Image Processing and Simulation Toolboxes of Microscopy Images of Bacterial Cells

Recent advances in microscopy imaging technology have allowed the characterization of the dynamics of cellular processes at the single-cell and single-molecule level. Particularly in bacterial cell studies, and using the E. coli as a case study, these techniques have been used to detect and track internal cell structures such as the Nucleoid and the Cell Wall and fluorescently tagged molecular aggregates such as FtsZ proteins, Min system proteins, inclusion bodies and all the different types of RNA molecules. These studies have been performed with using multi-modal, multi-process, time-lapse microscopy, producing both morphological and functional images. To facilitate the finding of relationships between cellular processes, from small-scale, such as gene expression, to large-scale, such as cell division, an image processing toolbox was implemented with several automatic and/or manual features such as, cell segmentation and tracking, intra-modal and intra-modal image registration, as well as the detection, counting and characterization of several cellular components. Two segmentation algorithms of cellular component were implemented, the first one based on the Gaussian Distribution and the second based on Thresholding and morphological structuring functions. These algorithms were used to perform the segmentation of Nucleoids and to identify the different stages of FtsZ Ring formation (allied with the use of machine learning algorithms), which allowed to understand how the temperature influences the physical properties of the Nucleoid and correlated those properties with the exclusion of protein aggregates from the center of the cell. Another study used the segmentation algorithms to study how the temperature affects the formation of the FtsZ Ring. The validation of the developed image processing methods and techniques has been based on benchmark databases manually produced and curated by experts. When dealing with thousands of cells and hundreds of images, these manually generated datasets can become the biggest cost in a research project. To expedite these studies in terms of time and lower the cost of the manual labour, an image simulation was implemented to generate realistic artificial images. The proposed image simulation toolbox can generate biologically inspired objects that mimic the spatial and temporal organization of bacterial cells and their processes, such as cell growth and division and cell motility, and cell morphology (shape, size and cluster organization). The image simulation toolbox was shown to be useful in the validation of three cell tracking algorithms: Simple Nearest-Neighbour, Nearest-Neighbour with Morphology and DBSCAN cluster identification algorithm. It was shown that the Simple Nearest-Neighbour still performed with great reliability when simulating objects with small velocities, while the other algorithms performed better for higher velocities and when there were larger clusters present

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

Introduction to Facial Micro Expressions Analysis Using Color and Depth Images: A Matlab Coding Approach (Second Edition, 2023)

The book attempts to introduce a gentle introduction to the field of Facial Micro Expressions Recognition (FMER) using Color and Depth images, with the aid of MATLAB programming environment. FMER is a subset of image processing and it is a multidisciplinary topic to analysis. So, it requires familiarity with other topics of Artifactual Intelligence (AI) such as machine learning, digital image processing, psychology and more. So, it is a great opportunity to write a book which covers all of these topics for beginner to professional readers in the field of AI and even without having background of AI. Our goal is to provide a standalone introduction in the field of MFER analysis in the form of theorical descriptions for readers with no background in image processing with reproducible Matlab practical examples. Also, we describe any basic definitions for FMER analysis and MATLAB library which is used in the text, that helps final reader to apply the experiments in the real-world applications. We believe that this book is suitable for students, researchers, and professionals alike, who need to develop practical skills, along with a basic understanding of the field. We expect that, after reading this book, the reader feels comfortable with different key stages such as color and depth image processing, color and depth image representation, classification, machine learning, facial micro-expressions recognition, feature extraction and dimensionality reduction. The book attempts to introduce a gentle introduction to the field of Facial Micro Expressions Recognition (FMER) using Color and Depth images, with the aid of MATLAB programming environment.Comment: This is the second edition of the boo

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 Framework for Vision-based Static Hand Gesture Recognition

In today’s technical world, the intellectual computing of a efficient human-computer interaction (HCI) or human alternative and augmentative communication (HAAC) is essential in our lives. Hand gesture recognition is one of the most important techniques that can be used to build up a gesture based interface system for HCI or HAAC application. Therefore, suitable development of gesture recognition method is necessary to design advance hand gesture recognition system for successful applications like robotics, assistive systems, sign language communication, virtual reality etc. However, the variation of illumination, rotation, position and size of gesture images, efficient feature representation, and classification are the main challenges towards the development of a real time gesture recognition system. The aim of this work is to develop a framework for vision based static hand gesture recognition which overcomes the challenges of illumination, rotation, size and position variation of the gesture images. In general, a framework for gesture recognition system which consists of preprocessing, feature extraction, feature selection, and classification stages is developed in this thesis work. The preprocessing stage involves the following sub-stages: image enhancement which enhances the image by compensating illumination variation; segmentation, which segments hand region from its background image and transforms it into binary silhouette; image rotation that makes the segmented gesture as rotation invariant; filtering that effectively removes background noise and object noise from binary image and provides a well defined segmented hand gesture. This work proposes an image rotation technique by coinciding the first principal component of the segmented hand gesture with vertical axes to make it as rotation invariant. In the feature extraction stage, this work extracts xi localized contour sequence (LCS) and block based features, and proposes a combined feature set by appending LCS features with block-based features to represent static hand gesture images. A discrete wavelets transform (DWT) and Fisher ratio (F-ratio) based feature set is also proposed for better representation of static hand gesture image. To extract this feature set, DWT is applied on resized and enhanced grayscale image and then the important DWT coefficient matrices are selected as features using proposed F-ratio based coefficient matrices selection technique. In sequel, a modified radial basis function neural network (RBF-NN) classifier based on k-mean and least mean square (LMS) algorithms is proposed in this work. In the proposed RBF-NN classifier, the centers are automatically selected using k-means algorithm and estimated weight matrix is updated utilizing LMS algorithm for better recognition of hand gesture images. A sigmoidal activation function based RBF-NN classifier is also proposed here for further improvement of recognition performance. The activation function of the proposed RBF-NN classifier is formed using a set of composite sigmoidal functions. Finally, the extracted features are applied as input to the classifier to recognize the class of static hand gesture images. Subsequently, a feature vector optimization technique based on genetic algorithm (GA) is also proposed to remove the redundant and irrelevant features. The proposed algorithms are tested on three static hand gesture databases which include grayscale images with uniform background (Database I and Database II) and color images with non-uniform background (Database III). Database I is a repository database which consists of hand gesture images of 25 Danish/international sign language (D/ISL) hand alphabets. Database II and III are indigenously developed using VGA Logitech Webcam (C120) with 24 American Sign Language (ASL) hand alphabets