Elastic map: interactive image segmentation using a few seed-points

Thesis supervisor: Dr. K. Palaniappan.Includes vita.Over the past two decades interactive methods for clinical and biomedical image segmentation have been investigated since the pioneering work of Live-Wire, Live-Lane [17] and Intelligent Scissors [1]. Fully automatic image segmentation is essential for quantitative analysis but remains an unsolved problem, so user driven interactive methods continue to be a powerful alternative when extremely precise segmentation is required. However, manual methods although routinely used are tedious, time-consuming, expensive, inconsistent between experts and error prone. In semi-supervised interactive segmentation the goal is for the user to provide a small amount of partial information or hints for an automatic algorithm to use in order to produce accurate boundaries suitable for the user. The coupled interaction between the user provided input and the semi-supervised segmentation algorithm should be minimal and robust. Commonly used drawing tools for interactive segmentation interfaces include active contour or boundary drawing, scribbles to identify foreground and background regions, and rectangles to outline the object of interest. But interactive segmentation using a sparse set of seed-points has not been widely investigated. In this work we investigate the use of sparse seed point-based for interactive image segmentation task. We have also proposed a new regression based framework, making use of Elastic Body Splines (EBS) to perform interactive image segmentation. Elastic Body Splines belonging to the family of 3D splines were recently introduced to capture tissue deformations within a physical model-based approach for non-rigid biomedical image registration [18]. ElasticMap model the displacement of points in a 3D homogeneous isotropic elastic body subject to forces. We propose a novel extension of using elastic body splines for interactive learning-based figure-ground segmentation. The task of interactive image segmentation, with user provided foreground-background labeled seeds or samples, is formulated as learning a spatially dependent interpolating pixel classification function that is then used to assign labels for all unlabeled pixels in the image. The spline function we chose to model the semisupervised pixel classifier is the ElasticMap which can use sparse point-scribble input from the user and has a closed form solution. Experimental results demonstrate the applicability of the EBS approach for image segmentation. The ElasticMap method for interactive foreground segmentation uses on an average just four to six labeled pixels as input from the user. Using such sparsely labeled information the proposed EBS method produces very accurate results with an average accuracy consistently exceeding 95 percent on three different benchmark datasets and outperforms eleven other popular interactive image segmentation methods.Includes bibliographical references (pages 110-120)

Atlas-Based Prostate Segmentation Using an Hybrid Registration

Purpose: This paper presents the preliminary results of a semi-automatic method for prostate segmentation of Magnetic Resonance Images (MRI) which aims to be incorporated in a navigation system for prostate brachytherapy. Methods: The method is based on the registration of an anatomical atlas computed from a population of 18 MRI exams onto a patient image. An hybrid registration framework which couples an intensity-based registration with a robust point-matching algorithm is used for both atlas building and atlas registration. Results: The method has been validated on the same dataset that the one used to construct the atlas using the "leave-one-out method". Results gives a mean error of 3.39 mm and a standard deviation of 1.95 mm with respect to expert segmentations. Conclusions: We think that this segmentation tool may be a very valuable help to the clinician for routine quantitative image exploitation.Comment: International Journal of Computer Assisted Radiology and Surgery (2008) 000-99

An Elastic Interaction-Based Loss Function for Medical Image Segmentation

Deep learning techniques have shown their success in medical image segmentation since they are easy to manipulate and robust to various types of datasets. The commonly used loss functions in the deep segmentation task are pixel-wise loss functions. This results in a bottleneck for these models to achieve high precision for complicated structures in biomedical images. For example, the predicted small blood vessels in retinal images are often disconnected or even missed under the supervision of the pixel-wise losses. This paper addresses this problem by introducing a long-range elastic interaction-based training strategy. In this strategy, convolutional neural network (CNN) learns the target region under the guidance of the elastic interaction energy between the boundary of the predicted region and that of the actual object. Under the supervision of the proposed loss, the boundary of the predicted region is attracted strongly by the object boundary and tends to stay connected. Experimental results show that our method is able to achieve considerable improvements compared to commonly used pixel-wise loss functions (cross entropy and dice Loss) and other recent loss functions on three retinal vessel segmentation datasets, DRIVE, STARE and CHASEDB1

Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i