Synchrotron-based x-ray tomography is a noninvasive imaging technique that allows for reconstructing the internal structure of materials at high spatial resolutions from tens of micrometers to a few nanometers. In order to resolve sample features at smaller length scales, however, a higher radiation dose is required. Therefore, the limitation on the achievable resolution is set primarily by noise at these length scales. We present TomoGAN, a denoising technique based on generative adversarial networks, for improving the quality of reconstructed images for low-dose imaging conditions. We evaluate our approach in two photon-budget-limited experimental conditions: (1) sufficient number of low-dose projections (based on Nyquist sampling), and (2) insufficient or limited number of high-dose projections. In both cases, the angular sampling is assumed to be isotropic, and the photon budget throughout the experiment is fixed based on the maximum allowable radiation dose on the sample. Evaluation with both simulated and experimental datasets shows that our approach can significantly reduce noise in reconstructed images, improving the structural similarity score of simulation and experimental data from 0.18 to 0.9 and from 0.18 to 0.41, respectively. Furthermore, the quality of the reconstructed images with filtered back projection followed by our denoising approach exceeds that of reconstructions with the simultaneous iterative reconstruction technique, showing the computational superiority of our approach.

TomoGAN: low-dose synchrotron x-ray tomography with generative adversarial networks: discussion.

Computed Tomography (CT) Image Reconstruction is an important technique used in a variety of domains, including medical imaging, electron microscopy, non-destructive testing and transportation security. Model-based Iterative Reconstruction (MBIR) using Iterative Coordinate Descent (ICD) is a CT algorithm that produces state-of-the-art results in terms of image quality. However, MBIR is highly computationally intensive and challenging to parallelize, and has traditionally been viewed as impractical in applications where reconstruction time is critical. We present the first GPU-based algorithm for ICD-based MBIR. The algorithm leverages the recently-proposed concept of SuperVoxels, and efficiently exploits the three levels of parallelism available in MBIR to better utilize the GPU hardware resources. We also explore data layout transformations to obtain more coalesced accesses and several GPU-specific optimizations for MBIR that boost performance. Across a suite of 3200 test cases, our GPU implementation obtains a geometric mean speedup of 4.43X over a state-of-the-art multi-core implementation on a 16-core iso-power CPU.

Model-based Iterative CT Image Reconstruction on GPUs

MBIR: A cryo-ET 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information.

Computed Tomographic (CT) image reconstruction is an important technique used in a wide range of applications. Among reconstruction methods, Model-Based Iterative Reconstruction (MBIR) is known to produce much higher quality CT images; however, the high computational requirements of MBIR greatly restrict their application. Currently, MBIR speed is primarily limited by irregular data access patterns, the difficulty of effective parallelization, and slow algorithmic convergence.This paper presents a new algorithm for MBIR, the Non-Uniform Parallel Super-Voxel (NU-PSV) algorithm, that regularizes the data access pattern, enables massive parallelism, and ensures fast convergence. We compare the NU-PSV algorithm with two state-of-the-art implementations on a 69632-core distributed system. Results indicate that the NU-PSV algorithm has an average speedup of 1665 compared to the fastest state-of-the-art implementations.

https://dl.acm.org/doi/pdf/10.1145/3126908.3126911

Massively parallel 3D image reconstruction

Modern synchrotron light sources and detectors produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used imaging techniques that generates data at tens of gigabytes per second is computed tomography (CT). Although CT experiments result in rapid data generation, the analysis and reconstruction of the collected data may require hours or even days of computation time with a medium-sized workstation, which hinders the scientific progress that relies on the results of analysis. We present Trace, a data-intensive computing engine that we have developed to enable high-performance implementation of iterative tomographic reconstruction algorithms for parallel computers. Trace provides fine-grained reconstruction of tomography datasets using both (thread-level) shared memory and (process-level) distributed memory parallelization. Trace utilizes a special data structure called replicated reconstruction object to maximize application performance. We also present the optimizations that we apply to the replicated reconstruction objects and evaluate them using tomography datasets collected at the Advanced Photon Source.
 Our experimental evaluations show that our optimizations and parallelization techniques can provide 158× speedup using 32 compute nodes (384 cores) over a single-core configuration and decrease the end-to-end processing time of a large sinogram (with 4501 × 1 × 22,400 dimensions) from 12.5 h to <5 min per iteration. The proposed tomographic reconstruction engine can efficiently process large-scale tomographic data using many compute nodes and minimize reconstruction times.

