PICS in Pics: Physics Informed Contour Selection for Rapid Image Segmentation

Effective training of deep image segmentation models is challenging due to the need for abundant, high-quality annotations. Generating annotations is laborious and time-consuming for human experts, especially in medical image segmentation. To facilitate image annotation, we introduce Physics Informed Contour Selection (PICS) - an interpretable, physics-informed algorithm for rapid image segmentation without relying on labeled data. PICS draws inspiration from physics-informed neural networks (PINNs) and an active contour model called snake. It is fast and computationally lightweight because it employs cubic splines instead of a deep neural network as a basis function. Its training parameters are physically interpretable because they directly represent control knots of the segmentation curve. Traditional snakes involve minimization of the edge-based loss functionals by deriving the Euler-Lagrange equation followed by its numerical solution. However, PICS directly minimizes the loss functional, bypassing the Euler Lagrange equations. It is the first snake variant to minimize a region-based loss function instead of traditional edge-based loss functions. PICS uniquely models the three-dimensional (3D) segmentation process with an unsteady partial differential equation (PDE), which allows accelerated segmentation via transfer learning. To demonstrate its effectiveness, we apply PICS for 3D segmentation of the left ventricle on a publicly available cardiac dataset. While doing so, we also introduce a new convexity-preserving loss term that encodes the shape information of the left ventricle to enhance PICS's segmentation quality. Overall, PICS presents several novelties in network architecture, transfer learning, and physics-inspired losses for image segmentation, thereby showing promising outcomes and potential for further refinement

Automatic segmentation of the left ventricle cavity and myocardium in MRI data

A novel approach for the automatic segmentation has been developed to extract the epi-cardium and endo-cardium boundaries of the left ventricle (lv) of the heart. The developed segmentation scheme takes multi-slice and multi-phase magnetic resonance (MR) images of the heart, transversing the short-axis length from the base to the apex. Each image is taken at one instance in the heart's phase. The images are segmented using a diffusion-based filter followed by an unsupervised clustering technique and the resulting labels are checked to locate the (lv) cavity. From cardiac anatomy, the closest pool of blood to the lv cavity is the right ventricle cavity. The wall between these two blood-pools (interventricular septum) is measured to give an approximate thickness for the myocardium. This value is used when a radial search is performed on a gradient image to find appropriate robust segments of the epi-cardium boundary. The robust edge segments are then joined using a normal spline curve. Experimental results are presented with very encouraging qualitative and quantitative results and a comparison is made against the state-of-the art level-sets method

Image segmentation and reconstruction of 3D surfaces from carotid ultrasound images

Tese de doutoramento. Engenharia Electrotécnica e de Computadores. Faculdade de Engenharia. Universidade do Porto. 200

تمثيل الإطار الخارجي للكلمات العربية بكفاءة من خلال الدمج بين نموذج الكنتور النشط وتحديد ونقاط الزوايا

Graphical curves and surfaces fitting are hot areas of research studies and application, such as artistic applications, analysis applications and encoding purposes. Outline capture of digital word images is important in most of the desktop publishing systems. The shapes of the characters are stored in the computer memory in terms of their outlines, and the outlines are expressed as Bezier curves. Existing methods for Arabic font outline description suffer from low fitting accuracy and efficiency. In our research, we developed a new method for outlining shapes using Bezier curves with minimal set of curve points. A distinguishing characteristic of our method is that it combines the active contour method (snake) with corner detection to achieve an initial set of points that is as close to the shape's boundaries as possible. The method links these points (snake + corner) into a compound Bezier curve, and iteratively improves the fitting of the curve over the actual boundaries of the shape. We implemented and tested our method using MATLAB. Test cases included various levels of shape complexity varying from simple, moderate, and high complexity depending on factors, such as: boundary concavities, number of corners. Results show that our method achieved average 86% of accuracy when measured relative to true shape boundary. When compared to other similar methods (Masood & Sarfraz, 2009; Sarfraz & Khan, 2002; Ferdous A Sohel, Karmakar, Dooley, & Bennamoun, 2010), our method performed comparatively well. Keywords: Bezier curves, shape descriptor, curvature, corner points, control points, Active Contour Model.تعتبر المنحنيات والأسطح الرسومية موضوعاً هاماً في الدراسات البحثية وفي التطبيقات البرمجية مثل التطبيقات الفنية، وتطبيقات تحليل وترميز البيانات. ويعتبر تخطيط الحدود الخارجية للكلمات عملية أساسية في غالبية تطبيقات النشر المكتبي. في هذه التطبيقات تخزن أشكال الأحرف في الذاكرة من حيث خطوطها الخارجية، وتمثل الخطوط الخارجية على هيئة منحنيات Bezier. الطرق المستخدمة حالياً لتحديد الخطوط الخارجية للكلمات العربية تنقصها دقة وكفاءة الملاءمة ما بين الحدود الحقيقية والمنحنى الرسومي الذي تقوم بتشكيله. في هذا البحث قمنا بتطوير طريقة جديدة لتخطيط الحدود الخارجية للكلمات تعتمد على منحنيات Bezier بمجموعة أقل من المنحنيات الجزئية. تتميز طريقتنا بخاصية مميزة وهي الدمج بين آلية لاستشعار الزوايا مع آلية نموذج الكنتور النشط (الأفعى). يتم الدمج بين نقاط الزوايا ونقاط الأفعى لتشكيل مجموعة موحدة من النقاط المبدئية قريبة قدر الإمكان من الحدود الحقيقية للشكل المراد تحديده. يتشكل منحنى Bezier من هذه المجموعة المدمجة، وتتم عملية تدريجية على دورات لملاءمة المنحنى على الحدود الحقيقية للشكل. قام الباحث بتنفيذ وتجربة الطريقة الجديدة باستخدام برنامج MATLAB. وتم اختيار أشكال رسومية كعينات اختبار تتصف بمستويات متباينة من التعقيد تتراوح ما بين بسيط إلى متوسط إلى عالي التعقيد على أساس عوامل مثل تقعرات الحدود، عدد نقاط الزوايا، الفتحات الداخلية، إلخ. وقد أظهرت نتائج الاختبار أن طريقتنا الجديدة حققت دقة في الملائمة تصل نسبتها إلى 86% مقارنة بالحدود الحقيقية للشكل المستهدف. وكذلك فقد كان أداء طريقتنا جيداً بالمقارنة مع طرق أخرى مماثلة

