Linear-Time Poisson-Disk Patterns

We present an algorithm for generating Poisson-disc patterns taking O(N) time to generate $N$ points. The method is based on a grid of regions which can contain no more than one point in the final pattern, and uses an explicit model of point arrival times under a uniform Poisson process.Comment: 4 pages, 2 figure

Dual channel rank-based intensity weighting for quantitative co-localization of microscopy images

BACKGROUND: Accurate quantitative co-localization is a key parameter in the context of understanding the spatial co-ordination of molecules and therefore their function in cells. Existing co-localization algorithms consider either the presence of co-occurring pixels or correlations of intensity in regions of interest. Depending on the image source, and the algorithm selected, the co-localization coefficients determined can be highly variable, and often inaccurate. Furthermore, this choice of whether co-occurrence or correlation is the best approach for quantifying co-localization remains controversial. RESULTS: We have developed a novel algorithm to quantify co-localization that improves on and addresses the major shortcomings of existing co-localization measures. This algorithm uses a non-parametric ranking of pixel intensities in each channel, and the difference in ranks of co-localizing pixel positions in the two channels is used to weight the coefficient. This weighting is applied to co-occurring pixels thereby efficiently combining both co-occurrence and correlation. Tests with synthetic data sets show that the algorithm is sensitive to both co-occurrence and correlation at varying levels of intensity. Analysis of biological data sets demonstrate that this new algorithm offers high sensitivity, and that it is capable of detecting subtle changes in co-localization, exemplified by studies on a well characterized cargo protein that moves through the secretory pathway of cells. CONCLUSIONS: This algorithm provides a novel way to efficiently combine co-occurrence and correlation components in biological images, thereby generating an accurate measure of co-localization. This approach of rank weighting of intensities also eliminates the need for manual thresholding of the image, which is often a cause of error in co-localization quantification. We envisage that this tool will facilitate the quantitative analysis of a wide range of biological data sets, including high resolution confocal images, live cell time-lapse recordings, and high-throughput screening data sets

Large-Scale Automatic Reconstruction of Neuronal Processes from Electron Microscopy Images

Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm scale can provide new insight into the fine grained structure of the brain. Segmentation of large-scale electron microscopy data is the main bottleneck in the analysis of these data sets. In this paper we present a pipeline that provides state-of-the art reconstruction performance while scaling to data sets in the GB-TB range. First, we train a random forest classifier on interactive sparse user annotations. The classifier output is combined with an anisotropic smoothing prior in a Conditional Random Field framework to generate multiple segmentation hypotheses per image. These segmentations are then combined into geometrically consistent 3D objects by segmentation fusion. We provide qualitative and quantitative evaluation of the automatic segmentation and demonstrate large-scale 3D reconstructions of neuronal processes from a $\mathbf{27,000}$ $\mathbf{\mu m^3}$ volume of brain tissue over a cube of $\mathbf{30 \; \mu m}$ in each dimension corresponding to 1000 consecutive image sections. We also introduce Mojo, a proofreading tool including semi-automated correction of merge errors based on sparse user scribbles

Non-Iterative, Feature-Preserving Mesh Smoothing

With the increasing use of geometry scanners to create 3D models, there is a rising need for fast and robust mesh smoothing to remove inevitable noise in the measurements. While most previous work has favored diffusion-based iterative techniques for feature-preserving smoothing, we propose a radically different approach, based on robust statistics and local first-order predictors of the surface. The robustness of our local estimates allows us to derive a non-iterative feature-preserving filtering technique applicable to arbitrary "triangle soups". We demonstrate its simplicity of implementation and its efficiency, which make it an excellent solution for smoothing large, noisy, and non-manifold meshes.Singapore-MIT Alliance (SMA

Antialiasing with Line Samples

Abstract. Antialiasing is a necessary component of any high quality renderer. An antialiased image is produced by convolving the scene with an antialiasing filter and sampling the result, or equivalently by solving the antialiasing integral at each pixel. Though methods for analytically computing this integral exist, they require the continuous two-dimensional result of visible-surface computations. Because these computations are expensive, most renderers use supersampling, a discontinuous approximation to the integral. We present a new algorithm, line sampling, combining a continuous approximation to the integral with a simple visible-surface algorithm. Line sampling provides high quality antialiasing at significantly lower cost than analytic methods while avoiding the visual artifacts caused by supersampling’s discontinuous nature. A line sample is a line segment in the image plane, centered at a pixel and spanning the footprint of the antialiasing filter. The segment is intersected with scene polygons, visible subsegments are determined, and the antialiasing integral is computed with those subsegments and a one-dimensional reparameterization of the integral. On simple scenes where edge directions can be precomputed, one correctly oriented line sample per pixel suffices for antialiasing. Complex scenes can be antialiased by combining multiple line samples weighted according to the orientation of the edges they intersect.

Adaptively sampled distance fields: A general representation of shape for computer graphics

Adaptively Sampled Distance Fields (ADFs) are a unifying representation of shape that integrate numerous concepts in computer graphics including the representation of geometry and volume data and a broad range of processing operations such as rendering, sculpting, level-of-detail management, surface offsetting, collision detection, and color gamut correction. Its structure is uncomplicated and direct, but is especially effective for quality reconstruction of complex shapes, e.g., artistic and organic forms, precision parts, volumes, high order functions, and fractals. We characterize one implementation of ADFs, illustrating its utility on two diverse applications: 1) artistic carving of fine detail, and 2) representing and rendering volume data and volumetric effects. Other applications are briefly presented