Automated artemia length measurement using U-shaped fully convolutional networks and second-order anisotropic Gaussian kernels

The brine shrimp Artemia, a small crustacean zooplankton organism, is universally used as live prey for larval fish and shrimps in aquaculture. In Artemia studies, it would be highly desired to have access to automated techniques to obtain the length information from Anemia images. However, this problem has so far not been addressed in literature. Moreover, conventional image-based length measurement approaches cannot be readily transferred to measure the Artemia length, due to the distortion of non-rigid bodies, the variation over growth stages and the interference from the antennae and other appendages. To address this problem, we compile a dataset containing 250 images as well as the corresponding label maps of length measuring lines. We propose an automated Anemia length measurement method using U-shaped fully convolutional networks (UNet) and second-order anisotropic Gaussian kernels. For a given Artemia image, the designed UNet model is used to extract a length measuring line structure, and, subsequently, the second-order Gaussian kernels are employed to transform the length measuring line structure into a thin measuring line. For comparison, we also follow conventional fish length measurement approaches and develop a non-learning-based method using mathematical morphology and polynomial curve fitting. We evaluate the proposed method and the competing methods on 100 test images taken from the dataset compiled. Experimental results show that the proposed method can accurately measure the length of Artemia objects in images, obtaining a mean absolute percentage error of 1.16%

Unsupervised cell segmentation and labelling in neural tissue images

Neurodegenerative diseases are a group of largely incurable disorders characterised by the progressive loss of neurons and for which often the molecular mechanisms are poorly understood. To bridge this gap, researchers employ a range of techniques. A very prominent and useful technique adopted across many different fields is imaging and the analysis of histopathological and fluorescent label tissue samples. Although image acquisition has been efficiently automated recently, automated analysis still presents a bottleneck. Although various methods have been developed to automate this task, they tend to make use of single-purpose machine learning models that require extensive training, imposing a significant workload on the experts and introducing variability in the analysis. Moreover, these methods are impractical to audit and adapt, as their internal parameters are difficult to interpret and change. Here, we present a novel unsupervised automated schema for object segmentation of images, exemplified on a dataset of tissue images. Our schema does not require training data, can be fully audited and is based on a series of understandable biological decisions. In order to evaluate and validate our schema, we compared it with a state-of-the-art automated segmentation method for post-mortem tissues of ALS patients

Quantitative analysis of incorporation dynamics of conserved Centriole proteins in Drosophila early embryos

To divide efficiently, cells of animals and many other higher eukaryotes, rely upon centrosomes to help nucleate the bipolar mitotic spindle. At each division, two centrosomes are required, such that one centrosome is ultimately inherited by each daughter cell. Consequently, centrosomes must duplicate precisely once during each cycle of cell division. At the core of each centrosome is a mother centriole that can duplicate by growing a new daughter centriole off its side, which will later mature into a mother and nucleate its own centrosome. The core components of the centriole are highly conserved across higher eukaryotes, despite this there is still a lack of detail regarding their function and their hierarchy of assembly. In this thesis, I perform a comparative analysis of the incorporation dynamics of several conserved centriole proteins, using both standard and super-resolution microscopy, and the Drosophila early embryo as a model. I show that the daughter centrioles in the Drosophila early embryo appear to begin assembling earlier than previously reported. Further, I provide evidence that several core centriole proteins may be recruited into a transient centrosomal primordial “soup” in addition to the centriole proper. In addition, I refine the order of assembly of the centriole - allowing incorporation of Sas-6, Ana2, Ana3, CEP135, Ana1 and Asl to be placed on a continuous timeline alongside the cell cycle. Finally, through the use of CEP135 mutants, I show that, CEP135 does not appear to be necessary to recruit Ana1 into centrioles, in contrast to previous findings. In summary, my work redefines the initial incorporation dynamics of centriole assembly, challenging several previous assumptions and providing new avenues for interrogation of the specific functions of the core centriole proteins

Image Feature Information Extraction for Interest Point Detection: A Comprehensive Review

Interest point detection is one of the most fundamental and critical problems in computer vision and image processing. In this paper, we carry out a comprehensive review on image feature information (IFI) extraction techniques for interest point detection. To systematically introduce how the existing interest point detection methods extract IFI from an input image, we propose a taxonomy of the IFI extraction techniques for interest point detection. According to this taxonomy, we discuss different types of IFI extraction techniques for interest point detection. Furthermore, we identify the main unresolved issues related to the existing IFI extraction techniques for interest point detection and any interest point detection methods that have not been discussed before. The existing popular datasets and evaluation standards are provided and the performances for eighteen state-of-the-art approaches are evaluated and discussed. Moreover, future research directions on IFI extraction techniques for interest point detection are elaborated

Influence of Rain on Vision-Based Algorithms in the Automotive Domain

The Automotive domain is a highly regulated domain with stringent requirements that characterize automotive systems’ performance and safety. Automotive applications are required to operate under all driving conditions and meet high levels of safety standards. Vision-based systems in the automotive domain are accordingly required to operate at all weather conditions, favorable or adverse. Rain is one of the most common types of adverse weather conditions that reduce quality images used in vision-based algorithms. Rain can be observed in an image in two forms, falling rain streaks or adherent raindrops. Both forms corrupt the input images and degrade the performance of vision-based algorithms. This dissertation describes the work we did to study the effect of rain on the quality images and the target vision systems that use them as the main input. To study falling rain, we developed a framework for simulating failing rain streaks. We also developed a de-raining algorithm that detects and removes rain streaks from the images. We studied the relation between image degradation due to adherent raindrops and the performance of the target vision algorithm and provided quantitive metrics to describe such a relation. We developed an adherent raindrop simulator that generates synthetic rained images, by adding generated raindrops to rain-free images. We used this simulator to generate rained image datasets, which we used to train some vision algorithms and evaluate the feasibility of using transfer-learning to improve DNN-based vision algorithms to improve performance under rainy conditions.Ph.D.College of Engineering & Computer ScienceUniversity of Michigan-Dearbornhttp://deepblue.lib.umich.edu/bitstream/2027.42/170924/1/Yazan Hamzeh final dissertation.pdfDescription of Yazan Hamzeh final dissertation.pdf : Dissertatio