Image Processing Techniques for Detecting Chromosome Abnormalities

With the increasing use of Fluorescence In Situ Hybridization (FISH) probes as markers for certain genetic sequences, the requirement of a proper image processing framework is becoming a necessity to accurately detect these probe signal locations in relation to the centerline of the chromosome. Automated detection and length measurements based on the centerline relative to the centromere and the telomere coordinates would highly assist in clinical diagnosis of genetic disorders and thus improve its efficiency significantly. Although many image processing techniques have been developed for chromosomal analysis such as ’’karyotype analysis” to assist in laboratory diagnosis, they fail to provide reliable results in segmenting and extracting the centerline of chromosomes due to the high variability in shape of chromosomes on microscope slides. In this thesis we propose a hybrid algorithm that utilizes Gradient Vector Flow active contours, Discrete Curve Evolution based skeleton pruning and morphological thinning to provide a robust and accurate centerline of the chromosome, which is then used for the measurement of the FISH probe signals. Then this centerline information is used to detect the centromere location of the chromosome and the probe signal location distances were measured with respective to these landmarks. The ability to accurately detect FISH probe locations with respective to its centerline and other landmarks can provide the cytogeneticists with detailed information that could lead to a faster diagnosis

ROAM: a Rich Object Appearance Model with Application to Rotoscoping

Rotoscoping, the detailed delineation of scene elements through a video shot, is a painstaking task of tremendous importance in professional post-production pipelines. While pixel-wise segmentation techniques can help for this task, professional rotoscoping tools rely on parametric curves that offer the artists a much better interactive control on the definition, editing and manipulation of the segments of interest. Sticking to this prevalent rotoscoping paradigm, we propose a novel framework to capture and track the visual aspect of an arbitrary object in a scene, given a first closed outline of this object. This model combines a collection of local foreground/background appearance models spread along the outline, a global appearance model of the enclosed object and a set of distinctive foreground landmarks. The structure of this rich appearance model allows simple initialization, efficient iterative optimization with exact minimization at each step, and on-line adaptation in videos. We demonstrate qualitatively and quantitatively the merit of this framework through comparisons with tools based on either dynamic segmentation with a closed curve or pixel-wise binary labelling

Accurate detection of dysmorphic nuclei using dynamic programming and supervised classification

A vast array of pathologies is typified by the presence of nuclei with an abnormal morphology. Dysmorphic nuclear phenotypes feature dramatic size changes or foldings, but also entail much subtler deviations such as nuclear protrusions called blebs. Due to their unpredictable size, shape and intensity, dysmorphic nuclei are often not accurately detected in standard image analysis routines. To enable accurate detection of dysmorphic nuclei in confocal and widefield fluorescence microscopy images, we have developed an automated segmentation algorithm, called Blebbed Nuclei Detector (BleND), which relies on two-pass thresholding for initial nuclear contour detection, and an optimal path finding algorithm, based on dynamic programming, for refining these contours. Using a robust error metric, we show that our method matches manual segmentation in terms of precision and outperforms state-of-the-art nuclear segmentation methods. Its high performance allowed for building and integrating a robust classifier that recognizes dysmorphic nuclei with an accuracy above 95%. The combined segmentation-classification routine is bound to facilitate nucleus-based diagnostics and enable real-time recognition of dysmorphic nuclei in intelligent microscopy workflows