Sharmishtaa Seshamani

Real-Time endoscopic mosaicking

With the advancement of minimally invasive techniques for surgical and diagnostic procedures, there is a growing need for the development of methods for improved visualization of internal body structures. Video mosaicking is one method for doing this. This approach provides a broader field of view of the scene by stitching together images in a video sequence. Of particular importance is the need for online processing to provide real-time feedback and visualization for image-guided surgery and diagnosis. We propose a method for online video mosaicking applied to endoscopic imagery, with examples in microscopic retinal imaging and catadioptric endometrial imaging.

Assessment of Crohn’s Disease Lesions in Wireless Capsule Endoscopy Images

Capsule endoscopy (CE) provides noninvasive access to a large part of the small bowel that is otherwise inaccessible without invasive and traumatic treatment. However, it also produces large amounts of data (approximately 50 000 images) that must be then manually reviewed by a clinician. Such large datasets provide an opportunity for application of image analysis and supervised learning methods. Automated analysis of CE images has only focused on detection, and often only for bleeding. Compared to these detection approaches, we explored assessment of discrete disease for lesions created by mucosal inflammation in Crohns disease (CD). Our work is the first study to systematically explore supervised classification for CD lesions, a classifier cascade to classify discrete lesions, as well as quantitative assessment of lesion severity. We used a well-developed database of 47 studies for evaluation of these methods. The developed methods show high agreement with ground truth severity ratings manually assigned by an expert, and good precision (>;90% for lesion detection) and recall (>;90%) for lesions of varying severity.

A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and an experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to current state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function.

A Method for handling intensity inhomogenieties in fMRI sequences of moving anatomy of the early developing brain

This paper presents a method for intensity inhomogeniety removal in fMRI studies of a moving subject. In such studies, subtle changes in signal as the subject moves in the presence of a bias field can be a significant confound for BOLD signal analysis. The proposed method avoids the need for a specific tissue model or assumptions about tissue homogeneity by making use of the multiple views of the underlying bias field provided by the subjects motion. A parametric bias field model is assumed and a regression model is used to estimate the basis function weights of this model. Quantitative evaluation of the effects of motion and noise in motion estimates are performed using simulated data. Results demonstrate the strength and robustness of the new method compared to the state of the art 4D nonparametric bias estimator (N4ITK). We also qualitatively demonstrate the impact of the method on resting state neuroimage analysis of a moving adult brain with simulated motion and bias fields, as well as on in vivo moving fetal fMRI.

Direct global adjustment methods for endoscopic mosaicking

Endoscopy is an invaluable tool for several surgical and diagnostic applications. It permits minimally invasive visualization of internal structures thus involving little or no injury to internal structures. This method of visualization however restricts the size of the imaging device and therefore compromises on the field of view captured in a single image. The problem of a narrow field of view can be solved by capturing video sequences and stitching them to generate a mosaic of the scene under consideration. Registration of images in the sequence is therefore a crucial step. Existing methods compute frame-to-frame registration estimates and use these to resample images in order to generate a mosaic. The complexity of the appearance of internal structures and accumulation of registration error in frame to frame estimates however can be large enough to cause a cumulative drift that can misrepresent the scene. These errors can be reduced by application of global adjustment schemes. In this paper, we present a set of techniques for overcoming this problem of drift for pixel based registration in order to achieve global consistency of mosaics. The algorithm uses the frame-to-frame estimate as an initialization and subsequently corrects these estimates by setting up a large scale optimization problem which simultaneously solves for all corrections of estimates. In addition we set up a graph and introduce loop closure constraints in order to ensure consistency of registration. We present our method and results in semi global and fully global graph based adjustment methods as well as validation of our results.

Detecting default mode networks in utero by integrated 4D fMRI reconstruction and analysis

Recently, there has been considerable interest, especially for in utero imaging, in the detection of functional connectivity in subjects whose motion cannot be controlled while in the MRI scanner. These cases require two advances over current studies: (1) multiecho acquisitions and (2) post processing and reconstruction that can deal with significant between slice motion during multislice protocols to allow for the ability to detect temporal correlations introduced by spatial scattering of slices into account. This article focuses on the estimation of a spatially and temporally regular time series from motion scattered slices of multiecho fMRI datasets using a full four‐dimensional (4D) iterative image reconstruction framework. The framework which includes quantitative MRI methods for artifact correction is evaluated using adult studies with and without motion to both refine parameter settings and evaluate the analysis pipeline. ICA analysis is then applied to the 4D image reconstruction of both adult and in utero fetal studies where resting state activity is perturbed by motion. Results indicate quantitative improvements in reconstruction quality when compared to the conventional 3D reconstruction approach (using simulated adult data) and demonstrate the ability to detect the default mode network in moving adults and fetuses with single‐subject and group analysis. Hum Brain Mapp 37:4158–4178, 2016.

A Meta Registration Framework for Lesion Matching

A variety of pixel and feature based methods have been proposed for registering multiple views of anatomy visible in studies obtained using diagnostic, minimally invasive imaging. A given registration method may outperform another depending on anatomical variations, imaging conditions, and imaging sensor performance, and it is often difficult a priori to determine the best registration method for a particular application. To address this problem, we propose a registration framework that pools the results of multiple registration methods using a decision function for validating registrations. We refer to this as meta registration. We demonstrate that our framework outperforms several individual registration methods on the task of registering multiple views of Crohns disease lesions sampled from a Capsule Endoscopy (CE) study database. We also report on preliminary work on assessing the quality of registrations obtained, and the possibility of using such assessment in the registration framework.

A Meta Method for Image Matching

This paper presents a novel system for image matching in optical endoscopy. The proposed metamatching system approaches the challenge of matching images in a complex scene by incorporating multiple matchers and a decision function. Experiments are presented for Crohns disease lesion matching in capsule endoscopy with a metamatcher consisting of five independent matchers. We compare the performance of six different types of decision functions. Results show that the F-measure of the metamatching system containing all five matchers is 4%-7% greater than the performance of using the best matcher only, with a maximum F-measure of 0.811. The robustness of the method is validated using simulated data generated by controlled deformations of the image. We also demonstrate how the addition of simulated data to the training set can be used to augment the performance of the metamatcher by up to 10%.

Learning disease severity for capsule endoscopy images

Wireless capsule endoscopy (CE) is increasing being used to assess several gastrointestinal(GI) diseases and disorders. Current clinical methods are based on subjective evaluation of images. In this paper, we develop a method for ranking lesions appearing in CE images. This ranking is based on pairwise comparisons among representative images supplied by an expert. With such sparse pairwise rank information for a small number of images, we investigate methods for creating and evaluating global ranking functions. In experiments with CE images, we train statistical classifiers using color and edge feature descriptors extracted frommanually annotated regions of interest. Experiments on a data set using Crohns disease lesions for lesion severity are presented with the developed ranking functions achieve high accuracy rates.

3D in utero quantification of T2* relaxation times in human fetal brain tissues for age optimized structural and functional MRI

Maximization of the blood oxygen level–dependent (BOLD) functional MRI (fMRI) contrast requires the echo time of the MR sequence to match the T2* value of the tissue of interest, which is expected to be higher in the fetal brain compared with the brain of a child or an adult.