Halide: a language and compiler for optimizing parallelism, locality, and recomputation in image processing pipelines

Image processing pipelines combine the challenges of stencil computations and stream programs. They are composed of large graphs of different stencil stages, as well as complex reductions, and stages with global or data-dependent access patterns. Because of their complex structure, the performance difference between a naive implementation of a pipeline and an optimized one is often an order of magnitude. Efficient implementations require optimization of both parallelism and locality, but due to the nature of stencils, there is a fundamental tension between parallelism, locality, and introducing redundant recomputation of shared values. We present a systematic model of the tradeoff space fundamental to stencil pipelines, a schedule representation which describes concrete points in this space for each stage in an image processing pipeline, and an optimizing compiler for the Halide image processing language that synthesizes high performance implementations from a Halide algorithm and a schedule. Combining this compiler with stochastic search over the space of schedules enables terse, composable programs to achieve state-of-the-art performance on a wide range of real image processing pipelines, and across different hardware architectures, including multicores with SIMD, and heterogeneous CPU+GPU execution. From simple Halide programs written in a few hours, we demonstrate performance up to 5x faster than hand-tuned C, intrinsics, and CUDA implementations optimized by experts over weeks or months, for image processing applications beyond the reach of past automatic compilers.United States. Dept. of Energy (Award DE-SC0005288)National Science Foundation (U.S.) (Grant 0964004)Intel CorporationCognex CorporationAdobe System

Halide: a language and compiler for optimizing parallelism, locality, and recomputation in image processing pipelines

Image processing pipelines combine the challenges of stencil computations and stream programs. They are composed of large graphs of different stencil stages, as well as complex reductions, and stages with global or data-dependent access patterns. Because of their complex structure, the performance difference between a naive implementation of a pipeline and an optimized one is often an order of magnitude. Efficient implementations require optimization of both parallelism and locality, but due to the nature of stencils, there is a fundamental tension between parallelism, locality, and introducing redundant recomputation of shared values. We present a systematic model of the tradeoff space fundamental to stencil pipelines, a schedule representation which describes concrete points in this space for each stage in an image processing pipeline, and an optimizing compiler for the Halide image processing language that synthesizes high performance implementations from a Halide algorithm and a schedule. Combining this compiler with stochastic search over the space of schedules enables terse, composable programs to achieve state-of-the-art performance on a wide range of real image processing pipelines, and across different hardware architectures, including multicores with SIMD, and heterogeneous CPU+GPU execution. From simple Halide programs written in a few hours, we demonstrate performance up to 5x faster than hand-tuned C, intrinsics, and CUDA implementations optimized by experts over weeks or months, for image processing applications beyond the reach of past automatic compilers.United States. Dept. of Energy (Award DE-SC0005288)National Science Foundation (U.S.) (Grant 0964004)Intel CorporationCognex CorporationAdobe System

Investigating the impact of supervoxel segmentation for unsupervised abnormal brain asymmetry detection

Several brain disorders are associated with abnormal brain asymmetries (asymmetric anomalies). Several computer-based methods aim to detect such anomalies automatically. Recent advances in this area use automatic unsupervised techniques that extract pairs of symmetric supervoxels in the hemispheres, model normal brain asymmetries for each pair from healthy subjects, and treat outliers as anomalies. Yet, there is no deep understanding of the impact of the supervoxel segmentation quality for abnormal asymmetry detection, especially for small anomalies, nor of the added value of using a specialized model for each supervoxel pair instead of a single global appearance model. We aim to answer these questions by a detailed evaluation of different scenarios for supervoxel segmentation and classification for detecting abnormal brain asymmetries. Experimental results on 3D MR-T1 brain images of stroke patients confirm the importance of high-quality supervoxels fit anomalies and the use of a specific classifier for each supervoxel. Next, we present a refinement of the detection method that reduces the number of false-positive supervoxels, thereby making the detection method easier to use for visual inspection and analysis of the found anomalies.</p

Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation

We describe and demonstrate an optimization-based x-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to and fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement

Pore Space Architecture of Particulate Materials: Characterization and Applications

The behavior of particulate materials is of overarching importance across multiple science and engineering fields, given its ubiquitous presence in nature. These materials are typically composed of two phases, solids and voids, and are therefore described as complex multi-phase materials that exhibit non-linear responses when subjected to varying boundary conditions. While the attributes of the solid phase of particulate materials have been extensively characterized both experimentally and numerically, there is much less understanding of the attributes and behavior of the pore phase. Furthermore, classical pore models incorporate idealized assumptions of feature geometries, limiting the accuracy of the information that can be obtained from these features. This study aims to advance digital characterization capabilities for particulate microstructures, focusing on characterizing the geometry and topology of the highly complex pore space within packed particle systems. A new and robust computational algorithm is proposed that quantifies various characteristics of the three-dimensional pore space of a given particulate media, which is unimpeded by assumptions of feature shapes or user dependency. The method is validated against packings of known pore geometries and implemented on real, simulated, and fabricated microstructures of different packing densities, particle sizes, shapes, gradation, and following different specimen preparation techniques to measure its ability in capturing multi-scale responses of microstructures. The study also leverages the emergence of machine learning techniques to scale up the findings to real-world field-scale applications comprising particle-pore systems with 10's of millions of particles. In this regard, the use of deep learning tools for the rapid estimation of pore space properties from three-dimensional images is sought. Finally, the developed techniques and tools are implemented on real granular soils to strengthen the understanding of macro-geomechanical phenomena. The findings highlight the importance of accounting for pore space properties when interpreting the macroscopic response of granular assemblies subjected to external mechanical and precipitational loading.Ph.D

Image Analysis for the Life Sciences - Computer-assisted Tumor Diagnostics and Digital Embryomics

Current research in the life sciences involves the analysis of such a huge amount of image data that automatization is required. This thesis presents several ways how pattern recognition techniques may contribute to improved tumor diagnostics and to the elucidation of vertebrate embryonic development. Chapter 1 studies an approach for exploiting spatial context for the improved estimation of metabolite concentrations from magnetic resonance spectroscopy imaging (MRSI) data with the aim of more robust tumor detection, and compares against a novel alternative. Chapter 2 describes a software library for training, testing and validating classification algorithms that estimate tumor probability based on MRSI. It allows flexible adaptation towards changed experimental conditions, classifier comparison and quality control without need for expertise in pattern recognition. Chapter 3 studies several models for learning tumor classifiers that allow for the common unreliability of human segmentations. For the first time, models are used for this task that additionally employ the objective image information. Chapter 4 encompasses two contributions to an image analysis pipeline for automatically reconstructing zebrafish embryonic development based on time-resolved microscopy: Two approaches for nucleus segmentation are experimentally compared, and a procedure for tracking nuclei over time is presented and evaluated

Multimodal MR Prediction Models for Late-Life Depression and Treatment Response

Currently, depression diagnosis relies primarily on behavioral symptoms and signs, instead of underlying brain characteristics, and treatment is guided by trial and error instead of individual suitability associated with underlying brain characteristics. Also, previous brain-imaging studies attempting to resolve this issue have traditionally focused on mid-life depression using a single imaging modality and region-based approach, which may not fully explain the complexity of the underlying brain characteristics; especially for late-life depression. We aimed to evaluate and compare underlying brain characteristics of late-life depression diagnosis and treatment response by estimating accurate prediction models using multi-modal magnetic resonance imaging and non-imaging measures. Based on our finding, late-life depression diagnosis and treatment response predictors involve measures from different imaging modalities, which are indicative of differences in underlying brain characteristics

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum