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

Leveraging Microtechnology to Study Multicellular Microvascular Systems and Macromolecular Interaction

Biological systems are large-scale, complex systems comprised of many hierarchical subsystems interacting physico-chemically in a dynamic and coordinated fashion. The complex interactions of subsystems (in micro-scale) lead to the formation of emergent properties (in macro-scale); these are properties that are not visible if individual subsystems are studied. The inherent high-throughput characteristics of microfabrication technology (microtechnology) along with its ability to manipulate biological species at the micro-scale makes it an ideal tool to elucidate the mechanisms leading to the formation of emergent properties at the macro-scale. In this dissertation, by combining microtechnologies with advanced computational algorithms, we demonstrate system-level analysis of biological systems in development and disease. The abundance of high quality molecular and genetic data along with the drastic increase in computational power resulted in considerable progress in genomics, epigenomics and proteomics, but not for the so-called cellomics as we define it here: high-throughput study of single-cell phenotype and heterotypic cell-cell interaction via micromanipulation and bioinformatics analysis. Lack of high-throughput robust experimental tools is the major roadblock to cellomics. Using microtechnologies, in the context of developmental biology we studied vascular tissue morphogenesis (vasculogenesis). Formation of microvessels is of critical significance in development and for vascularizing newly engineered tissues in regenerative medicine. First, we sought to map the heterogeneous morphodynamic behavior of individual clonal cells in the process of capillary-like structure (CLS) formation (Chapter 2 and 3). Then we looked into deciphering the role of extracellular matrix (ECM) mediated mechanical signals in deriving the process of CLS formation (Chapter 4). In the second half of this thesis, we demonstrated the capabilities of microtechnologies and advanced computational algorithms in tackling the challenging problems in disease: global health diagnostics and cancer drug screening. First, we studied the performance of microfluidic-based diagnostic as a large-scale complex system under real-world constraints (Chapter 5). Then, we present the development of two microfluidic-based platforms to study the heterotypic interaction of cells in both a biomimetic in vitro and a realistic in vivo setting. We developed an implantable construct carrying a densely-packed heterogeneous panel of tumor cells. This platform could ultimately be used to test anti-cancer drug efficacy against a large number of genotypes in an in vivo setting (Appendices A and B). Together, these methods provide a powerful suite of tools for high-throughput analysis of biological species at the micro-scale and could potentially unlock the mysteries behind the emergent properties observed at the macro-scale

HyperCell

This research believes that understanding the relationship between Interactive Architecture and the principles of biology will become a mainstream research area in future architectural design. Aiming towards achieving the goal of “making architecture as organic bodies”, almost all the current digital techniques in architectural design are executed using computational simulation: digital fabrication technologies and physical computing. Based on its’ main biological inspirations, Evolutionary Development Biology (Evo-Devo), this research intends to propose a novel bio-inspired design thinking wherein architecture should become analogs to the growing process of living organisms (Figure 6.1). Instead of being born from static optimization results most of the architecture seems content at aiming for nowadays, this research is looking towards designing dynamic architectural bodies which can adapt to the constantly changing environments and are thus seeking optimization in real-time. In other words, architecture should come “alive” as a living creature in order to actively optimize itself with respect to dynamic environmental conditions and user behavior’ requirements in real-time. Following the notion of “architecture as organic bodies”, six major topics were derived from the publication of “New Wombs: Electric Bodies and Architectural Disorders” (Palumbo, 2000). These topics are aimed at initiating critical discussions between body and space, which, are used here to re-interpret six main traits of being an interactive architecture: Dis-measurement, Uprooting, Fluidity, Visceral Nature, Virtuality, and Sensitivity. These six topics merge diverse key points from aforementioned chapters including outlining the vision of active interacting architecture, the transformation of human bodies under digital culture, the profound biological inspiration from Evo-Devo and the fundamental componential notion of swarm, which leads to the ultimate notion of embodying organic body-like interactive Bio-architecture. Dis-measurement: Acknowledging the premise of “architecture (technology) as an extension of human bodies” proposed by Marshall McLuhan (McLuhan, Understanding Media: The Extensions of Man, 1964), it is, still difficult to explicitly define the boundary of a space, especially in the context of a borderless cyberspace (the Internet). Space in such a context expands more than ever before and thus makes traditional measurements techniques unfeasible. With cyberspace, people can be virtually present in different places at the same time, thus breaking existing physical boundaries of a space. From another point of view, space as an extension of our bodies constantly adapting to environmental conditions and user demands, creates an intimate linkage between physical bodies and spatial bodies. Interaction in such instances can be seen from a micro-scale: between biological cells and intelligent architectural components to the macro-scale: between physical organic bodies and spatial bodies/architectural space. Uprooting: Apart from further extending the “Dis-measurement” idea by directly plugging into cyberspace (the Internet), “Uprooting” is also interpreted as adaptation devoid of any site/location constraints. In other words, the idea of “Uprooting” implies, generating an architecture that can adjust/modify in accordance with its existing surroundings by interactions between its smallest intelligent components like cells in a body searching for dynamic equilibrium. In this case, architecture has no particular reason to be designed as “rooted” on sites. Fluidity: With the neural system inside the body, most of the messages can be transmitted, received and sent within less than a millionth of a second. To envision architecture as an information processor, which has abilities to react to dynamic environmental conditions and user demands, efficient information protocols must be built into such an organic architectural body to create seamless exterior/interior transformations. Visceral Nature: Visceral can be interpreted in the form of an embodied organ. This implies envisioning architecture in the form of a living-entity. It is no longer the case of mimicking a natural form and thus claiming a building to be organic, but rather instigates one to look deeper into the principles of a natural form’s morphogenesis and apply these to generate a truly organic space. Through the study of Evo-Devo, several principles will be applied to generate an interactive organic Bio-architecture. It is thus not an organic looking shape that matters, but the principles behind the shape, which matter. For instance, principles of self-organization, self-assembly, and self-adaptation, providing possibilities of making body-like architectures with multi-directional and multi-modal communications both inside out and outside in. An intelligent architecture, should “live” in the environment just as how the body lives with its’ Visceral Nature. Virtuality: It is impossible to talk about physical space without mentioning virtual space nowadays. From cyberspace, augmented reality to virtual reality, “Virtuality” is related to “interaction” since the beginning and has gradually become an inevitable aspect of our daily lives. In fact, virtual space has to still use constraints from the physical world to enhance experiential aspects. The ultimate goal of virtual reality here is not to end up with a VR helmet and keep constantly being stimulated by electronic messages, but to bring the physical to the virtual and in the process, attempt to search for a dynamic balance between the virtual and real by merging them together. With the assistance of virtual reality, novel unrealistic space can still be realized into creative tangible immersive and fascinating spaces, which, earlier was not possible. Sensitivity: The notion of “architecture is an extension of human bodies”, is crucial to embrace, if we consider enhancing the sensing abilities of the space as a body not only externally but also internally. In a digital space, active sensing can be achieved by attaching specific devices. In an interactive space, like an organic body, the sensing capabilities of the space have to be fast, accurate, intuitive, and predictive. The sensing system should thus not only work externally to sense the surrounding environment but also internally in order to fulfill the users’ demands in time. With such a connection between human bodies and spatial bodies, it should become relatively understandable for the space to know the requirements of the users by means of hand gestures instead of verbal cues. The sensitivity, in this case, should rely on local information distribution as a bottom-up system rather than a top-down centralized demanding structure

