Review : Deep learning in electron microscopy

Deep learning is transforming most areas of science and technology, including electron microscopy. This review paper offers a practical perspective aimed at developers with limited familiarity. For context, we review popular applications of deep learning in electron microscopy. Following, we discuss hardware and software needed to get started with deep learning and interface with electron microscopes. We then review neural network components, popular architectures, and their optimization. Finally, we discuss future directions of deep learning in electron microscopy

Monte Carlo Method with Heuristic Adjustment for Irregularly Shaped Food Product Volume Measurement

Volume measurement plays an important role in the production and processing of food products. Various methods have been proposed to measure the volume of food products with irregular shapes based on 3D reconstruction. However, 3D reconstruction comes with a high-priced computational cost. Furthermore, some of the volume measurement methods based on 3D reconstruction have a low accuracy. Another method for measuring volume of objects uses Monte Carlo method. Monte Carlo method performs volume measurements using random points. Monte Carlo method only requires information regarding whether random points fall inside or outside an object and does not require a 3D reconstruction. This paper proposes volume measurement using a computer vision system for irregularly shaped food products without 3D reconstruction based on Monte Carlo method with heuristic adjustment. Five images of food product were captured using five cameras and processed to produce binary images. Monte Carlo integration with heuristic adjustment was performed to measure the volume based on the information extracted from binary images. The experimental results show that the proposed method provided high accuracy and precision compared to the water displacement method. In addition, the proposed method is more accurate and faster than the space carving method

Particle Swarm Optimization

Particle swarm optimization (PSO) is a population based stochastic optimization technique influenced by the social behavior of bird flocking or fish schooling.PSO shares many similarities with evolutionary computation techniques such as Genetic Algorithms (GA). The system is initialized with a population of random solutions and searches for optima by updating generations. However, unlike GA, PSO has no evolution operators such as crossover and mutation. In PSO, the potential solutions, called particles, fly through the problem space by following the current optimum particles. This book represents the contributions of the top researchers in this field and will serve as a valuable tool for professionals in this interdisciplinary field

Natural Fracture Evolution: Investigations into the Middle Devonian Marcellus Shale, Appalachian Basin, USA

Optimizing recovery from unconventional shale reservoirs has generated considerable research into optimal recovery methods through hydraulic fracturing design and shale reservoir characterization in the development of long-term hydrocarbon producers. Permeability at multiple scales from nanometer-scale pore sizes and nano-darcy permeability to completion-induced fractures defining a 100’s of meter stimulated reservoir volume plays a significant role in hydrocarbon flow during production in shale reservoirs. Preexisting cemented fractures in unconventional shale reservoirs are abundant and preferentially reactivate during induced hydraulic fracturing treatment to create necessary large-scale permeability. While previous investigations have significantly improved our knowledge of shale reservoirs, it has also highlighted the need for increased understanding of the geologic evolution and effect on hydraulic stimulation of pre-existing cemented fractures. This three-part dissertation examines natural fractures from four middle Devonian Marcellus Shale wells across the Appalachian basin through integration of visual core observation, thin section petrography, spectral gamma ray logs, borehole image logs, petrophysical logs, elemental data, and X-ray computed tomography cores. The research goals are: (1) to establish clues to assess natural fracture development in source rocks from kerogen maturation, relative timing, and hydrocarbon migration; (2) to investigate the relationship of natural fractures in wells of varying thermal maturity levels, and preferential fracture distribution in various clay types and redox environments; and (3) to characterize mineralized natural fractures in 3D using a medical CT-scan core to quantify volume and assess connectivity. This research indicates that overpressure from kerogen expulsion of hydrocarbon creates numerous cemented fractures filled with calcite and bitumen that achieve orientations related to the geologic burial stresses during their evolution, predominant in clay-rich units of certain redox conditions, cluster at geomechanical boundaries, and have inconsistent 3D volume changes within the core

Development of New Global Optimization Algorithms Using Stochastic Level Set Method with Application in: Topology Optimization, Path Planning and Image Processing

A unique mathematical tool is developed to deal with global optimization of a set of engineering problems. These include image processing, mechanical topology optimization, and optimal path planning in a variational framework, as well as some benchmark problems in parameter optimization. The optimization tool in these applications is based on the level set theory by which an evolving contour converges toward the optimum solution. Depending upon the application, the objective function is defined, and then the level set theory is used for optimization. Level set theory, as a member of active contour methods, is an extension of the steepest descent method in conventional parameter optimization to the variational framework. It intrinsically suffers from trapping in local solutions, a common drawback of gradient based optimization methods. In this thesis, methods are developed to deal with this drawbacks of the level set approach. By investigating the current global optimization methods, one can conclude that these methods usually cannot be extended to the variational framework; or if they can, the computational costs become drastically expensive. To cope with this complexity, a global optimization algorithm is first developed in parameter space and compared with the existing methods. This method is called "Spiral Bacterial Foraging Optimization" (SBFO) method because it is inspired by the aggregation process of a particular bacterium called, Dictyostelium Discoideum. Regardless of the real phenomenon behind the SBFO, it leads to new ideas in developing global optimization methods. According to these ideas, an effective global optimization method should have i) a stochastic operator, and/or ii) a multi-agent structure. These two properties are very common in the existing global optimization methods. To improve the computational time and costs, the algorithm may include gradient-based approaches to increase the convergence speed. This property is particularly available in SBFO and it is the basis on which SBFO can be extended to variational framework. To mitigate the computational costs of the algorithm, use of the gradient based approaches can be helpful. Therefore, SBFO as a multi-agent stochastic gradient based structure can be extended to multi-agent stochastic level set method. In three steps, the variational set up is formulated: i) A single stochastic level set method, called "Active Contours with Stochastic Fronts" (ACSF), ii) Multi-agent stochastic level set method (MSLSM), and iii) Stochastic level set method without gradient such as E-ARC algorithm. For image processing applications, the first two steps have been implemented and show significant improvement in the results. As expected, a multi agent structure is more accurate in terms of ability to find the global solution but it is much more computationally expensive. According to the results, if one uses an initial level set with enough holes in its topology, a single stochastic level set method can achieve almost the same level of accuracy as a multi-agent structure can obtain. Therefore, for a topology optimization problem for which a high level of calculations (at each iteration a finite element model should be solved) is required, only ACSF with initial guess with multiple holes is implemented. In some applications, such as optimal path planning, objective functions are usually very complicated; finding a closed-form equation for the objective function and its gradient is therefore impossible or sometimes very computationally expensive. In these situations, the level set theory and its extensions cannot be directly employed. As a result, the Evolving Arc algorithm that is inspired by "Electric Arc" in nature, is proposed. The results show that it can be a good solution for either unconstrained or constrained problems. Finally, a rigorous convergence analysis for SBFO and ACSF is presented that is new amongst global optimization methods in both parameter and variational framework

Emergence of self-organized amoeboid movement in a multi-agent approximation of Physarum polycephalum

The giant single-celled slime mould Physarum polycephalum exhibits complex morphological adaptation and amoeboid movement as it forages for food and may be seen as a minimal example of complex robotic behaviour. Swarm computation has previously been used to explore how spatio-temporal complexity can emerge from, and be distributed within, simple component parts and their interactions. Using a particle-based swarm approach we explore the question of how to generate collective amoeboid movement from simple non-oscillatory component parts in a model of P. polycephalum. The model collective behaves as a cohesive and deformable virtual material, approximating the local coupling within the plasmodium matrix. The collective generates de-novo and complex oscillatory patterns from simple local interactions. The origin of this motor behaviour distributed within the collective rendering is morphologically adaptive, amenable to external influence and robust to simulated environmental insult. We show how to gain external influence over the collective movement by simulated chemo-attraction (pulling towards nutrient stimuli) and simulated light irradiation hazards (pushing from stimuli). The amorphous and distributed properties of the collective are demonstrated by cleaving it into two independent entities and fusing two separate entities to form a single device, thus enabling it to traverse narrow, separate or tortuous paths. We conclude by summarizing the contribution of the model to swarm-based robotics and soft-bodied modular robotics and discuss the future potential of such material approaches to the field. © 2012 IOP Publishing Ltd

Advanced Knowledge Application in Practice

The integration and interdependency of the world economy leads towards the creation of a global market that offers more opportunities, but is also more complex and competitive than ever before. Therefore widespread research activity is necessary if one is to remain successful on the market. This book is the result of research and development activities from a number of researchers worldwide, covering concrete fields of research

A Comprehensive Review of Bio-Inspired Optimization Algorithms Including Applications in Microelectronics and Nanophotonics

The application of artificial intelligence in everyday life is becoming all-pervasive and unavoidable. Within that vast field, a special place belongs to biomimetic/bio-inspired algorithms for multiparameter optimization, which find their use in a large number of areas. Novel methods and advances are being published at an accelerated pace. Because of that, in spite of the fact that there are a lot of surveys and reviews in the field, they quickly become dated. Thus, it is of importance to keep pace with the current developments. In this review, we first consider a possible classification of bio-inspired multiparameter optimization methods because papers dedicated to that area are relatively scarce and often contradictory. We proceed by describing in some detail some more prominent approaches, as well as those most recently published. Finally, we consider the use of biomimetic algorithms in two related wide fields, namely microelectronics (including circuit design optimization) and nanophotonics (including inverse design of structures such as photonic crystals, nanoplasmonic configurations and metamaterials). We attempted to keep this broad survey self-contained so it can be of use not only to scholars in the related fields, but also to all those interested in the latest developments in this attractive area

A Comprehensive Survey on Particle Swarm Optimization Algorithm and Its Applications

Particle swarm optimization (PSO) is a heuristic global optimization method, proposed originally by Kennedy and Eberhart in 1995. It is now one of the most commonly used optimization techniques. This survey presented a comprehensive investigation of PSO. On one hand, we provided advances with PSO, including its modifications (including quantum-behaved PSO, bare-bones PSO, chaotic PSO, and fuzzy PSO), population topology (as fully connected, von Neumann, ring, star, random, etc.), hybridization (with genetic algorithm, simulated annealing, Tabu search, artificial immune system, ant colony algorithm, artificial bee colony, differential evolution, harmonic search, and biogeography-based optimization), extensions (to multiobjective, constrained, discrete, and binary optimization), theoretical analysis (parameter selection and tuning, and convergence analysis), and parallel implementation (in multicore, multiprocessor, GPU, and cloud computing forms). On the other hand, we offered a survey on applications of PSO to the following eight fields: electrical and electronic engineering, automation control systems, communication theory, operations research, mechanical engineering, fuel and energy, medicine, chemistry, and biology. It is hoped that this survey would be beneficial for the researchers studying PSO algorithms