BACKGROUND: Neuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, researchers relate a connectome's structure to neuronal function, often by studying individual neuron cell types. Vast libraries of fly driver lines expressing fluorescent reporter genes in sets of neurons have been created and imaged using confocal light microscopy (LM), enabling the targeting of neurons for experimentation. However, creating a fly line for driving gene expression within a single neuron found in an EM connectome remains a challenge, as it typically requires identifying a pair of driver lines where only the neuron of interest is expressed in both. This task and other emerging scientific workflows require finding similar neurons across large data sets imaged using different modalities. RESULTS: Here, we present NeuronBridge, a web application for easily and rapidly finding putative morphological matches between large data sets of neurons imaged using different modalities. We describe the functionality and construction of the NeuronBridge service, including its user-friendly graphical user interface (GUI), extensible data model, serverless cloud architecture, and massively parallel image search engine. CONCLUSIONS: NeuronBridge fills a critical gap in the Drosophila research workflow and is used by hundreds of neuroscience researchers around the world. We offer our software code, open APIs, and processed data sets for integration and reuse, and provide the application as a service at http://neuronbridge.janelia.org .

Heuristics that exploit bouning boxes are common in algorithms for rendering, modeling, and animation. While experience has shown that bounding boxes improve the performance of these algorithms in practice, the previous theoretical analysis has concluded that bounding boxes perform poorly in the worst case. This paper reconciles this discrepancy by analyzing intersections among n geometric objects in terms of two parameters: α an upper bound on the aspect ratio or elongatedness of each object; and σ an upper bound on the scale factor or size disparity between the largest and smallest objects. Letting K o and K b be the number of intersecting object pairs and bounding box pairs, respectively, we analyze a ratio measure of the bounding boxes' efficiency, ρ = K b / (n + K 0 ) . The analysis proves that ρ = O(α√σlog 2 σ) and ρ = Ω(α√σ) . One important consequence is that if α and σ are small constants (as is often the case in practice), then K b = O ( K o )+ O ( n , so an algorithm that uses bounding boxes has time complexity proportional to the number of actual object intersections. This theoretical result validates the efficiency that bounding boxes have demonstrated in practice. Another consequence of our analysis is a proof of the output-sensitivity of an algorithm for reporting all intersecting pairs in a set of n convex polyhedra with constant α and σ. The algorithm takes time O ( n log d -1 n + K o log d -1 n ) for dimension d = 2, 3. This running time improves on the performance of previous algorithms, which make no assumptions about α and σ.

This article presents the density estimation framework for generating view-independent global illumination solutions. It works by probabilistically simulating the light flow in an environment with light particles that trace random walks origination at luminaires and then using statistical density estimation techniques to reconstruct the lighting on each surface. By splitting the computation into separate transport and reconstruction stages, we gain many advantages including reduced memory usage, the ability to simulate nondiffuse transport, and natural parallelism. Solutions to several theoretical and practical difficulties in implementing this framework are also described. Light sources that vary spectrally and directionally are integrated into a spectral particle tracer using nonuniform rejection. A new local linear density estimation technique eliminates boundary bias and extends to arbitrary polygons. A mesh decimation algorithm with perceptual calibration is introduced to simplify the Gouraud-shaded representation of the solution for interactive display.

This article presentsa method for approximatingpolyhedralobjects to support a time-critical collision-detectionalgorithm.The approximationsare hierarchies of spheres, and they allow the time-critical algorithm to progressively refine the accuracy of its detection, stopping as needed to maintain the real-time performanceessential for interactive applications.The key to this approach is a preprocessthat automaticallybuilds tightly fitting hierarchies for rigid and articulatedobjects.The preprocessuses medial-axis surfaces, which are skeletal representations of objects.These skeletons guide an optimizationtechnique that gives the hierarchies accuracy properties appropriate for collision detection.In a sample application, hierarchies built this way allow the time-criticalcollision-detectionalgorithmto have acceptableaccuracy, improving significantly on that possible with hierarchies built by previous techniques.The performanceof the time-critical algorithm in this application is consistently 10 to 100 times better than a previous collision-detection algorithm, maintaining low latency and a nearIy constant frame rate of 10 frames per second on a conventional graphics workstation.The time-critical algorithm maintains its real-time performance as objects become more complicated, even as they exceed previously reported complexity levels by a factor of more than 10.

Collision detection and response are important for interactive graphics applications such as vehicle simulators and virtual reality. Unfortunately, previous collision detection algorithms are too slow for interactive use. The paper presents a new algorithm for rigid or articulated objects that meets performance goals through a form of time critical computing. The algorithm supports progressive refinement, detecting collisions between successively tighter approximations to object surfaces as the application allows it more processing time. The algorithm uses simple four dimensional geometry to approximate motion, and hierarchies of spheres to approximate three dimensional surfaces at multiple resolutions. In a sample application, the algorithm allows interactive performance that is not possible with a good previous algorithm. In particular, the new algorithm provides acceptable accuracy while maintaining a steady and high frame rate, which in some cases improves on the previous algorithm's rate by more than two orders of magnitude.>

No abstract available.

We present an interactive modeling and animation system that facilitates the integration of a variety of simulation and animation paradigms. This system permits the modeling of diverse objects that change in shape, appearance, and behaviour over time. Our system thus extends modeling tools to include animation controls. Changes can be effected by various methods of control, including scripted, gestural, and behavioral specification. The system is an extensible testbed that supports research in the interaction of disparate control methods embodied in controller objects. This paper discusses some of the issues involved in modeling such interactions and the mechanisms implemented to provide solutions to some of these issues.The system's object-oriented architecture uses delegation hierarchies to let objects change all of their attributes dynamically. Objects include displayable objects, controllers, cameras, lights, renderers, and user interfaces. Techniques used to obtain interactive performance include the use of data-dependency networks, lazy evaluation, and extensive caching to exploit inter- and intra-frame coherency.