Cheetah:a computational toolkit for cybergenetic control

Abstract Advances in microscopy, microfluidics, and optogenetics enable single-cell monitoring and environmental regulation and offer the means to control cellular phenotypes. The development of such systems is challenging and often results in bespoke setups that hinder reproducibility. To address this, we introduce Cheetah, a flexible computational toolkit that simplifies the integration of real-time microscopy analysis with algorithms for cellular control. Central to the platform is an image segmentation system based on the versatile U-Net convolutional neural network. This is supplemented with functionality to robustly count, characterize, and control cells over time. We demonstrate Cheetah’s core capabilities by analyzing long-term bacterial and mammalian cell growth and by dynamically controlling protein expression in mammalian cells. In all cases, Cheetah’s segmentation accuracy exceeds that of a commonly used thresholding-based method, allowing for more accurate control signals to be generated. Availability of this easy-to-use platform will make control engineering techniques more accessible and offer new ways to probe and manipulate living cells

VIDEO FOREGROUND LOCALIZATION FROM TRADITIONAL METHODS TO DEEP LEARNING

These days, detection of Visual Attention Regions (VAR), such as moving objects has become an integral part of many Computer Vision applications, viz. pattern recognition, object detection and classification, video surveillance, autonomous driving, human-machine interaction (HMI), and so forth. The moving object identification using bounding boxes has matured to the level of localizing the objects along their rigid borders and the process is called foreground localization (FGL). Over the decades, many image segmentation methodologies have been well studied, devised, and extended to suit the video FGL. Despite that, still, the problem of video foreground (FG) segmentation remains an intriguing task yet appealing due to its ill-posed nature and myriad of applications. Maintaining spatial and temporal coherence, particularly at object boundaries, persists challenging, and computationally burdensome. It even gets harder when the background possesses dynamic nature, like swaying tree branches or shimmering water body, and illumination variations, shadows cast by the moving objects, or when the video sequences have jittery frames caused by vibrating or unstable camera mounts on a surveillance post or moving robot. At the same time, in the analysis of traffic flow or human activity, the performance of an intelligent system substantially depends on its robustness of localizing the VAR, i.e., the FG. To this end, the natural question arises as what is the best way to deal with these challenges? Thus, the goal of this thesis is to investigate plausible real-time performant implementations from traditional approaches to modern-day deep learning (DL) models for FGL that can be applicable to many video content-aware applications (VCAA). It focuses mainly on improving existing methodologies through harnessing multimodal spatial and temporal cues for a delineated FGL. The first part of the dissertation is dedicated for enhancing conventional sample-based and Gaussian mixture model (GMM)-based video FGL using probability mass function (PMF), temporal median filtering, and fusing CIEDE2000 color similarity, color distortion, and illumination measures, and picking an appropriate adaptive threshold to extract the FG pixels. The subjective and objective evaluations are done to show the improvements over a number of similar conventional methods. The second part of the thesis focuses on exploiting and improving deep convolutional neural networks (DCNN) for the problem as mentioned earlier. Consequently, three models akin to encoder-decoder (EnDec) network are implemented with various innovative strategies to improve the quality of the FG segmentation. The strategies are not limited to double encoding - slow decoding feature learning, multi-view receptive field feature fusion, and incorporating spatiotemporal cues through long-shortterm memory (LSTM) units both in the subsampling and upsampling subnetworks. Experimental studies are carried out thoroughly on all conditions from baselines to challenging video sequences to prove the effectiveness of the proposed DCNNs. The analysis demonstrates that the architectural efficiency over other methods while quantitative and qualitative experiments show the competitive performance of the proposed models compared to the state-of-the-art

ReSCon '12, Research Student Conference: Book of Abstracts

The fifth SED Research Student Conference (ReSCon2012) was hosted over three days, 18-20 June 2012, in the Hamilton Centre at Brunel University. The conference consisted of 130 oral and 70 poster presentations, based on the high quality and diverse research being conducted within the School of Engineering and Design by postgraduate research students. The conference is held annually, and ReSCon plays a key role in contributing to research and innovations within the School

MATLAB

A well-known statement says that the PID controller is the "bread and butter" of the control engineer. This is indeed true, from a scientific standpoint. However, nowadays, in the era of computer science, when the paper and pencil have been replaced by the keyboard and the display of computers, one may equally say that MATLAB is the "bread" in the above statement. MATLAB has became a de facto tool for the modern system engineer. This book is written for both engineering students, as well as for practicing engineers. The wide range of applications in which MATLAB is the working framework, shows that it is a powerful, comprehensive and easy-to-use environment for performing technical computations. The book includes various excellent applications in which MATLAB is employed: from pure algebraic computations to data acquisition in real-life experiments, from control strategies to image processing algorithms, from graphical user interface design for educational purposes to Simulink embedded systems

