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Publication Metadata only A Variational Joint Segmentation and Registration Framework for Multimodal Images(Springer, 2020) Ademaj, Adela; Rada, Lavdie; Ibrahim, Mazlinda; Chen, Ke; Zheng, Y.; Williams, B.M.; Chen, K.; Ademaj, Adela, Department of Biomedical Engineering, Universität Heidelberg, Heidelberg, Germany; Rada, Lavdie, Department of Biomedical Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Ibrahim, Mazlinda, National Defense University of Malaysia, Kuala Lumpur, Malaysia; Chen, Ke, Centre for Mathematical Imaging Techniques and Department of Mathematical Sciences, University of Liverpool, Liverpool, United KingdomImage segmentation and registration are closely related image processing techniques and often required as simultaneous tasks. In this work, we introduce an optimization-based approach to a joint registration and segmentation model for multimodal images deformation. The model combines an active contour variational term with a mutual information smoothing fitting term and solves in this way the difficulties of simultaneously performed segmentation and registration models for multimodal images. This combination takes into account the image structure boundaries and the movement of the objects, leading in this way to a robust dynamic scheme that links the object boundaries information that changes over time. Comparison of our model with state of art shows that our method leads to more consistent registrations and accurate results. © 2020 Elsevier B.V., All rights reserved.Publication Metadata only Quantifying the grounding probability in narrow waterways(CRC Press/Balkema, 2020) Özlem, Şirin; Altan, Yigit C.; Otay, Emre N.; Or, İlhan; Soares, C.G.; Özlem, Şirin, MEF University, Istanbul, Turkey; Altan, Yigit C., Bahçeşehir Üniversitesi, Istanbul, Turkey; Otay, Emre N., Boğaziçi Üniversitesi, Bebek, Turkey; Or, İlhan, Boğaziçi Üniversitesi, Bebek, TurkeyThe aim of this paper is to estimate the grounding probability of vessels while navigating in narrow waterways. In this study, the grounding probability is modelled as a combination the geometric probability, defined as vessel being on a grounding course and the causation probability, defined as the probability that the vessel is unable to avoid a grounding while being on a grounding course. A mathematical model is developed to estimate the geometric probability where the causation probability is estimated through a specially designed Bayesian network. The Strait of Istanbul, one of the narrowest waterways in the world, is used as a test case. The resulting grounding and ramming accidents are 2.8 times the ship collisions. The most critical causes of grounding accidents are the machine failure, steering inadequacy and lack of pilot support, respectively. With different input parameters, the proposed approach may be applied to other narrow waterways. © 2020 Elsevier B.V., All rights reserved.Publication Metadata only Label-free imaging of exosomes using depth scanning correlation (DSC) interferometric microscopy(SPIE spie@spie.org, 2020) Aygün, Ugur; Yalcin Ozkumur, Ayca; Durmuş, Naside Gozde; Demirci, Utkan; Ürey, Hakan; Shaked, N.T.; Hayden, O.; Aygün, Ugur, Department of Electrical and Electronic Engineering, Koç Üniversitesi, Istanbul, Turkey, Research Center for Translational Medicine, Koç Üniversitesi, Istanbul, Turkey; Yalcin Ozkumur, Ayca, Department of Electrical and Electronic Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey, Boston University College of Engineering, Boston, United States; Durmuş, Naside Gozde, Stanford University, Stanford, United States; Demirci, Utkan, Stanford University, Stanford, United States; Ürey, Hakan, Department of Electrical and Electronic Engineering, Koç Üniversitesi, Istanbul, Turkey, Research Center for Translational Medicine, Koç Üniversitesi, Istanbul, TurkeyDirect visualization and characterization of nanosized biological particles such as viruses, vesicles and protein aggregates are important for various applications in medicine. Specifically, exosomes (30-150 nm in diameter) gained huge interest due to their potential role as a biomarker in cancer diagnosis and prognosis, however direct detection of these particles is challenging due to their small size. Interferometric microscopy allows detection of these particles without using any labels. We show that visibility of nanoparticles can be enhanced in interferometric microscopy by utilizing defocused images. In this paper, with the proposed method Depth Scanning Correlation, we demonstrate label-free detection of individual exosomes isolated from breast cancer cell culture isolated by using Exosome Total Isolation Chip (ExoTIC). Proposed imaging system combined with an isolation tool, can be used in a wide range of applications, where label-free detection of single biological nanoparticles is needed. © 2020 Elsevier B.V., All rights reserved.Publication Metadata only Students’ Approach to Recycling and Sustainability: A Design Study on Affordable Container Houses(Springer, 2020) Ceylan, Salih; Charytonowicz, J.; Ceylan, Salih, Department of Architecture, Bahçeşehir Üniversitesi, Istanbul, TurkeyThe world has been suffering from serious environmental problems