Textural Analysis of a Fibronectin Network During Early Embryogenesis

Fibronectin is a major extracellular matrix molecular component that plays a critical role in embryonic cell motility and morphogenesis. During early development, the fibronectin molecular network is nearly ubiquitous in distribution across the entire embryonic volume. As a result, the embryonic fibronectin distribution is functionally relevant to both cell motility and organogenesis. Despite its biological importance, the structural attributes of embryonic fibronectin distribution are poorly understood. The textural features of an extracellular matrix network like that of fibronectin is not known. By marking the embryonic tissue, obtained during specific stages of development, using fibronectin indirect immunofluorescence, fluorescent microscopy images capturing the embryonic fibronectin distribution were obtained. Using the properties of the gray scale co-occurrence matrix, textural attributes of a fibronectin network was derived for quail embryos during their early stages of morphogenesis. As a result, textural properties like inertia, correlation, uniformity, entropy and homogeneity were assessed for the medial (including the embryonic anteroposterior axis) and lateral (excluding the embryonic anteroposterior axis) fibronectin . The results not only demonstrated a noticeable heterogeneity of fibronectin textural properties across the embryonic regions examined, but also across the developmental stages that were studied. The spatial anisotropy and the temporal evolution across the developmental span in the textural attributes of embryonic fibronectin may have functional consequences for cell motility and morphogenesis. With this thesis, textural analysis has found yet another application, viz. the study of the surface structural attributes of an extracellular matrix protein network in the context of developmental biology. The work presented in this thesis is the first of its kind in applying texture analysis with gray scale co-occurrence matrix method to study the spatial distribution of fibronectin matrix within a given stage of embryonic development and the temporal textural changes as the embryonic development progresses from stage 5 through stage 9

Learning to Read by Spelling: Towards Unsupervised Text Recognition

This work presents a method for visual text recognition without using any paired supervisory data. We formulate the text recognition task as one of aligning the conditional distribution of strings predicted from given text images, with lexically valid strings sampled from target corpora. This enables fully automated, and unsupervised learning from just line-level text-images, and unpaired text-string samples, obviating the need for large aligned datasets. We present detailed analysis for various aspects of the proposed method, namely - (1) impact of the length of training sequences on convergence, (2) relation between character frequencies and the order in which they are learnt, (3) generalisation ability of our recognition network to inputs of arbitrary lengths, and (4) impact of varying the text corpus on recognition accuracy. Finally, we demonstrate excellent text recognition accuracy on both synthetically generated text images, and scanned images of real printed books, using no labelled training examples

Image processing methods for computer-aided interpretation of microscopic images

Ankara : The Department of Electrical and Electronics Engineering and the Graduate School of Engineering and Science of Bilkent University, 2012.Thesis (Master's) -- Bilkent University, 2012.Includes bibliographical refences.Image processing algorithms for automated analysis of microscopic images have become increasingly popular in the last decade with the remarkable growth in computational power. The advent of high-throughput scanning devices allows for computer-assisted evaluation of microscopic images, resulting in a quick and unbiased image interpretation that will facilitate the clinical decision-making process. In this thesis, new methods are proposed to provide solution to two image analysis problems in biology and histopathology. The first problem is the classification of human carcinoma cell line images. Cancer cell lines are widely used for research purposes in laboratories all over the world. In molecular biology studies, researchers deal with a large number of specimens whose identity have to be checked at various points in time. A novel computerized method is presented for cancer cell line image classification. Microscopic images containing irregular carcinoma cell patterns are represented by subwindows which correspond to foreground pixels. For each subwindow, a covariance descriptor utilizing the dual-tree complex wavelet transform (DTCWT) coefficients as pixel features is computed. A Support Vector Machine (SVM) classifier with radial basis function (RBF) kernel is employed for final classification. For 14 different classes, we achieve an overall accuracy of 98%, which outperforms the classical covariance based methods. Histopathological image analysis problem is related to the grading of follicular lymphoma (FL) disease. FL is one of the commonly encountered cancer types in the lymph system. FL grading is based on histological examination of hematoxilin and eosin (H&E) stained tissue sections by pathologists who make clinical decisions by manually counting the malignant centroblast (CB) cells. This grading method is subject to substantial inter- and intra-reader variability and sampling bias. A computer-assisted method is presented for detection of CB cells in H&Estained FL tissue samples. The proposed algorithm takes advantage of the scalespace representation of FL images to detect blob-like cell regions which reside in the scale-space extrema of the difference-of-Gaussian images. Multi-stage false positive elimination strategy is employed with some statistical region properties and textural features such as gray-level co-occurrence matrix (GLCM), gray-level run-length matrix (GLRLM) and Scale Invariant Feature Transform (SIFT). The algorithm is evaluated on 30 images and 90% CB detection accuracy is obtained, which outperforms the average accuracy of expert hematopathologists.Keskin, Musa FurkanM.S

