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

DTI denoising for data with low signal to noise ratios

Low signal to noise ratio (SNR) experiments in diffusion tensor imaging (DTI) give key information about tracking and anisotropy, e. g., by measurements with small voxel sizes or with high b values. However, due to the complicated and dominating impact of thermal noise such data are still seldom analysed. In this paper Monte Carlo simulations are presented which investigate the distributions of noise for different DTI variables in low SNR situations. Based on this study a strategy for the application of spatial smoothing is derived. Optimal prerequisites for spatial filters are unbiased, bell shaped distributions with uniform variance, but, only few variables have a statistics close to that. To construct a convenient filter a chain of nonlinear Gaussian filters is adapted to peculiarities of DTI and a bias correction is introduced. This edge preserving three dimensional filter is then validated via a quasi realistic model. Further, it is shown that for small sample sizes the filter is as effective as a maximum likelihood estimator and produces reliable results down to a local SNR of approximately 1. The filter is finally applied to very recent data with isotropic voxels of the size 1×1×1mm^3 which corresponds to a spatially mean SNR of 2.5. This application demonstrates the statistical robustness of the filter method. Though the Rician noise model is only approximately realized in the data, the gain of information by spatial smoothing is considerable

A Convex Model for Edge-Histogram Specification with Applications to Edge-preserving Smoothing

The goal of edge-histogram specification is to find an image whose edge image has a histogram that matches a given edge-histogram as much as possible. Mignotte has proposed a non-convex model for the problem [M. Mignotte. An energy-based model for the image edge-histogram specification problem. IEEE Transactions on Image Processing, 21(1):379--386, 2012]. In his work, edge magnitudes of an input image are first modified by histogram specification to match the given edge-histogram. Then, a non-convex model is minimized to find an output image whose edge-histogram matches the modified edge-histogram. The non-convexity of the model hinders the computations and the inclusion of useful constraints such as the dynamic range constraint. In this paper, instead of considering edge magnitudes, we directly consider the image gradients and propose a convex model based on them. Furthermore, we include additional constraints in our model based on different applications. The convexity of our model allows us to compute the output image efficiently using either Alternating Direction Method of Multipliers or Fast Iterative Shrinkage-Thresholding Algorithm. We consider several applications in edge-preserving smoothing including image abstraction, edge extraction, details exaggeration, and documents scan-through removal. Numerical results are given to illustrate that our method successfully produces decent results efficiently

Spatial Smoothing for Diffusion Tensor Imaging with low Signal to Noise Ratios

Though low signal to noise ratio (SNR) experiments in DTI give key information about tracking and anisotropy, e.g. by measurements with very small voxel sizes, due to the complicated impact of thermal noise such experiments are up to now seldom analysed. In this paper Monte Carlo simulations are presented which investigate the random fields of noise for different DTI variables in low SNR situations. Based on this study a strategy for spatial smoothing, which demands essentially uniform noise, is derived. To construct a convenient filter the weights of the nonlinear Aurich chain are adapted to DTI. This edge preserving three dimensional filter is then validated in different variants via a quasi realistic model and is applied to very new data with isotropic voxels of the size 1x1x1 mm3 which correspond to a spatial mean SNR of approximately 3

An adaptive noise removal approach for restoration of digital images corrupted by multimodal noise

Data smoothing algorithms are commonly applied to reduce the level of noise and eliminate the weak textures contained in digital images. Anisotropic diffusion algorithms form a distinct category of noise removal approaches that implement the smoothing process locally in agreement with image features such as edges that are typically determined by applying diverse partial differential equation (PDE) models. While this approach is opportune since it allows the implementation of feature-preserving data smoothing strategies, the inclusion of the PDE models in the formulation of the data smoothing process compromises the performance of the anisotropic diffusion schemes when applied to data corrupted by non-Gaussian and multimodal image noise. In this paper we first evaluate the positive aspects related to the inclusion of a multi-scale edge detector based on the generalisation of the Di Zenzo operator into the formulation of the anisotropic diffusion process. Then, we introduce a new approach that embeds the vector median filtering into the discrete implementation of the anisotropic diffusion in order to improve the performance of the noise removal algorithm when applied to multimodal noise suppression. To evaluate the performance of the proposed data smoothing strategy, a large number of experiments on various types of digital images corrupted by multimodal noise were conducted.Keywords — Anisotropic diffusion, vector median filtering, feature preservation, multimodal noise, noise removal

Image Segmentation with Eigenfunctions of an Anisotropic Diffusion Operator

We propose the eigenvalue problem of an anisotropic diffusion operator for image segmentation. The diffusion matrix is defined based on the input image. The eigenfunctions and the projection of the input image in some eigenspace capture key features of the input image. An important property of the model is that for many input images, the first few eigenfunctions are close to being piecewise constant, which makes them useful as the basis for a variety of applications such as image segmentation and edge detection. The eigenvalue problem is shown to be related to the algebraic eigenvalue problems resulting from several commonly used discrete spectral clustering models. The relation provides a better understanding and helps developing more efficient numerical implementation and rigorous numerical analysis for discrete spectral segmentation methods. The new continuous model is also different from energy-minimization methods such as geodesic active contour in that no initial guess is required for in the current model. The multi-scale feature is a natural consequence of the anisotropic diffusion operator so there is no need to solve the eigenvalue problem at multiple levels. A numerical implementation based on a finite element method with an anisotropic mesh adaptation strategy is presented. It is shown that the numerical scheme gives much more accurate results on eigenfunctions than uniform meshes. Several interesting features of the model are examined in numerical examples and possible applications are discussed

Robust Feature Detection and Local Classification for Surfaces Based on Moment Analysis

The stable local classification of discrete surfaces with respect to features such as edges and corners or concave and convex regions, respectively, is as quite difficult as well as indispensable for many surface processing applications. Usually, the feature detection is done via a local curvature analysis. If concerned with large triangular and irregular grids, e.g., generated via a marching cube algorithm, the detectors are tedious to treat and a robust classification is hard to achieve. Here, a local classification method on surfaces is presented which avoids the evaluation of discretized curvature quantities. Moreover, it provides an indicator for smoothness of a given discrete surface and comes together with a built-in multiscale. The proposed classification tool is based on local zero and first moments on the discrete surface. The corresponding integral quantities are stable to compute and they give less noisy results compared to discrete curvature quantities. The stencil width for the integration of the moments turns out to be the scale parameter. Prospective surface processing applications are the segmentation on surfaces, surface comparison, and matching and surface modeling. Here, a method for feature preserving fairing of surfaces is discussed to underline the applicability of the presented approach.