As neuroimaging algorithms and technology continue to grow faster than CPU performance in complexity and image resolution, data-parallel computing methods will be increasingly important. The high performance, data-parallel architecture of modern graphical processing units (GPUs) can reduce computational times by orders of magnitude. However, its massively threaded architecture introduces challenges when GPU resources are exceeded. This paper presents optimization strategies for compute- and memory-bound algorithms for the CUDA architecture. For compute-bound algorithms, the registers are reduced through variable reuse via shared memory and the data throughput is increased through heavier thread workloads and maximizing the thread configuration for a single thread block per multiprocessor. For memory-bound algorithms, fitting the data into the fast but limited GPU resources is achieved through reorganizing the data into self-contained structures and employing a multi-pass approach. Memory latencies are reduced by selecting memory resources whose cache performance are optimized for the algorithm's access patterns. We demonstrate the strategies on two computationally expensive algorithms and achieve optimized GPU implementations that perform up to 6× faster than unoptimized ones. Compared to CPU implementations, we achieve peak GPU speedups of 129× for the 3D unbiased nonlinear image registration technique and 93× for the non-local means surface denoising algorithm.

BackgroundDigital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data.ResultsThe MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data.ConclusionsMBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows.

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Resupplying forward-deployed units in rugged terrain in the presence of hostile forces creates a high threat to manned air and ground vehicles. An autonomous unmanned ground vehicle (UGV) capable of navigating stealthily at night in offroad and on-road terrain could significantly increase the safety and success rate of such resupply missions for warfighters. Passive night-time perception of terrain and obstacle features is a vital requirement for such missions. As part of the ONR 30 Autonomy Team, the Jet Propulsion Laboratory developed a passive, low-cost night-time perception system under the ONR Expeditionary Maneuver Warfare and Combating Terrorism Applied Research program. Using a stereo pair of forward looking LWIR uncooled microbolometer cameras, the perception system generates disparity maps using a local window-based stereo correlator to achieve real-time performance while maintaining low power consumption. To overcome the lower signal-to-noise ratio and spatial resolution of LWIR thermal imaging technologies, a series of pre-filters were applied to the input images to increase the image contrast and stereo correlator enhancements were applied to increase the disparity density. To overcome false positives generated by mixed pixels, noisy disparities from repeated textures, and uncertainty in far range measurements, a series of consistency, multi-resolution, and temporal based post-filters were employed to improve the fidelity of the output range measurements. The stereo processing leverages multi-core processors and runs under the Robot Operating System (ROS). The night-time passive perception system was tested and evaluated on fully autonomous testbed ground vehicles at SPAWAR Systems Center Pacific (SSC Pacific) and Marine Corps Base Camp Pendleton, California. This paper describes the challenges, techniques, and experimental results of developing a passive, low-cost perception system for night-time autonomous navigation.

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