RSVP Keyboard
People with severe speech and physical impairments can benefit from a direct brain computer interface for their communication needs. This project aims to develop an AAC interface using noninvasive EEG sensors to infer the user\\\'s intent regarding desired letters and symbols during text generation. The designed RSVP Keyboard system will utilize rapid serial visual presentation of letter sequences coupled with probabilistic and adaptive open vocabulary language models and EEG signal processing and classification algorithms. The designed brain interface relies on event related potentials including the P300 signal. The project design tightly couples feedback from locked-in consultants who will test the system design at regular intervals and provide critical feedback in future design improvements.
RSVP iconCHAT
Most existing BCI research for assistive communication interfaces focus on the use letters to generate written text. This requires the subjects to be literate and comfortable with typing in general. As an alternative approach, in this project, we seek to design a BCI that enables the user to generate language using an iconic language called iconCHAT developed by Dr. Rupal Patel. Expected benefits include increased speed of communication as each icon might represent a word or phrase so equal number of item selection can construct a sentence instead of a word compared to RSVP Keyboard. A potential drawback is the necessity for the subject to become familiar with the icon set; this also means a closed vocabulary language generation system which is suitable for limited context interactions. An option to switch to letters for open vocabulary text generation can be incorporated to the final design for users that prefer to have this option.
Augmented Cognition Computer Games
This project aims to develop interactive computer games that are aware of the user\'s cognitive state and engagement in order to adjust its challenge level automatically for the purpose of maintaining a predetermined effective mental effort level. The system features a fusion of passive BCI that assesses the neurological markers in relationship to behavioral markers as well as performance indices specifically designed to measure cognitive engagement. These customized games are specifically designed to be simultaneously entertaining and engaging in a manner that emulates established batteries of cognitive tests and exercises.
SSVEP-based BCI Design
Steady state visually evoked potentials (SSVEP) of the visual cortex provide an alternative means for enabling communication between a brain and a computer system. Being relatively easy to induce, and requiring almost no subject training and minimal calibration time, SSVEP signals are prime candidates for developing BCI controlled applications. We are exploring the use of SSVEP inducing stimuli and associated signal processing and classification algorithms primarily in environmental control applications such as navigating a robot/wheelchair. The reliable and robust nature of these signals also make them ideal for undergraduate research activities in BCI technology and application development .
Real Time Lung Tumor Tracking
Radiotherapy is an effective treatment technique for lung cancer. However, the movement of lung tumors during normal respiration makes it difficult to accurately irradiate the tumor. Precise lung tumor localization is vital to efficiently treating the tumor and avoiding unnecessary radiation exposure of normal tissues. Estimating the motion model of the tumor may lead to improved treatment planning and dose calculation throughout the therapy. 4D Computed Tomography (CT) images taken prior to treatment (to develop the patient\'s treatment plan) provide valuable information about the movement of the thoracic organs and the tumor. For each radiotherapy treatment session, a set of kilovoltage X-ray images (kV images) are acquired to aid in the alignment of the treatment target relative to the radiation beam. This project focuses on real time lung tumor tracking by incorporating information and labels from 4DCT on kV x-ray videos for treatment-day specific tumor motion models.
Predicting Migration of Cancer Cells using Diffusion Tensor Imaging
Diffusion tensor Magnetic Resonance Imaging (MRI) is a biomedical visualization technique, which shows direction of water diffusion. Diffusion Tensor Imaging (DTI) is an application of diffusion MRI aiming to extract and characterize diffusion anisotropy affects. When applied to brain, DTI shows the motion flow in the white matter of brain. Radiotherapy is widely used intreatment of malignant brain lesions. Current treatment plans include a fixed length margin around the tumor region of interest to account for the possible tumor spread. However, progressive tumors might occur outside of these margins, which requires more analysis about the spread of brain tumors. In this project, we are interested in predicting migration of cancer cells by using diffusion tensor MRI and finding out whether neuronal fiber pathways might provide possible routes for the spread of cancer cells. The outcome will help creating improved anisotropic margins for radiation treatment of brain tumors.
