SVM for density estimation and application to medical image segmentation

A method of medical image segmentation based on support vector machine (SVM) for density estimation is presented. We used this estimator to construct a prior model of the image intensity and curvature profile of the structure from training images. When segmenting a novel image similar to the training images, the technique of narrow level set method is used. The higher dimensional surface evolution metric is defined by the prior model instead of by energy minimization function. This method offers several advantages. First, SVM for density estimation is consistent and its solution is sparse. Second, compared to the traditional level set methods, this method incorporates shape information on the object to be segmented into the segmentation process. Segmentation results are demonstrated on synthetic images, MR images and ultrasonic images

<it>Sanjeevini: </it>a freely accessible web-server for target directed lead molecule discovery

<p>Abstract</p> <p>Background</p> <p>Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to design improved lead molecules for the target.</p> <p>Results</p> <p><it>Sanjeevini </it>represents a massive on-going scientific endeavor to provide to the user, a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. It builds in several features, including automated detection of active sites, scanning against a million compound library for identifying hit molecules, all atom based docking and scoring and various other utilities to design molecules with desired affinity and specificity against biomolecular targets. Each of the modules is thoroughly validated on a large dataset of protein/DNA drug targets.</p> <p>Conclusions</p> <p>The article presents <it>Sanjeevini</it>, a freely accessible user friendly web-server, to aid in drug discovery. It is implemented on a tera flop cluster and made accessible via a web-interface at <url>http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp</url>. A brief description of various modules, their scientific basis, validation, and how to use the server to develop <it>in silico </it>suggestions of lead molecules is provided.</p

Robust Nonrigid Multimodal Image Registration Using Local Frequency Maps

Automatic multi-modal image registration is central to numerous tasks in medical imaging today and has a vast range of applications e.g., image guidance, atlas construction, etc. In this paper, we present a novel multi-modal 3D non-rigid registration algorithm where in 3D images to be registered are represented by their corresponding local frequency maps efficiently computed using the Riesz transform as opposed to the popularly used Gabor filters. The non-rigid registration between these local frequency maps is formulated in a statistically robust framework involving the minimization of the integral squared error a.k.a. L2E (L2 error). This error is expressed as the squared difference between the true density of the residual (which is the squared difference between the non-rigidly transformed reference and the target local frequency representations) and a Gaussian or mixture of Gaussians density approximation of the same. The non-rigid transformation is expressed in a B-spline basis to achieve the desired smoothness in the transformation as well as computational efficiency. The key contributions of this work are (i) the use of Riesz transform to achieve better efficiency in computing the local frequency representation in comparison to Gabor filter-based approaches, (ii) new mathematical model for local-frequency based non-rigid registration, (iii) analytic computation of the gradient of the robust non-rigid registration cost function to achieve efficient and accurate registration. The proposed non-rigid L2E-based registration is a significant extension of research reported in literature to date. We present experimental results for registering several real data sets with synthetic and real non-rigid misalignments.