Ayelet Akselrod-Ballin

Automatic Segmentation and Classification of Multiple Sclerosis in Multichannel MRI

We introduce a multiscale approach that combines segmentation with classification to detect abnormal brain structures in medical imagery, and demonstrate its utility in automatically detecting multiple sclerosis (MS) lesions in 3-D multichannel magnetic resonance (MR) images. Our method uses segmentation to obtain a hierarchical decomposition of a multichannel, anisotropic MR scans. It then produces a rich set of features describing the segments in terms of intensity, shape, location, neighborhood relations, and anatomical context. These features are then fed into a decision forest classifier, trained with data labeled by experts, enabling the detection of lesions at all scales. Unlike common approaches that use voxel-by-voxel analysis, our system can utilize regional properties that are often important for characterizing abnormal brain structures. We provide experiments on two types of real MR images: a multichannel proton-density-, T2-, and T1-weighted dataset of 25 MS patients and a single-channel fluid attenuated inversion recovery (FLAIR) dataset of 16 MS patients. Comparing our results with lesion delineation by a human expert and with previously extensively validated results shows the promise of the approach.

Atlas guided identification of brain structures by combining 3d segmentation and SVM classification

This study presents a novel automatic approach for the identification of anatomical brain structures in magnetic resonance images (MRI). The method combines a fast multiscale multi-channel three dimensional (3D) segmentation algorithm providing a rich feature vocabulary together with a support vector machine (SVM) based classifier. The segmentation produces a full hierarchy of segments, expressed by an irregular pyramid with only linear time complexity. The pyramid provides a rich, adaptive representation of the image, enabling detection of various anatomical structures at different scales. A key aspect of the approach is the thorough set of multiscale measures employed throughout the segmentation process which are also provided at its end for clinical analysis. These features include in particular the prior probability knowledge of anatomic structures due to the use of an MRI probabilistic atlas. An SVM classifier is trained based on this set of features to identify the brain structures. We validated the approach using a gold standard real brain MRI data set. Comparison of the results with existing algorithms displays the promise of our approach.

An Integrated Segmentation and Classification Approach Applied to Multiple Sclerosis Analysis

We present a novel multiscale approach that combines segmentation with classification to detect abnormal brain structures in medical imagery, and demonstrate its utility in detecting multiple sclerosis lesions in 3D MRI data. Our method uses segmentation to obtain a hierarchical decomposition of a multi-channel, anisotropic MRI scan. It then produces a rich set of features describing the segments in terms of intensity, shape, location, and neighborhood relations. These features are then fed into a decision tree-based classifier, trained with data labeled by experts, enabling the detection of lesions in all scales. Unlike common approaches that use voxel-by-voxel analysis, our system can utilize regional properties that are often important for characterizing abnormal brain structures. We provide experiments showing successful detections of lesions in both simulated and real MR images.

Prior knowledge driven multiscale segmentation of brain MRI

We present a novel automatic multiscale algorithm applied to segmentation of anatomical structures in brain MRI. The algorithm which is derived from algebraic multigrid, uses a graph representation of the image and performs a coarsening process that produces a full hierarchy of segments. Our main contribution is the incorporation of prior knowledge information into the multiscale framework through a Bayesian formulation. The probabilistic information is based on an atlas prior and on a likelihood function estimated from a manually labeled training set. The significance of our new approach is that the constructed pyramid, reflects the prior knowledge formulated. This leads to an accurate and efficient methodology for detection of various anatomical structures simultaneously. Quantitative validation results on gold standard MRI show the benefit of our approach.