Tractography Techniques for Tubular Structures with Automated Bifurcation Detection
Tree and graph structures consisting of tubular segments are omnipresent in biological systems; consider the axons and dendritic trees of neurons, vascular networks in various organs, bronchial tree in the lungs, river and road networks in geospatial imagery (a 2-dimensional instantiation of the same concept). Biomedical 3-dimensional (3D) imagery obtained using various imaging modalities including confocal microscopy, computerized tomography (CT), magnetic resonance imaging (MRI) can be utilized to analyze and extract the 3D structure of tubular object networks which could be used to model and simulate such networks structurally and functionally, as well as design virtual endoscopy type diagnostic applications. We are currently focusing on confocal microscopy imagery of neural networks and their dendritic tree structures. Especially, we have been working with Brainbow imagery. Automatic extraction of dendritic tree structures is an important first step in processing massive image data to be used in improving our understanding of how the brain and the nervous system works.
Semi-supervised Segmentation of Organs and Tumors in 4D-CT
Radiation therapy of tumors relies on 3D-CT and 4D-CT treatment planning imagery which is manually segmented (delineated) and labeled prior to the optimization of the dose delivery plan. Automatic segmentation of all regions of interest has been a topic of intense research interest yet clinical practitioners are unsatisfied with the performance of existing solutions. It is our goal to keep the clinician in the loop during the process and design an interactive segmentation tool that fuses inputs from the expert user with low level features in imagery to speed up the manual delineation process. One important goal is to accurately transfer object boundaries from one respiration phase of 4D-CT to the other without performing 3D-to-3D deformable registration.
Interaction of Nanoparticles with Lipid Vesicles
Novel properties of nanoparticles have numerous potential technological applications but at the same time underlie new kinds of biological effects. Uniqueness of nano particles and nano materials requires a new experimental methodology in order to acquire knowledge about their toxic effect on biological systems and environment in general. Much evidence suggests that nano particles affect cell membrane stability and subsequently exert toxic effects. To explore these effects, we propose an in vitro experiment with a simple biological system, a simulation of cell membrane - lipid vesicle. Giant lipid vesicles are a promising choice due to controllability and repeatability of experimental conditions. Due to their size, which is on the same order of magnitude as the size of cells, vesicles can be directly observed under the light microscope. Vesicles\' shape changes and fluctuations have been widely investigated by various techniques, however microscopy imaging is among most common. Most researchers focus on recording single vesicles throughout the exposure period and observing changes in their morphology. Instead, we propose recording populations of vesicles at various times of exposure and calculating statistical analysis of the vesicles size and morphological distributions. The hypothesis is that different nano particles have different potential to interfere with lipid membranes. We expect that this will be manifested as vesicles\' shape transformation. Our preliminary experiments already showed that changes in populations of vesicles can be detected with this approach. Our future direction is toward improving existing approaches to capturing of images and their post processing.
Tensor Decomposition Analysis
A tensor is a multiway array of scalars; in this context it is a generalization of scalars (order-0), vectors (order-1), and matrices (order-2) to higher-order structures. Tensor analysis is an increasingly relevant and interesting field of inquiry in signal processing and machine learning as generalizations of rank-1 decompositions of matrices such as the singular value decomposition (or eigendecomposition of symmetric matrices) have found considerable application and success. Decompositions of tensors emerge and become relevant when high-order data or statistics are analyzed. Canonical decomposition (also called parallel factor analysis) and other decomposition methodologies exist and exhibit useful properties such as uniqueness. However, this particular decomposition lacks structure in its vector frame that forms the rank-one decomposition components, which prevents recursive solution formulations as in deflation of principal components. The goal of this project is to develop a non-redundant tensor decomposition, which can be interpreted as a generalization of the spherical coordinate system of vectors and the orthogonal matrix group based on a predetermined frame of basis vectors. This imposed structure prevents the decomposition from achieving the minimum cross-product tensor rank as canonical decomposition does; however, we think it provides a solution that is more suitable for recursive calculations that is useful and important in dimension reduction applications.
Principal Curves and Surfaces
Principal, saddle, and minor surfaces are critical surfaces of various dimensions that underlie functions which represent data density over some suitable space; this could be color or other feature distribution over space for images or probability density for arbitrary features in a statistical machine learning setting. We present a generalization of the local maximum, minimum, or saddle point concept as the fundamental definition of such surfaces in an attempt to frame the problem of manifold learning (and related problems with various names) as a geometrical structure identification problem. Our definition of the principal surface of a function is as follows: a point is an element of the principal surface if that point is a local maximum of the function in the orthogonal subspace at that point. This modifies Hastie\'s definition of self-consistent principal surfaces by replacing the mean-in-the-orthogonal-subspace with local maximum. The advantages are: (i) the definition is local and is only concerned with local derivatives of the function, (ii) it is trivial to define other critical surfaces such as saddle and minor surfaces, which generalize critical points (0-dimensional critical surfaces) to any dimensionality, (iii) since given the function (for instance the pdf) we can calculate the gradient, Hessian, etc at any point, we can know whether a point is on this principal surface or not without solving for the whole surface (as in manifold learning for instance). This latter property is very useful in designing manifold learning algorithms as well as dimension reduction techniques. The definition also easily handles bifurcations, graphs, trees that underlie the structure; most manifold learning algorithms assume a globally smooth manifold and fail to handle singularities easily or rigorously.