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Proceedings of the 2021 DigitalFUTURES

This open access book is a compilation of selected papers from 2021 DigitalFUTURES—The 3rd International Conference on Computational Design and Robotic Fabrication (CDRF 2021). The work focuses on novel techniques for computational design and robotic fabrication. The contents make valuable contributions to academic researchers, designers, and engineers in the industry. As well, readers encounter new ideas about understanding material intelligence in architecture

Proceedings of the 9th Conference on Autonomous Robot Systems and Competitions

Welcome to ROBOTICA 2009. This is the 9th edition of the conference on Autonomous Robot Systems and Competitions, the third time with IEEE‐Robotics and Automation Society Technical Co‐Sponsorship. Previous editions were held since 2001 in Guimarães, Aveiro, Porto, Lisboa, Coimbra and Algarve. ROBOTICA 2009 is held on the 7th May, 2009, in Castelo Branco , Portugal. ROBOTICA has received 32 paper submissions, from 10 countries, in South America, Asia and Europe. To evaluate each submission, three reviews by paper were performed by the international program committee. 23 papers were published in the proceedings and presented at the conference. Of these, 14 papers were selected for oral presentation and 9 papers were selected for poster presentation. The global acceptance ratio was 72%. After the conference, eighth papers will be published in the Portuguese journal Robótica, and the best student paper will be published in IEEE Multidisciplinary Engineering Education Magazine. Three prizes will be awarded in the conference for: the best conference paper, the best student paper and the best presentation. The last two, sponsored by the IEEE Education Society ‐ Student Activities Committee. We would like to express our thanks to all participants. First of all to the authors, whose quality work is the essence of this conference. Next, to all the members of the international program committee and reviewers, who helped us with their expertise and valuable time. We would also like to deeply thank the invited speaker, Jean Paul Laumond, LAAS‐CNRS France, for their excellent contribution in the field of humanoid robots. Finally, a word of appreciation for the hard work of the secretariat and volunteers. Our deep gratitude goes to the Scientific Organisations that kindly agreed to sponsor the Conference, and made it come true. We look forward to seeing more results of R&D work on Robotics at ROBOTICA 2010, somewhere in Portugal

HyperCell: A Bio-inspired Design Framework for Real-time Interactive Architectures