/pdf/trace-a-high-throughput-tomographic-reconstruction-engine-40jxnsfmyq.pdf

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets.

Computed Tomography (CT) Image Reconstruction is an important technique used in a wide range of applications, ranging from explosive detection, medical imaging to scientific imaging. Among available reconstruction methods, Model Based Iterative Reconstruction (MBIR) produces higher quality images and allows for the use of more general CT scanner geometries than is possible with more commonly used methods. The high computational cost of MBIR, however, often makes it impractical in applications for which it would otherwise be ideal. This paper describes a new MBIR implementation that significantly reduces the computational cost of MBIR while retaining its benefits. It describes a novel organization of the scanner data into super-voxels (SV) that, combined with a super-voxel buffer (SVB), dramatically increase locality and prefetching, enable parallelism across SVs and lead to an average speedup of 187 on 20 cores.

/pdf/high-performance-model-based-image-reconstruction-4umbdwwu1t.pdf

High performance model based image reconstruction

Model-Based Image Reconstruction (MBIR) methods significantly enhance the quality of computed tomographic (CT) reconstructions relative to analytical techniques, but are limited by high computational cost. In this article, we propose a multi-agent consensus equilibrium (MACE) algorithm for distributing both the computation and memory of MBIR reconstruction across a large number of parallel nodes. In MACE, each node stores only a sparse subset of views and a small portion of the system matrix, and each parallel node performs a local sparse-view reconstruction, which based on repeated feedback from other nodes, converges to the global optimum. Our distributed approach can also incorporate advanced denoisers as priors to enhance reconstruction quality. In this case, we obtain a parallel solution to the serial framework of Plug-n-play (PnP) priors, which we call MACE-PnP. In order to make MACE practical, we introduce a partial update method that eliminates nested iterations and prove that it converges to the same global solution. Finally, we validate our approach on a distributed memory system with real CT data. We also demonstrate an implementation of our approach on a massive supercomputer that can perform large-scale reconstruction in real-time.

Distributed Iterative CT Reconstruction Using Multi-Agent Consensus Equilibrium

Computed tomography (CT) image reconstruction is a crucial technique for many imaging applications. Among various reconstruction methods, Model-Based Iterative Reconstruction (MBIR) enables super-resolution with superior image quality. MBIR, however, has a high memory requirement that limits the achievable image resolution, and the parallelization for MBIR suffers from limited scalability. In this paper, we propose Asynchronous Consensus MBIR (AC-MBIR) that uses Consensus Equilibrium (CE) to provide a super-resolution algorithm with a small memory footprint, low communication overhead and a high scalability. Super-resolution experiments show that AC-MBIR has a 6.8 times smaller memory footprint and 16 times more scalability, compared with the state-of-the-art MBIR implementation, and maintains a 100% strong scaling efficiency at 146880 cores. In addition, AC-MBIR achieves an average bandwidth of 3.5 petabytes per second at 587520 cores.

https://dl.acm.org/doi/pdf/10.1145/3295500.3356142

Xiao Wang

Papers

High performance model based image reconstruction

Model-based Iterative CT Image Reconstruction on GPUs

Massively parallel 3D image reconstruction

Distributed Iterative CT Reconstruction Using Multi-Agent Consensus Equilibrium

Consensus equilibrium framework for super-resolution and extreme-scale CT reconstruction