http://midag.cs.unc.edu/pubs/papers/Neuroimage06_Yushkevich.pdf

User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients—manually annotated by up to four raters—and to 65 comparable scans generated using tumor image simulation software Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%–85%), illustrating the difficulty of this task We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource

/pdf/the-multimodal-brain-tumor-image-segmentation-benchmark-2gfraj98dk.pdf

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

The rapid increase in the performance of graphics hardware, coupled with recent improvements in its programmability, have made graphics hardware a compelling platform for computationally demanding tasks in a wide variety of application domains. In this report, we describe, summarize, and analyze the latest research in mapping general-purpose computation to graphics hardware. We begin with the technical motivations that underlie general-purpose computation on graphics processors (GPGPU) and describe the hardware and software developments that have led to the recent interest in this field. We then aim the main body of this report at two separate audiences. First, we describe the techniques used in mapping general-purpose computation to graphics hardware. We believe these techniques will be generally useful for researchers who plan to develop the next generation of GPGPU algorithms and techniques. Second, we survey and categorize the latest developments in general-purpose application development on graphics hardware. This survey should be of particular interest to researchers who are interested in using the latest GPGPU applications in their systems of interest.

/pdf/a-survey-of-general-purpose-computation-on-graphics-hardware-2phx1q9xxr.pdf

A Survey of General-Purpose Computation on Graphics Hardware

Characterizing the performance of image segmentation approaches has been a persistent challenge. Performance analysis is important since segmentation algorithms often have limited accuracy and precision. Interactive drawing of the desired segmentation by human raters has often been the only acceptable approach, and yet suffers from intra-rater and inter-rater variability. Automated algorithms have been sought in order to remove the variability introduced by raters, but such algorithms must be assessed to ensure they are suitable for the task. The performance of raters (human or algorithmic) generating segmentations of medical images has been difficult to quantify because of the difficulty of obtaining or estimating a known true segmentation for clinical data. Although physical and digital phantoms can be constructed for which ground truth is known or readily estimated, such phantoms do not fully reflect clinical images due to the difficulty of constructing phantoms which reproduce the full range of imaging characteristics and normal and pathological anatomical variability observed in clinical data. Comparison to a collection of segmentations by raters is an attractive alternative since it can be carried out directly on the relevant clinical imaging data. However, the most appropriate measure or set of measures with which to compare such segmentations has not been clarified and several measures are used in practice. We present here an expectation-maximization algorithm for simultaneous truth and performance level estimation (STAPLE). The algorithm considers a collection of segmentations and computes a probabilistic estimate of the true segmentation and a measure of the performance level represented by each segmentation. The source of each segmentation in the collection may be an appropriately trained human rater or raters, or may be an automated segmentation algorithm. The probabilistic estimate of the true segmentation is formed by estimating an optimal combination of the segmentations, weighting each segmentation depending upon the estimated performance level, and incorporating a prior model for the spatial distribution of structures being segmented as well as spatial homogeneity constraints. STAPLE is straightforward to apply to clinical imaging data, it readily enables assessment of the performance of an automated image segmentation algorithm, and enables direct comparison of human rater and algorithm performance.

/pdf/simultaneous-truth-and-performance-level-estimation-staple-2ww9ut6c5n.pdf

Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation

Genetic programming (GP) is a systematic, domain-independent method for getting computers to solve problems automatically starting from a high-level statement of what needs to be done. Using ideas from natural evolution, GP starts from an ooze of random computer programs, and progressively refines them through processes of mutation and sexual recombination, until high-fitness solutions emerge. All this without the user having to know or specify the form or structure of solutions in advance. GP has generated a plethora of human-competitive results and applications, including novel scientific discoveries and patentable inventions. This unique overview of this exciting technique is written by three of the most active scientists in GP. See www.gp-field-guide.org.uk for more information on the book.

/pdf/a-field-guide-to-genetic-programming-3wkkmsw81n.pdf

A Field Guide to Genetic Programming

A Survey of General-Purpose Computation on Graphics Hardware.

The tremendous evolution of programmable graphics hardware has made high-quality real-time volume graphics a reality. In addition to the traditional application of rendering volume data in scientific visualization, the interest in applying these techniques for real-time rendering of atmospheric phenomena and participating media such as fire, smoke, and clouds is growing rapidly. This course covers both applications in scientific visualization, e.g., medical volume data, and real-time rendering, such as advanced effects and illumination in computer games, in detail. Course participants will learn techniques for harnessing the power of consumer graphics hardware and high-level shading languages for real-time rendering of volumetric data and effects. Beginning with basic texture-based approaches including hardware ray casting, the algorithms are improved and expanded incrementally, covering local and global illumination, scattering, pre-integration, implicit surfaces and non-polygonal isosurfaces, transfer function design, volume animation and deformation, dealing with large volumes, high-quality volume clipping, rendering segmented volumes, higher-order filtering, and non-photorealistic volume rendering. Course participants are provided with documented source code covering details usually omitted in publications.

Real-Time Volume Graphics

The graphics processor (GPU) on today's commodity video cards has evolved into an extremely powerful and flexible processor. The latest graphics architectures provide tremendous memory bandwidth and computational horsepower, with fully programmable vertex and pixel processing units that support vector operations up to full IEEE floating point precision. High level languages have emerged for graphics hardware, making this computational power accessible. Architecturally, GPUs are highly parallel streaming processors optimized for vector operations, with both MIMD (vertex) and SIMD (pixel) pipelines. Not surprisingly, these processors are capable of general-purpose computation beyond the graphics applications for which they were designed. Researchers have found that exploiting the GPU can accelerate some problems by over an order of magnitude over the CPU.However, significant barriers still exist for the developer who wishes to use the inexpensive power of commodity graphics hardware, whether for in-game simulation of physics of for conventional computational science. These chips are designed for and driven by video game development; the programming model is unusual, the programming environment is tightly constrained, and the underlying architectures are largely secret. The GPU developer must be an expert in computer graphics and its computational idioms to make effective use of the hardware, and still pitfalls abound. This course provides a detailed introduction to general purpose computation on graphics hardware (GPGPU). We emphasize core computational building blocks, ranging from linear algebra to database queries, and review the tools, perils, and tricks of the trade in GPU programming. Finally we present some interesting and important case studies on general-purpose applications of graphics hardware.The course presenters are experts on general-purpose GPU computation from academia and industry, and have presented papers and tutorials on the topic at SIGGRAPH, Graphics Hardware, Game Developers Conference, and elsewhere.

GPGPU: general purpose computation on graphics hardware

Due to our familiarity with how fluids move and interact, as well as their complexity, plausible animation of fluids remains a challenging problem. We present a particle interaction method for simulating fluids. The underlying equations of fluid motion are discretized using moving particles and their interactions. The method allows simulation and modeling of mixing fluids with different physical properties, fluid interactions with stationary objects, and fluids that exhibit significant interface breakup and fragmentation. The gridless computational method is suited for medium scale problems since computational elements exist only where needed. The method fits well into the current user interaction paradigm and allows easy user control over the desired fluid motion.

/pdf/particle-based-simulation-of-fluids-4pnv77qyzz.pdf

Aaron Lefohn

Papers

A Survey of General-Purpose Computation on Graphics Hardware

A Survey of General-Purpose Computation on Graphics Hardware.

Real-Time Volume Graphics

GPGPU: general purpose computation on graphics hardware

Particle-Based Simulation of Fluids