A "Do-It-Yourself" phenotyping system:measuring growth and morphology throughout the diel cycle in rosette shaped plants

Abstract Background Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here we present a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle. Results We constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry Pi NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. Our software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate our system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 min throughout the 24 h light–dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. Conclusion Our methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments

Entropy-based framework for combinatorial optimization problems and enabling the grid of the future

This thesis is divided into two parts. In the first part, I describe efficient meta-heuristic algorithms for a series of combinatorially complex optimization problems, while the second part is concerned with robust and scalable control architecture for a network of paralleled converter/inverter systems (DC/AC microgrids). Combinatorial optimization problems arise in many applications in various forms in seemingly unrelated areas such as data compression, pattern recognition, image segmentation, resource allocation, routing, and scheduling, graph aggregation, and graph partition problems. These optimization problems are characterized by a combinatorial number of configurations, where a cost value can be assigned to each configuration, and the goal is to find the configuration that minimizes the cost. Moreover, these optimization problems are largely non-convex, computationally complex and suffer from multiple local minima that riddle the cost surface. Most heuristics to these optimization problems are very sensitive to initial guess solutions, and efforts to make them robust to initializations typically come at significant computational costs such that the algorithms lose practicality in many applications. In our work, we are motivated by solutions that are employed by nature to similar combinatorial optimization problems; well described in terms of laws such as maximum entropy principle (MEP) in statistical physics literature. We propose to use MEP in solving a variety of combinatorial optimization problems. Our main current contributions are threefold - (i) First we provide a clustering or resource allocation viewpoint to several combinatorial optimization problems: (a) data clustering, (b) graph partitioning (such as clustering of power networks), (c) traveling salesman problem (TSP) and its variants, and (d) hard problems on graphs, such as multiway $k$-cut. This viewpoint enables a unified approach to handle a broad class of problems, and therefore efficient MEP based heuristics can be leveraged to obtain high-quality solutions. (ii) Second, we explore MEP based ideas to clustering problems specified by pairwise distances. Many problems in graph theory are indeed specified in terms of the corresponding edge-weight matrices (and not in terms of the nodal locational coordinates). (iii) Finally, our framework allows for inclusion of several constraints in the clustering/resource allocation problems. These constraints may correspond to capacity constraints in case of resource allocations where capacity of each resource is limited, or minimum-tour length constraints in case of traveling salesman problems (TSPs) and its variants. In the second part of this thesis, we describe a novel distributed, robust and optimal control architecture for both DC as well as AC microgrids. Microgrids are grid systems that allow integration of local power sources, such as photovoltaics (PVs), wind, battery and other distributed energy resources (DERs) with local loads connected at the DC-link or the point of common coupling (PCC). Microgrids are hypothesized as viable alternatives to the traditional electric grid. In a microgrid, the main goals of the control design are to regulate voltage and frequency at the PCC and ensuring a prescribed sharing of power among different sources; for instance, economic considerations can dictate that power provided by the sources should be in a certain proportion or according to a prescribed priority. The main challenges arise from the uncertainties in the size and the schedules of loads, the complexity of a coupled multi-converter network, the uncertainties in the model parameters at each converter, and the adverse effects of interfacing DC power sources with AC loads, such as the $120$Hz ripple that must be provided by the DC sources. A systematic control design that addresses all the challenges and objectives for the multi-converter/inverter control is still lacking in the existing literature. The main contribution of the control architecture proposed by us is its capability to addresses all the primary objectives - a) voltage and frequency regulation at the PCC with guaranteed robustness margins, b) prescribed time-varying power sharing in a network of parallel converters, c) controlling the tradeoff between 120Hz ripple on the total current provided by the power sources and the ripple on the DC-link voltage. An important contribution of our work is that our control architecture allows for closed-loop analysis and robust control synthesis for the entire grid network. We introduce a structure in the control architecture, whereby, we show that analysis of the entire multi-component microgrid can be simplified to that of an equivalent {\em single-component} system. Besides analysis, this simplification facilitates using robust and optimal control tools for achieving multiple objectives simultaneously; in contrast in existing architectures, closed-loop analysis for entire networks is typically difficult, and posing optimal control and robustness objectives for the entire network practically untenable

Summer 2011 Research Symposium Abstract Book

Summer 2011 volume of abstracts for science research projects conducted by Trinity College students

Optimisation of Mobile Communication Networks - OMCO NET

The mini conference “Optimisation of Mobile Communication Networks” focuses on advanced methods for search and optimisation applied to wireless communication networks. It is sponsored by Research & Enterprise Fund Southampton Solent University. The conference strives to widen knowledge on advanced search methods capable of optimisation of wireless communications networks. The aim is to provide a forum for exchange of recent knowledge, new ideas and trends in this progressive and challenging area. The conference will popularise new successful approaches on resolving hard tasks such as minimisation of transmit power, cooperative and optimal routing