This pioneering research focuses on Biomimetic Interactive Architecture using “Computation”, “Embodiment”, and “Biology” to generate an intimate embodied convergence to propose a novel rule-based design framework for creating organic architectures composed of swarm-based intelligent components. Furthermore, the research boldly claims that Interactive Architecture should emerge as the next truly Organic Architecture. As the world and society are dynamically changing, especially in this digital era, the research dares to challenge the Utilitas, Firmitas, and Venustas of the traditional architectural Weltanschauung, and rejects them by adopting the novel notion that architecture should be dynamic, fluid, and interactive. This project reflects a trajectory from the 1960’s with the advent of the avant-garde architectural design group, Archigram, and its numerous intriguing and pioneering visionary projects. Archigram’s non-standard, mobile, and interactive projects profoundly influenced a new generation of architects to explore the connection between technology and their architectural projects. This research continues this trend of exploring novel design thinking and the framework of Interactive Architecture by discovering the interrelationship amongst three major topics: “Computation”, “Embodiment”, and “Biology”. The project aims to elucidate pioneering research combining these three topics in one discourse: “Bio-inspired digital architectural design”. These three major topics will be introduced in this Summary.   “Computation”, is any type of calculation that includes both arithmetical and nonarithmetical steps and follows a well-defined model understood and described as, for example, an algorithm. But, in this research, refers to the use of data storage, parametric design application, and physical computing for developing informed architectural designs. “Form” has always been the most critical focus in architectural design, and this focus has also been a major driver behind the application computational design in Architecture. Nonetheless, this research will interpret the term “Form” in architecture as a continual “information processor” rather than the result of information processing. In other words, “Form” should not be perceived only as an expressive appearance based computational outcome but rather as a real-time process of information processing, akin to organic “Formation”. Architecture embodying kinetic ability for adjusting or changing its shape with the ability to process the surroundings and feedback in accordance with its free will with an inherent interactive intelligent movement of a living body. Additionally, it is also crucial to address the question of whether computational technologies are being properly harnessed, if they are only used for form-generating purposes in architecture design, or should this be replaced with real-time information communication and control systems to produce interactive architectures, with embodied computation abilities?   “Embodiment” in the context of this research is embedded in Umberto Eco’s vision on Semiotics, theories underlying media studies in Marshall McLuhan’s “Body Extension” (McLuhan, 1964), the contemporary philosophical thought of “Body Without Organs” (Gilles Deleuze and Félix Guattari, 1983), the computational Logic of ‘Swarm Behavior’ and the philosophical notion of “Monadology” proposed by Gottfried Leibniz (Leibniz, 1714). Embodied computation and design are predominant today within the wearable computing and smart living domains, which combine Virtual and Real worlds. Technical progress and prowess in VR development also contribute to advancing 3D smart architectural design and display solutions. The proposed ‘Organic body-like architectural spaces’ emphasize upon the realization of a body-like interactive space. Developing Interactive Architecture will imply eliciting the collective intelligence prevalent in nature and the virtual world of Big Data. Interactive Architecture shall thus embody integrated Information exchange protocols and decision-making systems in order to possess organic body-like qualities.   “Biology”, in this research explores biomimetic principles intended to create purposedriven kinetic and organic architecture. This involves a detailed study/critique of organic architecture, generating organic shapes, performance optimization based digital fabrication techniques and kinetic systems. A holistic bio-inspired architecture embodies multiple performance criteria akin to natural systems, which integrate structural, infrastructure performances throughout the growth of an organic body. Such a natural morphogenesis process of architectural design explores what Janine M. Benyus described as “learning the natural process”. Profoundly influenced by the processes behind morphogenesis, the research further explores Evolutionary Development Biology (Evo-Devo) explaining how embryological regulation strongly affect the resulting formations. Evo-Devo in interactive architecture implies the development of architecture based on three fundamental principles: “Simple to Complex”, “Geometric Information Distribution”, and “On/Off Switch and Trigger.” The research seeks to create a relatively intelligent architectural body, and the tactile interactive spatial environment by applying the extracted knowledge from the study of the aforementioned principles of Evo-Devo in the following fashion: A. Extract a Self-Similar Componential System based approach from the “Simple to Complex” principle of Evo-Devo B. Extract the idea of “Collective Intelligence” from “Geometric information Distribution” principle of Evo-Devo C. Extract the principle of “Assembly Regulation” from “On/Off switch and trigger” principle of Evo-Devo The “HyperCell” research, through an elaborate investigation on the three aforementioned topics, develops a design framework for developing real-time adaptive spatial systems. HyperCell does this, by developing a system of transformable cubic elements which can self-organize, adapt and interact in real-time. These Hypercells shall comprise an organic space which can adjust itself in relation to our human bodies. The furniture system is literally reified and embodied to develop an intra-active space that proactively provokes human movement. The space thus acquires an emotive dimension and can become your pet, partner, or even friend, and might also involve multiple usabilities of the same space. The research and its progression were also had actively connected with a 5-year collaborative European Culture project: “MetaBody”. The research thus involves exploration of Interactive Architecture from the following perspectives: architectural design, digital architectural history trajectory, computational technology, philosophical discourse related to the embodiment, media and digital culture, current VR and body-related technology, and Evolutionary Developmental Biology. “HyperCell” will encourage young architects to pursue interdisciplinary design initiatives via the fusion of computational design, embodiment, and biology for developing bio-inspired organic architectures