VolRoverN: Enhancing Surface and Volumetric Reconstruction for Realistic Dynamical Simulation of Cellular and Subcellular Function

Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons and glia at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type and are used here on spiny dendrites with complex morphology and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models

A feature-based reverse engineering system using artificial neural networks

Reverse Engineering (RE) is the process of reconstructing CAD models from scanned data of a physical part acquired using 3D scanners. RE has attracted a great deal of research interest over the last decade. However, a review of the literature reveals that most research work have focused on creation of free form surfaces from point cloud data. Representing geometry in terms of surface patches is adequate to represent positional information, but can not capture any of the higher level structure of the part. Reconstructing solid models is of importance since the resulting solid models can be directly imported into commercial solid modellers for various manufacturing activities such as process planning, integral property computation, assembly analysis, and other applications. This research discusses the novel methodology of extracting geometric features directly from a data set of 3D scanned points, which utilises the concepts of artificial neural networks (ANNs). In order to design and develop a generic feature-based RE system for prismatic parts, the following five main tasks were investigated. (1) point data processing algorithms; (2) edge detection strategies; (3) a feature recogniser using ANNs; (4) a feature extraction module; (5) a CAD model exchanger into other CAD/CAM systems via IGES. A key feature of this research is the incorporation of ANN in feature recognition. The use of ANN approach has enabled the development of a flexible feature-based RE methodology that can be trained to deal with new features. ANNs require parallel input patterns. In this research, four geometric attributes extracted from a point set are input to the ANN module for feature recognition: chain codes, convex/concave, circular/rectangular and open/closed attribute. Recognising each feature requires the determination of these attributes. New and robust algorithms are developed for determining these attributes for each of the features. This feature-based approach currently focuses on solving the feature recognition problem based on 2.5D shapes such as block pocket, step, slot, hole, and boss, which are common and crucial in mechanical engineering products. This approach is validated using a set of industrial components. The test results show that the strategy for recognising features is reliable

A reduced-order model for segregated fluid-structure interaction solvers based on an ALE approach

This article presents a Galerkin projection model order reduction approach for fluid-structure interaction (FSI) problems in the Finite Volume context. The reduced-order model (ROM) is based on proper orthogonal decomposition (POD), where a reduced basis is formed using energy-dominant POD modes. The reduced basis also consists of characteristics of the POD time modes derived from the POD time modes coefficients. In addition, the solution state vector comprises the mesh deformation, considering the structural motion in FSI. The results are obtained by applying the proposed method to time-dependent problems governed by the 2D incompressible Navier-Stokes equations. The main objective of this work is to introduce a hybrid technique mixing up the classical Galerkin-projection approach with a data-driven method to obtain a versatile and accurate algorithm for resolving FSI problems with moving meshes. The effectiveness of this approach is demonstrated in the case study of vortex-induced vibrations (VIV) of a cylinder at Reynolds number Re = 200. The results show the stability and accuracy of the proposed method with respect to the high-dimensional model by capturing transient flow fields and, more importantly, the forces acting on the moving objects

Generalizable automated pixel-level structural segmentation of medical and biological data

Over the years, the rapid expansion in imaging techniques and equipments has driven the demand for more automation in handling large medical and biological data sets. A wealth of approaches have been suggested as optimal solutions for their respective imaging types. These solutions span various image resolutions, modalities and contrast (staining) mechanisms. Few approaches generalise well across multiple image types, contrasts or resolution. This thesis proposes an automated pixel-level framework that addresses 2D, 2D+t and 3D structural segmentation in a more generalizable manner, yet has enough adaptability to address a number of specific image modalities, spanning retinal funduscopy, sequential fluorescein angiography and two-photon microscopy. The pixel-level segmentation scheme involves: i ) constructing a phase-invariant orientation field of the local spatial neighbourhood; ii ) combining local feature maps with intensity-based measures in a structural patch context; iii ) using a complex supervised learning process to interpret the combination of all the elements in the patch in order to reach a classification decision. This has the advantage of transferability from retinal blood vessels in 2D to neural structures in 3D. To process the temporal components in non-standard 2D+t retinal angiography sequences, we first introduce a co-registration procedure: at the pairwise level, we combine projective RANSAC with a quadratic homography transformation to map the coordinate systems between any two frames. At the joint level, we construct a hierarchical approach in order for each individual frame to be registered to the global reference intra- and inter- sequence(s). We then take a non-training approach that searches in both the spatial neighbourhood of each pixel and the filter output across varying scales to locate and link microvascular centrelines to (sub-) pixel accuracy. In essence, this \link while extract" piece-wise segmentation approach combines the local phase-invariant orientation field information with additional local phase estimates to obtain a soft classification of the centreline (sub-) pixel locations. Unlike retinal segmentation problems where vasculature is the main focus, 3D neural segmentation requires additional exibility, allowing a variety of structures of anatomical importance yet with different geometric properties to be differentiated both from the background and against other structures. Notably, cellular structures, such as Purkinje cells, neural dendrites and interneurons, all display certain elongation along their medial axes, yet each class has a characteristic shape captured by an orientation field that distinguishes it from other structures. To take this into consideration, we introduce a 5D orientation mapping to capture these orientation properties. This mapping is incorporated into the local feature map description prior to a learning machine. Extensive performance evaluations and validation of each of the techniques presented in this thesis is carried out. For retinal fundus images, we compute Receiver Operating Characteristic (ROC) curves on existing public databases (DRIVE & STARE) to assess and compare our algorithms with other benchmark methods. For 2D+t retinal angiography sequences, we compute the error metrics ("Centreline Error") of our scheme with other benchmark methods. For microscopic cortical data stacks, we present segmentation results on both surrogate data with known ground-truth and experimental rat cerebellar cortex two-photon microscopic tissue stacks.Open Acces

Analyzing and controlling large nanosystems with physics-trained neural networks

In dieser Arbeit wird untersucht, wie Neuronale Netze genutzt werden können, um die Auswertung von Experimenten durch Minimierung des Simulationsaufwandes beschleunigen zu können. Für die Rekonstruktion von Silber-Nanoclustern aus Einzelschuss-Weitwinkel-Streubildern können diese bereits aus kleinen Datenätzen allgemeine Rekonstruktionsregeln ableiten und ermöglichen durch direktes Training auf der Streuphysik unerreichte Detailtiefen. Für Giant-Dipole-Zustände von Rydbergexzitonen in Kupferoxydul wird mittels Deep Reinforcement Learning ein Anregungsschema aus Simulationen hergeleitet.This thesis investigates the possible application of neural networks in accelerating the evaluation of physical experiments while minimizing the required simulation effort. Neural networks are capable of inferring universal reconstruction rules for reconstructing silver nanoclusters from single wide-angle scattering patterns from a small set of simulated data and when trained directly on scattering theory reaching unmatched accuracy. A dynamic excitation for giant dipole states of Rydberg excitons in cuprous oxide is derived through deep reinforcement learning interacting and simulation data

Modelling, Monitoring, Control and Optimization for Complex Industrial Processes

This reprint includes 22 research papers and an editorial, collected from the Special Issue "Modelling, Monitoring, Control and Optimization for Complex Industrial Processes", highlighting recent research advances and emerging research directions in complex industrial processes. This reprint aims to promote the research field and benefit the readers from both academic communities and industrial sectors

Measurements, Models, Systems and Design

531 s.