise ratio are calculated. Through simulated phantoms and OPT data of in vivo zebrafish embryo, SIRT consistently outperforms FBP in terms of reduced artifacts and enhanced image contrast especially when the projection numbers are reduced. SIRT method can provide high-quality reconstruction with 50 or fewer projections, thereby significantly reducing the minimum acquisition time and light dose while maintaining reconstruction quality. Through optimization and GPU acceleration, the SIRT algorithm can converge faster so as to reduce the image processing time. To our knowledge, this is the first time one SIRT algorithm is used for reconstruction of sparse OPT data. The experimental results show that SIRT algorithm outperform FBP especially when the number of projections is reduced. In addition, SIRT performs better in the preservation of vascular signal, which is significant for the monitoring of angiogenesis.

OA158] Noise equivalent number of quanta (NEQ): A tool for choosing the optimal reconstruction algorithm in computed tomography (CT)

In this paper, we developed an accelerated algorithm for the classical simultaneous iterative reconstruction technique (SIRT) method applied in CT image reconstruction. The proposed algorithm possesses the following two features. First, it can flexibly handle the image reconstruction problem where projection data is contaminated by Poisson noise. This property makes it successful in compensating the disadvantage of the typical algebraic reconstruction technique (ART) method. Second, we utilize Passty's proximal splitting framework to construct a row-action type accelerated iterative algorithm to minimize the cost function. The accelerating strategy makes it successful in compensating the disadvantage of the famous SIRT method. We proved that the new algorithm can achieve significant image quality with noise reduction in less than 10 iterations, while SIRT needs more than 200 iterations. Both digital phantom and clinical abdominal CT image were reconstructed for demonstrating the efficiency of the proposed method.

Algebraic Reconstruction Technique (ART) is an age-old method used for solving the problem of three-dimensional (3-D) reconstruction from projections in electron microscopy and radiology. In medical applications, direct 3-D reconstruction is at the forefront of investigation. The simultaneous iterative reconstruction technique (SIRT) is an ART-type algorithm with the potential of generating in a few iterations tomographic images of a quality comparable to that of convolution backprojection (CBP) methods. Pixel-based reconstruction (PBR) is similar to SIRT reconstruction, and it has been shown that PBR algorithms give better quality pictures compared to those produced by SIRT algorithms. In this work, we propose a few modifications to the PBR algorithms. The modified algorithms are shown to give better quality pictures compared to PBR algorithms. The PBR algorithm and the modified PBR algorithms are highly compute intensive, Not many attempts have been made to reconstruct objects in the true 3-D sense because of the high computational overhead. In this study, we have developed parallel two-dimensional (2-D) and 3-D reconstruction algorithms based on modified PBR. We attempt to solve the two problems encountered by the PBR and modified PBR algorithms, i.e., the long computational time and the large memory requirements, by parallelizing the algorithm on a multiprocessor system. We investigate the possible task and data partitioning schemes by exploiting the potential parallelism in the PBR algorithm subject to minimizing the memory requirement. We have implemented an extended hypercube (EH) architecture for the high-speed execution of the 3-D reconstruction algorithm using the commercially available fast floating point digital signal processor (DSP) chips as the processing elements (PEs) and dual-port random access memories (DPR) as channels between the PEs. We discuss and compare the performances of the PBR algorithm on an IBM 6000 RISC workstation, on a Silicon Graphics Indigo 2 workstation, and on an EH system. The results show that an EH(3,1) using DSP chips as PEs executes the modified PBR algorithm about 100 times faster than an LBM 6000 RISC workstation. We have executed the algorithms on a 4-node IBM SP2 parallel computer. The results show that execution time of the algorithm on an EH(3,1) is better than that of a 4-node IBM SP2 system. The speed-up of an EH(3,1) system with eight PEs and one network controller is approximately 7.85.

A comparison of algebraic reconstruction techniques for a single-detector muon computed tomography system

The use of transmission electron tomography for three dimensional morphology analysis of nanostructured materials has grown significantly in recent years due to the improved robustness of automated image collection, alignment and reconstruction routines. Although the amount of published 3D electron tomography data has increased accordingly, in many cases the data is used purely for visualization purposes, due to the difficulty of making quantitative measurements from the as-reconstructed data. This is due to the traditionally difficult step of segmentation of the 3D image volume, which has been hindered due to noise, artifacts and lack of necessary image detail or sharpness. In this work the Simultaneous Iterative Reconstruction Technique (SIRT) is used to reconstruct High Angle Annular Dark Field-Scanning Transmission Electron Microscopy (HAADF-STEM) tomography data. The number of SIRT iterations is varied to optimize the reconstruction for segmentation. In particular, signal to noise ratio, signal to artifact ratio, and image blur are identified as parameters which each contribute to the suitability of the reconstruction for segmentation. The Expectation Maximization/ Maximization of Posterior Marginals image segmentation algorithm is applied to the SIRT reconstructions, and the resulting Average Intensity Projection (AIP) of the segmented image stack is compared to the raw tomography projection data.

ABSTRACTA hybrid algorithm, combining Monte‐Carlo optimization with simultaneous iterative reconstructive technique (SIRT) tomography, is used to invert first arrival traveltimes from seismic data for building a velocity model. Stochastic algorithms may localize a point around the global minimum of the misfit function but are not suitable for identifying the precise solution. On the other hand, a tomographic model reconstruction, based on a local linearization, will only be successful if an initial model already close to the best solution is available. To overcome these problems, in the method proposed here, a first model obtained using a classical Monte Carlo‐based optimization is used as a good initial guess for starting the local search with the SIRT tomographic reconstruction. In the forward problem, the first‐break times are calculated by solving the eikonal equation through a velocity model with a fast finite‐difference method instead of the traditional slow ray‐tracing technique. In addition, for the SIRT tomography the seismic energy from sources to receivers is propagated by applying a fast Fresnel volume approach which when combined with turning rays can handle models with both positive and negative velocity gradients. The performance of this two‐step optimization scheme has been tested on synthetic and field data for building a geologically plausible velocity model.This is an efficient and fast search mechanism, which permits insertion of geophysical, geological and geodynamic a priori constraints into the grid model and ray path is completed avoided. Extension of the technique to 3D data and also to the solution of ‘static correction’ problems is easily feasible.

