Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images

Detecting Multilingual Lines of Text with Fusion Moves

This thesis proposes an optimization-based algorithm for detecting lines of text in images taken by hand-held cameras. The majority of existing methods for this problem assume alphabet-based texts (e.g. in Latin or Greek) and they use heuristics specific to such texts: proximity between letters within one line, larger distance between separate lines, etc. We are interested in a more challenging problem where images combine alphabet and logographic characters from multiple languages where typographic rules vary a lot (e.g. English, Korean, and Chinese). Significantly higher complexity of fitting multiple lines of text in different languages calls for an energy-based formulation combining a data fidelity term and a regularization prior. Our data cost combines geometric errors and likelihoods given by a classifier trained to low-level features in each language. Our regularization term encourages sparsity based on label costs. Our energy can be efficiently minimized by fusion moves. The algorithm was evaluated on a database of images from the subway of metropolitan area of Seoul and was proven to be robust

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images

Hidden Markov models for robust recognition of vehicle licence plates

In this dissertation the problem of recognising vehicle licence plates of which the sym¬bols can not be segmented by standard image processing techniques is addressed. Most licence plate recognition systems proposed in the literature do not compensate for dis¬torted, obscured and damaged licence plates. We implemented a novel system which uses a neural network/ hidden Markov model hybrid for licence plate recognition. We implemented a region growing algorithm, which was shown to work well when used to extract the licence plate from a vehicle image. Our vertical edges algorithm was not as successful. We also used the region growing algorithm to separate the symbols in the licence plate. Where the region growing algorithm failed, possible symbol borders were identified by calculating local minima of a vertical projection of the region. A multilayer perceptron neural network was used to estimate symbol probabilities of all the possible symbols in the region. The licence plate symbols were the inputs of the neural network, and were scaled to a constant size. We found that 7 x 12 gave the best character recognition rate. Out of 2117 licence plate symbols we achieved a symbol recognition rate of 99.53%. By using the vertical projection of a licence plate image, we were able to separate the licence plate symbols out of images for which the region growing algorithm failed. Legal licence plate sequences were used to construct a hidden Markov model contain¬ing all allowed symbol orderings. By adapting the Viterbi algorithm with sequencing constraints, the most likely licence plate symbol sequences were calculated, along with a confidence measure. The confidence measure enabled us to use more than one licence plate and symbol segmentation technique. Our recognition rate increased dramatically when we com¬bined the different techniques. The results obtained showed that the system developed worked well, and achieved a licence plate recognition rate of 93.7%.Dissertation (MEng (Computer Engineering))--University of Pretoria, 2002.Electrical, Electronic and Computer Engineeringunrestricte

Motion patterns of subviral particles: Digital tracking, image data processing and analysis

At the Institute of Virology, Philipps-University, Marburg, Germany, currently research on the understanding of the transport mechanisms of Ebola- and Marburgvirus nucleocapsids is carried out. This research demands a profound knowledge about the various motion characteristics of the nucleocapids. The analysis of large amounts of samples by conventional manual evaluation is a laborious task and does not always lead to reproducible and comparable results. In a cooperation between the Institute of Virology, Marburg, and the Institute for Biomedical Engineering, University of Applied Sciences, Giessen, Germany, algorithms are developed and programmed that enable an automatic tracking of subviral particles in fluorescence microscopic image sequences. The algorithms form an interface between the biologic and the algorithmic domain. Furthermore, methods to automatically parameterize and classify subviral particle motions are created. Geometric and mathematical approaches, like curvature-, fractal dimension- and mean squared displacement-determination are applied. Statistical methods are used to compare the measured subviral particle motion parameters between different biological samples. In this thesis, the biological, mathematical and algorithmic basics are described and the state of the art methods of other research groups are presented and compared. The algorithms to track, parameterize, classify and statistically analyze subviral particle tracks are presented in the Methods section. All methods are evaluated with simulated data and/or compared to data validated by a virologist. The methods are applied to a set of real fluorescence microscopic image sequences of Marburgvirus infected live-cells. The Results chapter shows that subviral particle motion can be successfully analyzed using the presented tracking and analysis methods. Furthermore, differences between the subviral particle motions in the analyzed groups could be detected. However, further optimization with manually evaluated data can improve the results. The methods developed in this project enhance the knowledge about nucleocapsid transport and may be valuable for the development of effective antiviral agents to cure Ebola- and Marburgvirus diseases. The thesis concludes with a chapter Discussion and Conclusions