in the last decades. However, there are also ongoing attempts to reduce harmful human impact on nature. All those attempts require interdisciplinary work by various professions, one of them being architecture regarding its role and responsibility in environmental issues. Architecture discipline is required to formulate new methods and strategies to maintain harmony between natural and built environments. Furthermore, the academy in the field of architecture has the mission of training future architects with the notion to meet the expectations of contemporary societies. Accordingly, sustainable design and energy efficiency in buildings have become important fields in architectural education. This paper presents container housing as an educational theme in the design studio for first-year architecture students as a reliable method for environmentally responsive design. The findings of the case study point out that using a design topic that promotes sustainability and energy efficiency has a significant effect on the students’ awareness about the issues. © 2020 Elsevier B.V., All rights reserved.Publication Metadata only Using virtual reality to improve visual recognition skills of first year architecture students: A comparative study(SciTePress, 2020) Ceylan, Salih; Lane, H.C.; Zvacek, S.; Uhomoibhi, J.; Ceylan, Salih, Department of Architecture, Bahçeşehir Üniversitesi, Istanbul, TurkeyThe use of virtual reality (VR) technologies is getting widespread throughout the world in the last years. Architecture as a prominent discipline in using digital technologies has a lot to promise about the use of VR in different areas of the profession. It can be used as a design or a representation instrument, as well as a tool in the construction processes. Accordingly, as architectural education needs to keep itself up-to-date about new technologies, the implementation of VR technologies into the architecture curriculum is supposed to be a subject to be studied by researchers working in the educational domain of architecture. This paper presents a comparative study on the use of VR technologies in the first year of architectural education to improve the visual and spatial recognition skills of students. The findings of the study indicate that VR technologies can be beneficial in various aspects like the perception of certain physical characteristics of a model, and students’ enthusiasm to participate in the design studio courses. © 2020 Elsevier B.V., All rights reserved.Publication Metadata only Initial study towards the integrated design of bone scaffolds based on cell diffusion, growth factor release and tissue regeneration(American Society of Mechanical Engineers (ASME), 2020) Sahin, Mervenaz; Tabak, Ahmet Fatih; Sendur, Gullu Kiziltas; Sahin, Mervenaz, Materials Science and Nano Engineering, Sabancı Üniversitesi, Tuzla, Turkey; Tabak, Ahmet Fatih, Mechatronics Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Sendur, Gullu Kiziltas, Mechatronics Engineering, Sabancı Üniversitesi, Tuzla, Turkey, Nanotechnology Research and Application Center, Sabancı Üniversitesi, Tuzla, TurkeyThree-dimensional (3D) porous tissue scaffolds combined with bioactive molecules and cells offer key advantages for bone repair mechanisms. A functional bone tissue scaffold should provide mechanical support with an adequate combination of porosity and permeability for nutrients, oxygen supply, waste removal, and growth factors release as well as controlled degradation. Although a vast amount of work exist to address these challenges, to the best of our knowledge, a design framework taking tissue differentiation, diffusion, and growth factor (GF) release into account in time-domain simultaneously does not exist. In this paper, we provide an initial effort to address such a need by laying down the foundations for a simulation framework incorporating these effects within a Finite Element Analysis (FEA) model in COMSOL Multiphysics® software. The effectiveness of the numerical model is demonstrated via preliminary mechano-biology analyses on a simulated 3D poroelastic bone scaffold. Initial time-dependent results demonstrate the suitability of this model for an optimization framework. More specifically, it is demonstrated that coupled Multiphysics equations of diffusion, GF release, and differentiation could provide valuable inputs for ideal bone scaffold systems for effective bone repair tasks in the future. © 2021 Elsevier B.V., All rights reserved.Publication Metadata only A case study about facebook usage for visually impaired using the android platforms(IADIS, 2020) Uslu, Arda; Boluk, Pinar Sarisaray; Uslu, Arda, Computer Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Boluk, Pinar Sarisaray, Department of Software Engineering, Bahçeşehir Üniversitesi, Istanbul, TurkeyThe use of social media plays an important role in our lives. It is crucial that visually impaired (VI) can likewise take part in various social media platforms. In this paper, we tried to discover the problems and interactions faced by VI on Facebook with the help of tasks that are prepared beforehand. We, researchers helped the participant to pass the steps required to complete these predetermined tasks if the participant encountered a