Cone-beam computed tomography (CBCT) technique is largely used in medical diagnostic imaging and nondestructive materials testing, especially in cases which require fast times and high accuracy level. In this paper, the pros and cons of Feldkamp-Davis-Kress (FDK) and simultaneous iterative reconstruction technique (SIRT) algorithms used in CBCT technique is studied. The method of simulating CBCT systems is also used to provide richer projection data, which helps the research to evaluate many aspects of algorithms.

Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.

Noninvasive X-ray imaging of nanoscale three-dimensional objects, such as integrated circuits (ICs), generally requires two types of scanning: ptychographic, which is translational and returns estimates of the complex electromagnetic field through the IC; combined with a tomographic scan, which collects these complex field projections from multiple angles. Here, we present Attentional Ptycho-Tomography (APT), an approach to drastically reduce the amount of angular scanning, and thus the total acquisition time. APT is machine learning-based, utilizing axial self-Attention for Ptycho-Tomographic reconstruction. APT is trained to obtain accurate reconstructions of the ICs, despite the incompleteness of the measurements. The training process includes regularizing priors in the form of typical patterns found in IC interiors, and the physics of X-ray propagation through the IC. We show that APT with ×12 reduced angles achieves fidelity comparable to the gold standard Simultaneous Algebraic Reconstruction Technique (SART) with the original set of angles. When using the same set of reduced angles, then APT also outperforms Filtered Back Projection (FBP), Simultaneous Iterative Reconstruction Technique (SIRT) and SART. The time needed to compute the reconstruction is also reduced, because the trained neural network is a forward operation, unlike the iterative nature of these alternatives. Our experiments show that, without loss in quality, for a 4.48 × 93.2 × 3.92 µm3 IC (≃6 × 108 voxels), APT reduces the total data acquisition and computation time from 67.96 h to 38 min. We expect our physics-assisted and attention-utilizing machine learning framework to be applicable to other branches of nanoscale imaging, including materials science and biological imaging.

Electron tomography based on a total variation minimization reconstruction technique

Gamma emission tomography (GET) detects fuel rods that emit gamma rays for potential use as verification tools in nuclear safeguards. In GET, iterative reconstruction algorithms are often used to reconstruct passive gamma-ray emitter source distributions. Generally, using noisy sinogram data, the iterative reconstruction algorithms increase the noise level on a reconstruction image with iterations. Thus, it is important to evaluate how performances of representative iterative reconstruction algorithms change with noisy sinogram data. The passive gamma-ray source distributions inside the mock-up of the water-water energetic reactor (WWER) fuel assembly having missing fuel rods were reconstructed by using the following algorithms: gradient method, steepest descent method, conjugate gradient reconstruction method, algebraic reconstruction technique, simultaneous iterative reconstruction technique, and maximum likelihood expectation maximization (MLEM). Consequently, MLEM algorithm yielded a higher contrast reconstruction image and was regarded as higher reliable algorithm to discriminate the fuel rods from the passive gamma-ray emitter source distribution.

Denoising reconstruction techniques can introduce nonlinear properties into computed tomography (CT) systems. These nonlinear algorithms introduce distortion which affects the assessment of the resolution of the system. The purpose of the present study was to decouple and investigate amplitude modulation and waveform distortion in reconstruction algorithms in CT. The methodology developed by Wells, J. R. and Dobbins, J. T. III [Frequency response and distortion properties of nonlinear image processing algorithms and the importance of imaging context. Med. Phys. 40, 091906 (2013)] was adapted to CT reconstruction algorithms. The CT simulating program ASTRA Toolbox© for MATLAB™ was used for the reconstruction of the sinusoidal wave functions. Filtered back projection and the simultaneous iterative reconstruction technique were investigated with simple nonlinear mechanisms: a median filter and a non-negative constraint, respectively. The native reconstruction algorithms were not free from nonlinear waveform distortion, however, none of the metrics showed any dependence on the contrast-to-noise ratio (CNR). Furthermore, the algorithms including nonlinear mechanisms showed a clear and specific CNR dependence, indicating the necessity for distortion analysis in nonlinear CT reconstruction.

To obtain useful knowledge and experience of CCERT under different excitation patterns, the image reconstruction performance of a 12-electrode CCERT sensor under five different excitation patterns (1-electrode excitation pattern, 2-electrode excitation pattern, 3-electrode excitation pattern, 4-electrode excitation pattern, and 5-electrode excitation pattern) are investigated and compared. A 12-electrode CCERT prototype, which can implement different excitation patterns, is developed to obtain the practical experiment data. Four typical image reconstruction algorithms (Linear Back Projection (LBP) algorithm, Landweber’s iteration algorithm, Algebraic Reconstruction Technique (ART) algorithm, and Simultaneous Iterative Reconstruction Technique (SIRT) algorithm) are introduced to investigate and compare the image reconstruction performance with the experimental data obtained from the CCERT prototype. Research results show that the 1-electrode excitation pattern and the 2-electrode excitation pattern have better global image reconstruction performance. These two excitation patterns are better choices, while the 3-electrode excitation pattern, the 4-electrode excitation pattern, and the 5-electrode excitation pattern are not recommended.