Affect Analysis using fMRI
Emotion Analysis using Multimodal Sensing
Stereotypy Analysis in Autism
Meditative State Analysis
Mind-body medicine such as meditation and yoga is the most commonly used type of complementary and alternative medicine treatment. However, the evidence for efficacy is not compelling and stems from several problems including inadequate controls, inappropriate and highly variable outcome measures, and lack of measures for intervention adherence. An additional problem includes the lack of a measure for practice ability which would improve analysis of intervention trial data. Mindfulness meditation (MM) is one mind-body approach that is popular and teaches skills applicable to everyday life situations. A key facet of MM is attending to the present moment in a non-judgmental way. Specific examples of MM intervention have already been formally studied and applied in a variety of clinical conditions. In order to develop better mind-body research methodology, it would be useful to demonstrate a measure of meditation ability. There have been some studies analyzing self-rated meditation ability using self- rated measures. While some physical mind-body interventions have used objective ability measures, e.g., video- ecording, the meditation intervention literature lacks any sort of objective adherence or meditation ability measures. Objectively assessing meditation ability might shed light on why meditation trials succeed or fail. There has been some evidence of Electroencephalography (EEG) changes during meditation. EEG is altered during meditation, primarily shown with expert meditators and not as well shown with novices. These meditative state changes likely overlap with relaxation changes. There has been interest in EEG synchrony as a meditation measure. The original synchrony analyses were based on using wavelets. We performed a randomized controlled intervention of MM in a population of older people with high stress levels, a population we have shown benefiting from a MM intervention. A physiological measure of meditation ability has not been established in the meditation research field, and studies often rely on self-report to gauge meditation experiences. Our plan was to define a novel measure of quality of meditation ability practice using a physiologic panel including respiration and EEG.
Motor Imagery BCI
Brain-Controlled Robots
Transcranial Current Stimulation
Protein Folding Analysis using SAXS
Detecting Clinical Laboratory Errors
Primate Behavior Analysis from Audio-Visual Sensors
Primate Behavior Analysis from Audio-Visual Sensors
Cell Tracking
Interactive Segmentation
Vessel Segmentation
Retina Vasculature Analysis
Blood Flow Analysis in Tongue Vessels
Principal Surfaces
Manifold Unwrapping
Error Dependent Risk
Feature Dimension Reduction
Sensor Decision Fusion
MEDITATION
Mind-body medicine such as meditation and yoga is the most commonly used type of complementary and alternative medicine treatment. However, the evidence for efficacy is not compelling and stems from several problems including inadequate controls, inappropriate and highly variable outcome measures, and lack of measures for intervention adherence. An additional problem includes the lack of a measure for practice ability which would improve analysis of intervention trial data. Mindfulness meditation (MM) is one mind-body approach that is popular and teaches skills applicable to everyday life situations. A key facet of MM is attending to the present moment in a non-judgmental way. Specific examples of MM intervention have already been formally studied and applied in a variety of clinical conditions. In order to develop better mind-body research methodology, it would be useful to demonstrate a measure of meditation ability. There have been some studies analyzing self-rated meditation ability using self- ated measures. While some physical mind-body interventions have used objective ability measures, e.g., video-recording, the meditation intervention literature lacks any sort of objective adherence or meditation ability measures. Objectively assessing meditation ability might shed light on why meditation trials succeed or fail. There has been some evidence of Electroencephalography (EEG) changes during meditation. EEG is altered during meditation, primarily shown with expert meditators and not as well shown with novices. These meditative state changes likely overlap with relaxation changes. There has been interest in EEG synchrony as a meditation measure. The original synchrony analyses were based on using wavelets. We performed a randomized controlled intervention of MM in a population of older people with high stress levels, a population we have shown benefiting from a MM intervention. A physiological measure of meditation ability has not been established in the meditation research field, and studies often rely on self-report to gauge meditation experiences. Our plan was to define a novel measure of quality of meditation ability practice using a physiologic panel including respiration and EEG.