3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Frequency Analysis and Sheared Reconstruction for Rendering Motion Blur

International audienceMotion blur is crucial for high-quality rendering but is also very expensive. Our first contribution is a frequency analysis of motion-blurred scenes, including moving objects, specular reflections, and shadows. We show that motion induces a shear in the frequency domain, and that the spectrum of moving scenes is usually contained in a wedge. This allows us to compute adaptive space-time sampling rates, to accelerate rendering. For uniform velocities and standard axis-aligned reconstruction, we show that the product of spatial and temporal bandlimits or sampling rates is constant, independent of velocity. Our second contribution is a novel sheared reconstruction filter that tightly packs the wedge of frequencies in the Fourier domain, and enables even lower sampling rates. We present a rendering algorithm that computes a sheared reconstruction filter per pixel, without any intermediate Fourier representation. This often permits synthesis of motion-blurred images with far fewer rendering samples than standard techniques require

Genetic characterization of Barbari goats using microsatellite markers

Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining. The number of alleles ranged from 4 to 11, with allele sizes ranging from 88 to 220 bp. The distribution of allele frequencies was between 0.0104 and 0.5208. Polymorphism information content varied from 0.5563 to 0.8348. The population was not in Hardy-Weinberg equilibrium for all except two microsatellite loci (ILSTS044 and ILSTS060). The observed heterozygosity ranged from 0.8478 to 1.0000 while the expected heterozygosity ranged from 0.6208 to 0.8509. Based on the results of the present study, there is a good scope for exploiting the genetic variability in the Barbari goats for further improvement of performance

Microgeometry capture using an elastomeric sensor

We describe a system for capturing microscopic surface geometry. The system extends the retrographic sensor [Johnson and Adelson 2009] to the microscopic domain, demonstrating spatial resolution as small as 2 microns. In contrast to existing microgeometry capture techniques, the system is not affected by the optical characteristics of the surface being measured---it captures the same geometry whether the object is matte, glossy, or transparent. In addition, the hardware design allows for a variety of form factors, including a hand-held device that can be used to capture high-resolution surface geometry in the field. We achieve these results with a combination of improved sensor materials, illumination design, and reconstruction algorithm, as compared to the original sensor of Johnson and Adelson [2009].National Science Foundation (U.S.) (Grant 0739255)National Institutes of Health (U.S.) (Contract 1-R01-EY019292-01

Multi-resolution isotropic strain limiting

In this paper we describe a fast strain-limiting method that allows stiff, incompliant materials to be simulated efficiently. Unlike prior approaches, which act on springs or individual strain components, this method acts on the strain tensors in a coordinate-invariant fashion allowing isotropic behavior. Our method applies to both two-and three-dimensional strains, and only requires computing the singular value decomposition of the deformation gradient, either a small 2x2 or 3x3 matrix, for each element. We demonstrate its use with triangular and tetrahedral linear-basis elements. For triangulated surfaces in three-dimensional space, we also describe a complementary edge-angle-limiting method to limit out-of-plane bending. All of the limits are enforced through an iterative, non-linear, Gauss-Seidel-like constraint procedure. To accelerate convergence, we propose a novel multi-resolution algorithm that enforces fitted limits at each level of a non-conforming hierarchy. Compared with other constraint-based techniques, our isotropic multi-resolution strain-limiting method is straightforward to implement, efficient to use, and applicable to a wide range of shell and solid materials. © 2010 ACM

Photo-antagonism of the GABAA receptor

Neurotransmitter receptor trafficking is fundamentally important for synaptic transmission and neural network activity. GABAA receptors and inhibitory synapses are vital components of brain function, yet much of our knowledge regarding receptor mobility and function at inhibitory synapses is derived indirectly from using recombinant receptors, antibody-tagged native receptors and pharmacological treatments. Here we describe the use of a set of research tools that can irreversibly bind to and affect the function of recombinant and neuronal GABAA receptors following ultraviolet photoactivation. These compounds are based on the competitive antagonist gabazine and incorporate a variety of photoactive groups. By using site-directed mutagenesis and ligand-docking studies, they reveal new areas of the GABA binding site at the interface between receptor β and α subunits. These compounds enable the selected inactivation of native GABAA receptor populations providing new insight into the function of inhibitory synapses and extrasynaptic receptors in controlling neuronal excitation

Data compression on the sphere

Large data-sets defined on the sphere arise in many fields. In particular, recent and forthcoming observations of the anisotropies of the cosmic microwave background (CMB) made on the celestial sphere contain approximately three and fifty mega-pixels respectively. The compression of such data is therefore becoming increasingly important. We develop algorithms to compress data defined on the sphere. A Haar wavelet transform on the sphere is used as an energy compression stage to reduce the entropy of the data, followed by Huffman and run-length encoding stages. Lossless and lossy compression algorithms are developed. We evaluate compression performance on simulated CMB data, Earth topography data and environmental illumination maps used in computer graphics. The CMB data can be compressed to approximately 40% of its original size for essentially no loss to the cosmological information content of the data, and to approximately 20% if a small cosmological information loss is tolerated. For the topographic and illumination data compression ratios of approximately 40:1 can be achieved when a small degradation in quality is allowed. We make our SZIP program that implements these compression algorithms available publicly.Comment: 13 pages, 8 figures, accepted for publication by A&A; We make our SZIP program that implements these compression algorithms available publicly from http://www.szip.org.u

Analysis of Sample Correlations for Monte Carlo Rendering

Modern physically based rendering techniques critically depend on approximating integrals of high dimensional functions representing radiant light energy. Monte Carlo based integrators are the choice for complex scenes and effects. These integrators work by sampling the integrand at sample point locations. The distribution of these sample points determines convergence rates and noise in the final renderings. The characteristics of such distributions can be uniquely represented in terms of correlations of sampling point locations. Hence, it is essential to study these correlations to understand and adapt sample distributions for low error in integral approximation. In this work, we aim at providing a comprehensive and accessible overview of the techniques developed over the last decades to analyze such correlations, relate them to error in integrators, and understand when and how to use existing sampling algorithms for effective rendering workflows.publishe