Evaluation of texture features for analysis of ovarian follicular development

Ovarian follicles in women are fluid-filled structures in the ovary that contain oocytes (eggs). A dominant follicle is physiologically selected and ovulates during the menstrual cycle. We examined the echotexture in ultrasonographic images of the follicle wall of dominant ovulatory follicles in women during natural menstrual cycles and dominant anovulatory follicles which developed in women using oral contraceptives (OC). Texture features of follicle wall regions of both ovulatory and anovulatory dominant follicles were evaluated over a period of seven days before ovulation (natural cycles) or peak estradiol concentrations (OC cycles). Differences in echotexture between the two classes of follicles were found for two co-occurrence matrix derived texture features and two edge-frequency based texture features. Co-occurrence energy and homogeneity were significantly lower for ovulatory follicles while edge density and edge contrast were higher for ovulatory follicles. In the each feature space, the two classes of follicle were adequately separable.This thesis employed several statistical approaches to analyses of texture features, such as plotting method and the Mann-Kendall method. A distinct change of feature trend was detected 3 or 4 days before the day of ovulation for ovulatory follicles in the two co-occurrence matrix derived texture features and two edge-frequency-based texture features. Anovulatory follicles, exhibited the biggest variation of the feature value 3 or 4 days before the day on which dominant follicles developed to maximum size. This discovery is believed to correspond to the ovarian follicles responding to system hormonal changes leading to presumptive ovulation

Texture analysis and Its applications in biomedical imaging: a survey

Texture analysis describes a variety of image analysis techniques that quantify the variation in intensity and pattern. This paper provides an overview of several texture analysis approaches addressing the rationale supporting them, their advantages, drawbacks, and applications. This survey’s emphasis is in collecting and categorising over five decades of active research on texture analysis.Brief descriptions of different approaches are presented along with application examples. From a broad range of texture analysis applications, this survey’s final focus is on biomedical image analysis. An up-to-date list of biological tissues and organs in which disorders produce texture changes that may be used to spot disease onset and progression is provided. Finally, the role of texture analysis methods as biomarkers of disease is summarised.Manuscript received February 3, 2021; revised June 23, 2021; accepted September 21, 2021. Date of publication September 27, 2021; date of current version January 24, 2022. This work was supported in part by the Portuguese Foundation for Science and Technology (FCT) under Grants PTDC/EMD-EMD/28039/2017, UIDB/04950/2020, PestUID/NEU/04539/2019, and CENTRO-01-0145-FEDER-000016 and by FEDER-COMPETE under Grant POCI-01-0145-FEDER-028039. (Corresponding author: Rui Bernardes.)info:eu-repo/semantics/publishedVersio

Making decisions based on context: models and applications in cognitive sciences and natural language processing

It is known that humans are capable of making decisions based on context and generalizing what they have learned. This dissertation considers two related problem areas and proposes different models that take context information into account. By including the context, the proposed models exhibit strong performance in each of the problem areas considered. The first problem area focuses on a context association task studied in cognitive science, which evaluates the ability of a learning agent to associate specific stimuli with an appropriate response in particular spatial contexts. Four neural circuit models are proposed to model how the stimulus and context information are processed to produce a response. The neural networks are trained by modifying the strength of neural connections (weights) using principles of Hebbian learning. Such learning is considered biologically plausible, in contrast to back propagation techniques that do not have a solid neurophysiological basis. A series of theoretical results for the neural circuit models are established, guaranteeing convergence to an optimal configuration when all the stimulus-context pairs are provided during training. Among all the models, a specific model based on ideas from recommender systems trained with a primal-dual update rule, achieves perfect performance in learning and generalizing the mapping from context-stimulus pairs to correct responses. The second problem area considered in the thesis focuses on clinical natural language processing (NLP). A particular application is the development of deep-learning models for analyzing radiology reports. Four NLP tasks are considered including anatomy named entity recognition, negation detection, incidental finding detection, and clinical concept extraction. A hierarchical Recurrent Neural Network (RNN) is proposed for anatomy named entity recognition, which is then used to produce a set of features for incidental finding detection of pulmonary nodules. A clinical context word embedding model is obtained, which is used with an RNN to model clinical concept extraction. Finally, feature-enriched RNN and transformer-based models with contextual word embedding are proposed for negation detection. All these models take the (clinical) context information into account. The models are evaluated on different datasets and are shown to achieve strong performance, largely outperforming the state-of-art

Computer-Assisted Algorithms for Ultrasound Imaging Systems

Ultrasound imaging works on the principle of transmitting ultrasound waves into the body and reconstructs the images of internal organs based on the strength of the echoes. Ultrasound imaging is considered to be safer, economical and can image the organs in real-time, which makes it widely used diagnostic imaging modality in health-care. Ultrasound imaging covers the broad spectrum of medical diagnostics; these include diagnosis of kidney, liver, pancreas, fetal monitoring, etc. Currently, the diagnosis through ultrasound scanning is clinic-centered, and the patients who are in need of ultrasound scanning has to visit the hospitals for getting the diagnosis. The services of an ultrasound system are constrained to hospitals and did not translate to its potential in remote health-care and point-of-care diagnostics due to its high form factor, shortage of sonographers, low signal to noise ratio, high diagnostic subjectivity, etc. In this thesis, we address these issues with an objective of making ultrasound imaging more reliable to use in point-of-care and remote health-care applications. To achieve the goal, we propose (i) computer-assisted algorithms to improve diagnostic accuracy and assist semi-skilled persons in scanning, (ii) speckle suppression algorithms to improve the diagnostic quality of ultrasound image, (iii) a reliable telesonography framework to address the shortage of sonographers, and (iv) a programmable portable ultrasound scanner to operate in point-of-care and remote health-care applications