Exploring polynomial based interpolation schemes for photoacoustic tomographic image reconstruction

Photoacoustic tomography (PAT) imaging employing polynomial-based interpolation methods is discussed. Nearest-neighbor, bilinear, bicubic and biquintic algorithms were implemented for the construction of the model matrix, and images were formed using the Tikhonov regularization and total variation (TV) minimization procedures. The performance of the interpolation methods was assessed by comparing the reconstructed images of three numerical and two experimental phantoms. The numerical and experimental studies demonstrate that the performance of the interpolation schemes is nearly equal for large PA sources. The simplest nearest-neighbor technique provides better image reconstruction for a sparse source compared to the others. The nearest-neighbor protocol may be adopted in practice for vascular imaging using PAT.

Реализация и производительность алгоритмов волновой томографии на вычислительных платформах SIMD CPU и GPU

This paper is concerned with implementation of wave tomography algorithms on modern SIMD CPU and GPU computing platforms. The field of wave tomography, which is currently under development, requires powerful computing resources. Main applications of wave tomography are medical imaging, nondestructive testing, seismic studies. Practical applications depend on computing hardware. Tomographic image reconstruction via wave tomography technique involves solving coefficient inverse problems for the wave equation. Such problems can be solved using iterative gradient-based methods, which rely on repeated numerical simulation of wave propagation process. In this study, finite-difference time-domain (FDTD) method is employed for wave simulation. This paper discusses software implementation of the algorithms and compares the performance of various computing devices: multi-core Intel and ARM-based CPUs, NVidia graphics processors. В данной статье рассматривается реализация алгоритмов волновой томографии на современных вычислительных платформах SIMD CPU и GPU. Область волновой томографии, которая в настоящее время находится в стадии разработки, требует мощных вычислительных ресурсов. Основные области применения волновой томографии - это медицинская визуализация, неразрушающий контроль, сейсмические исследования. Практические приложения зависят от вычислительного оборудования. Восстановление томографического изображения методом волновой томографии включает решение коэффициентов обратной задачи для волнового уравнения. Такие проблемы могут быть решены с помощью итерационных градиентных методов, основанных на многократном численном моделировании процесса распространения волн. В этом исследовании для моделирования волн используется метод конечных разностей во временной области (FDTD). В статье обсуждается программная реализация алгоритмов и сравнивается производительность различных вычислительных устройств: многоядерных процессоров Intel и ARM, графических процессоров NVidia.

Optical Tomographic Image Reconstruction Based on Gradient Tree Calculation Method

Optical coherence tomography is a new imaging method, which is widely used in many fields. This article introduces an iterative image reconstruction algorithm based on gradient trees. It also discusses image reconstruction methods containing void-like regions. It is proved that the image reconstruction based on the transportation model can overcome the shortcomings of the diffusion equation, and it can accurately reconstruct the optical tomographic image.

Synergistic tomographic image reconstruction: part 2

This special issue is the second part of a themed issue that focuses on synergistic tomographic image reconstruction and includes a range of contributions in multiple disciplines and application areas. The primary subject of study lies within inverse problems which are tackled with various methods including statistical and computational approaches. This volume covers algorithms and methods for a wide range of imaging techniques such as spectral X-ray computed tomography (CT), positron emission tomography combined with CT or magnetic resonance imaging, bioluminescence imaging and fluorescence-mediated imaging as well as diffuse optical tomography combined with ultrasound. Some of the articles demonstrate their utility on real-world challenges, either medical applications (e.g. motion compensation for imaging patients) or applications in material sciences (e.g. material decomposition and characterization). One of the desired outcomes of the special issues is to bring together different scientific communities which do not usually interact as they do not share the same platforms such as journals and conferences. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.

Synergistic multi-spectral CT reconstruction with directional total variation

This work considers synergistic multi-spectral CT reconstruction where information from all available energy channels is combined to improve the reconstruction of each individual channel. We propose to fuse these available data (represented by a single sinogram) to obtain a polyenergetic image which keeps structural information shared by the energy channels with increased signal-to-noise ratio. This new image is used as prior information during a channel-by-channel minimization process through the directional total variation. We analyse the use of directional total variation within variational regularization and iterative regularization. Our numerical results on simulated and experimental data show improvements in terms of image quality and in computational speed. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.

Musiré: multimodal simulation and reconstruction framework for the radiological imaging sciences

A software-based workflow is proposed for managing the execution of simulation and image reconstruction for SPECT, PET, CBCT, MRI, BLI and FMI packages in single and multimodal biomedical imaging applications. The workflow is composed of a Bash script, the purpose of which is to provide an interface to the user, and to organize data flow between dedicated programs for simulation and reconstruction. The currently incorporated simulation programs comprise GATE for Monte Carlo simulation of SPECT, PET and CBCT, SpinScenario for simulating MRI, and Lipros for Monte Carlo simulation of BLI and FMI. Currently incorporated image reconstruction programs include CASToR for SPECT and PET as well as RTK for CBCT. MetaImage (mhd) standard is used for voxelized phantom and image data format. Meshlab project (mlp) containers incorporating polygon meshes and point clouds defined by the Stanford triangle format (ply) are employed to represent anatomical structures for optical simulation, and to represent tumour cell inserts. A number of auxiliary programs have been developed for data transformation and adaptive parameter assignment. The software workflow uses fully automatic distribution to, and consolidation from, any number of Linux workstations and CPU cores. Example data are presented for clinical SPECT, PET and MRI systems using the Mida head phantom and for preclinical X-ray, PET and BLI systems employing the Digimouse phantom. The presented method unifies and simplifies multimodal simulation setup and image reconstruction management and might be of value for synergistic image research. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.

Motion estimation and correction for simultaneous PET/MR using SIRF and CIL

SIRF is a powerful PET/MR image reconstruction research tool for processing data and developing new algorithms. In this research, new developments to SIRF are presented, with focus on motion estimation and correction. SIRF’s recent inclusion of the adjoint of the resampling operator allows gradient propagation through resampling, enabling the MCIR technique. Another enhancement enabled registering and resampling of complex images, suitable for MRI. Furthermore, SIRF’s integration with the optimization library CIL enables the use of novel algorithms. Finally, SPM is now supported, in addition to NiftyReg, for registration. Results of MR and PET MCIR reconstructions are presented, using FISTA and PDHG, respectively. These demonstrate the advantages of incorporating motion correction and variational and structural priors. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.

Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography

The newly developed core imaging library (CIL) is a flexible plug and play library for tomographic imaging with a specific focus on iterative reconstruction. CIL provides building blocks for tailored regularized reconstruction algorithms and explicitly supports multichannel tomographic data. In the first part of this two-part publication, we introduced the fundamentals of CIL. This paper focuses on applications of CIL for multichannel data, e.g. dynamic and spectral. We formalize different optimization problems for colour processing, dynamic and hyperspectral tomography and demonstrate CIL’s capabilities for designing state-of-the-art reconstruction methods through case studies and code snapshots. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.