Accelerating Image Registration With the Johnson–Lindenstrauss Lemma: Application to Imaging 3-D Neural Ultrastructure With Electron Microscopy

We present a novel algorithm to accelerate feature based registration, and demonstrate the utility of the algorithm for the alignment of large transmission electron microscopy (TEM) images to create 3-D images of neural ultrastructure. In contrast to the most similar algorithms, which achieve small computation times by truncated search, our algorithm uses a novel randomized projection to accelerate feature comparison and to enable global search. Further, we demonstrate robust estimation of nonrigid transformations with a novel probabilistic correspondence framework, that enables large TEM images to be rapidly brought into alignment, removing characteristic distortions of the tissue fixation and imaging process. We analyze the impact of randomized projections upon correspondence detection, and upon transformation accuracy, and demonstrate that accuracy is maintained. We provide experimental results that demonstrate significant reduction in computation time and successful alignment of TEM images.

Improved registration for large electron microscopy images

In this paper we introduce a novel algorithm for alignment of Electron Microscopy images for 3D reconstruction. The algorithm extends the Expectation Maximization - Iterative Closest Points (EM-ICP) algorithm to go from point matching to patch matching. We utilize local patch characteristics to achieve improved registration. The method is applied to enable 3D reconstruction of Transmission Electron Microscopy (TEM) images. We demonstrate results on large TEM images and show the increased alignment accuracy of our approach.

MR imaging–derived oxygen-hemoglobin dissociation curves and fetal-placental oxygen-hemoglobin affinities

The authors of this study present a noninvasive approach for obtaining MR imaging–based oxygen-hemoglobin dissociation curves and for deriving oxygen tension values at which hemoglobin is 50% saturated and maps for the placenta and fetus in pregnant mice.

Accelerating Feature Based Registration Using the Johnson-Lindenstrauss Lemma

We introduce an efficient search strategy to substantially accelerate feature based registration. Previous feature based registration algorithms often use truncated search strategies in order to achieve small computation times. Our new accelerated search strategy is based on the realization that the search for corresponding features can be dramatically accelerated by utilizing Johnson-Lindenstrauss dimension reduction. Order of magnitude calculations for the search strategy we propose here indicate that the algorithm proposed is more than a million times faster than previously utilized naive search strategies, and this advantage in speed is directly translated into an advantage in accuracy as the fast speed enables more comparisons to be made in the same amount of time. We describe the accelerated scheme together with a full complexity analysis. The registration algorithm was applied to large transmission electron microscopy (TEM) images of neural ultrastructure. Our experiments demonstrate that our algorithm enables alignment of TEM images with increased accuracy and efficiency compared to previous algorithms.

Distinctive and compact features

We consider the problem of extracting features for multi-class recognition problems. The features are required to make fine distinctions between similar classes, combined with tolerance for distortions and missing information. We define and compare two general approaches, both based on maximizing the delivered information for recognition: one divides the problem into multiple binary classification tasks, while the other uses a single multi-class scheme. The two strategies result in markedly different sets of features, which we apply to face identification and detection. We show that the first produces a sparse set of distinctive features that are specific to an individual face, and are highly tolerant to distortions and missing input. The second produces compact features, each shared by about half of the faces, which perform better in general face detection. The results show the advantage of distinctive features for making fine distinctions in a robust manner. They also show that different features are optimal for recognition tasks at different levels of specificity.

Multimodal Correlative Preclinical Whole Body Imaging and Segmentation

Segmentation of anatomical structures and particularly abdominal organs is a fundamental problem for quantitative image analysis in preclinical research. This paper presents a novel approach for whole body segmentation of small animals in a multimodal setting of MR, CT and optical imaging. The algorithm integrates multiple imaging sequences into a machine learning framework, which generates supervoxels by an efficient hierarchical agglomerative strategy and utilizes multiple SVM-kNN classifiers each constrained by a heatmap prior region to compose the segmentation. We demonstrate results showing segmentation of mice images into several structures including the heart, lungs, liver, kidneys, stomach, vena cava, bladder, tumor, and skeleton structures. Experimental validation on a large set of mice and organs, indicated that our system outperforms alternative state of the art approaches. The system proposed can be generalized to various tissues and imaging modalities to produce automatic atlas-free segmentation, thereby enabling a wide range of applications in preclinical studies of small animal imaging.