The Girl with the Peanut Necklace: Experiences of Infertility and in vitro Fertilization in China

A 2014-2015 William Prize for best essay in East Asian Studies was awarded to Ruoxi Yu (Berkeley College \u2715) for her essay submitted to the Department of Anthropology, “The Girl with the Peanut Necklace: Experiences of Infertility and in vitro Fertilization in China.” (Marcia Inhorn, William K. Lanman Jr. Professor of Anthropology, advisor; Susan Brownell, Professor of Anthropology at USML, secondary reader.) Ruoxi Yu’s essay, “The Girl with the Peanut Necklace: Experiences of Infertility and in vitro Fertilization in China,” situates original research within the history of the one-child birth control policy and the tension between the demands of the family and the state. The first thing that strikes one about this senior essay is that, at 130 pages, it is not far from being a dissertation. It is based on 10 weeks of ethnographic fieldwork in an infertility clinic in Tianjin combined with two semesters of library research and writing. The quality of the ethnographic research is remarkable for an undergraduate. The setting was very sensitive and required sitting around the clinic waiting for an opportunity to draw a patient into conversation, eventually asking for permission to conduct an interview. Ruoxi’s social skills and facility in Chinese enabled her to interview a number of women who divulged intimate details of their lives. Even many anthropology Ph.D. students find it difficult to pull meaningful information out of the messiness of real life and to organize it within academic frameworks. In the end, Ruoxi is able to successfully draw from medical anthropology and feminist theory to link her research results with time-honored anthropological debates about the Chinese family, and also with recent thinking about medical technologies and their relationship with the state

A multiple criteria route recommendation system

The work to be developed in this dissertation is part of a larger project called Sustainable Tourism Crowding (STC), which motivation is based on two negative impacts caused by the tourism overload that happens, particularly, in the historic neighborhoods of Lisbon. The goal of this dissertation is then to mitigate those problems: reduce the tourist burden of points of interest in a city that, in addition to the degradation of the tourist experience, causes sustainability problems in different aspects (environmental, social and local). Within the scope of this dissertation, the implementation of one component of a recommendation system is the proposed solution. It is based on a multi-criteria algorithm for recommending pedestrian routes that minimize the passage through more crowded places and maximizes the visit to sustainable points of interest. These routes will be personalized for each user, as they consider their explicit preferences (e.g. time, budget, physical effort) and several constraints taken from other microservices that are part of the global system architecture mentioned above (e.g. weather conditions, crowding levels, points of interest, sustainability). We conclude it is possible to develop a microservice that recommend personalized routes and communicate with other microservices that are part of the global system architecture mentioned above. The analysis of the experimental data from the recommendation system, allows us to conclude that it is possible to obtain a more balanced distribution of the tourist visit, by increasing the visit to more sustainable places of interest and avoiding crowded paths.O trabalho a desenvolver nesta dissertação insere-se num projeto de maior dimensão denominado Sustainable Tourism Crowding (STC), cuja motivação assenta, essencialmente, em dois impactos negativos provocados pela sobrecarga turística que se verifica, nomeadamente, nos bairros históricos de Lisboa. O objetivo desta dissertação é, então, mitigar esses problemas: reduzir a sobrecarga turística dos pontos de interesse mais visitados numa cidade que, além da degradação da experiência turística, causa problemas de sustentabilidade em diversos aspetos (ambiental, social e local). No âmbito desta dissertação, a implementação de um componente de um sistema de recomendação é a solução proposta. Baseia-se num algoritmo multicritério de recomendação de percursos pedonais que minimiza a passagem por locais mais apinhados e maximizam a visita a pontos de interesse mais sustentáveis. Essas rotas serão personalizadas para cada utilizador, pois consideram as suas preferências (por exemplo, tempo, orçamento, nível de esforço físico) e várias restrições retiradas de outros microsserviços que fazem parte da arquitetura do sistema global mencionado acima (por exemplo, condições meteorológicas, níveis de apinhamento, pontos de interesse, níveis de sustentabilidade). Concluímos que é possível desenvolver um microsserviço que recomenda rotas personalizadas e que comunica com outros microsserviços que fazem parte da arquitetura global do sistema mencionada acima. A análise dos dados experimentais do sistema de recomendação, permite-nos concluir que é possível obter uma distribuição mais equilibrada da visita turística, aumentando a visita a pontos de interesse mais sustentáveis e evitando percursos mais apinhados