problem. According to the first factor, the results are displayed in terms of points attributed to the steps. Secondly, the time required to complete the task is checked. The third factor is if the participant had already known it before or not. As a result, findings in terms of usability and accessibility are discussed. Hence, we tried to find out what can be done to address these issues. © 2021 Elsevier B.V., All rights reserved.Publication Metadata only Republic of Turkey Identity Card (TCKK): Banking Use Case in Authentication & Customer Onboarding(Association for Computing Machinery, 2020) Keleş, Mehmet Klvllclm; Demirel, Şenay; Keleş, Mehmet Klvllclm, Vaklfbank VLAB RandD Center, T.C. Maltepe Universitesi, Istanbul, Turkey, Bahçeşehir Üniversitesi, Istanbul, Turkey; Demirel, Şenay, T.C. Maltepe Universitesi, Istanbul, TurkeyThe Republic of Turkey Identity Cards (TCKK) were issued on March 2016 to enable the electronic identity and electronic services for the citizens. TCKK includes personal and biometric information which allows authentication process to be enhanced with visual and electronic security elements of the highest standards. In this paper, we present a remote customer onboarding scenario and the usage of The Republic of Turkey Identity Card (TCKK) authentication with face recognition. We also explore the case for Near Field Communication (NFC) capable mobile devices which enable to take the colorful face image to improve the face recognition rate. The authentication steps are described in detail to further employ this usage. TCKK allows authentication process to be enhanced with visual and electronic security elements of the highest standards that can be applicable for many other digital banking scenarios or new applications in the financial sector. © 2022 Elsevier B.V., All rights reserved.Publication Metadata only User participation in housing regeneration projects(WITPress marketing@witpress.com, 2020) Asan, Hatice Sadikoglu; Özsoy, Ahsen; Hadjri, K.; Asan, Hatice Sadikoglu, Faculty of Architecture and Design, Bahçeşehir Üniversitesi, Istanbul, Turkey; Özsoy, Ahsen, Faculty of Architecture, İstanbul Teknik Üniversitesi, Istanbul, TurkeyThe quality of existing residential buildings is one of the biggest problems today. There are a number of different approaches to improve the quality of existing housing stock with user participation. Regeneration policies for the existing housing stock can create opportunities for improving spatial standards, and can preserve the social-cultural and economic value of the stock. Europe is rich in terms of housing estates that were designed based on modernist ideas after the World Wars as a means of solving housing problems. European countries have developed policies for improving the quality of those neighbourhoods. Nowadays, most regeneration policies focus on design, construction methods materials and financial resources, but they should also focus on user participation issues. The methodology of this research is built on examining the approaches and implementations related to the participation in housing regeneration projects in European countries and Turkey. The kind of policies and implementations related to user participation that exist in Europe and how such participation is organized in the projects has been examined. The research consists of a literature review on European regeneration projects, plus a survey and in-depth interviews on a modern housing settlement in Turkey to discuss the potential of user participation. A research case study was conducted on a modern housing project, in the Levent District, which was built in the 1950s. Questionnaires and in-depth interviews were employed to understand the users’ attitudes to a regeneration project. As part of studying the process of the selected projects, the participation type will be analysed in order to underline the importance of user participation on regeneration projects, and user participation potential will be discussed. © 2020 Elsevier B.V., All rights reserved.Publication Metadata only Adaptive Motion Control of Modified E. Coli(Institute of Electrical and Electronics Engineers Inc., 2020) Tabak, Ahmet Fatih; Tabak, Ahmet Fatih, Mechatronics Engineering, Bahçeşehir Üniversitesi, Istanbul, TurkeyMicro robotic systems are of growing interest for biomedical applications. The widely preferred means of locomotion for untethered microrobots is swimming via mimicry of single-celled organisms. Furthermore, such organisms are recently considered to be integrated into a micro-robotic system to achieve biocompatibility. The motion control of such bio-hybrid systems poses a considerable challenge due to their size and taxis-behavior. Here, an adaptive motion control scheme is investigated with a simulated coupled system of open kinematic chain and bacterium under in vitro conditions. The said control is achieved through magnetic coupling between the two via a single permanent magnet. The main focus of the study is the effect of the adaptive component and its ability to change the swimming direction of a single E. Coli minicell. Simulation results show that it is theoretically possible to achieve motion control via such an approach. © 2020 Elsevier B.V., All rights reserved.