Visualization and Intelligent Systems Laboratory
VISLab

 

 

Contact Information

VISLab
Winston Chung Hall Room 216
University of California, Riverside
900 University Avenue
Riverside, CA 92521-0425


Tel: (951)-827-3954

CRIS
Bourns College of Engineering
UCR
NSF IGERT on Video Bioinformatics

UCR Collaborators:
CSE
ECE
ME
STAT
PSYC
ENTM
BIOL
BPSC
ECON
MATH
BIOENG
MGNT

Other Collaborators:
Keio University

Other Activities:
IEEE Biometrics Workshop 2014
IEEE Biometrics Workshop 2013
Worshop on DVSN 2009
Multibiometrics Book

Webmaster Contact Information:
Alex Shin
wshin@ece.ucr.edu

Last updated: July 1, 2017

 

 

Brain

Spatio-temporal pattern recognition of dendritic spines and protein dynamics using live multichannel fluorescence microscopy

Actin-regulating proteins, such as cofilin, are essential in regulating the shape of dendritic spines, and synaptic plasticity in both neuronal functionality as well as in neurodegeneration related to aging. Presented is a novel automated pattern recognition system to analyze protein trafficking in neurons. Using spatio-temporal information present in multichannel fluorescence videos, the system generates a temporal maximum intensity projection that enhances the signal-to-noise ratio of important biological structures, segments and tracks dendritic spines, and quantifies the flux and density of proteins in spines. The temporal dynamics of spines is used to generate spine energy images which are used to automatically classify the shape of dendritic spines as stubby, mushroom, or thin. By tracking these spines over time and using their intensity profiles, the system is able to analyze the flux patterns of cofilin and other fluorescently stained proteins.

Dynamic Low-Level Context for the Detection of Mild Traumatic Brain Injury

T2 weighted MR image of half a coronal slice from the rat model dataset. A) Original T2 weighted image. B) Manual detection of the mTBI lesion (highlighted in red). Mild traumatic brain injury (mTBI) appears as low contrast lesions in magnetic resonance (MR) imaging. Standard automated detection approaches cannot detect the subtle changes caused by the lesions. We have are proposed and integrated new context features to improve the detection of mTBI lesions. The approach is validated on a temporal mTBI rat model dataset and shown to have improved dice score and convergence compared to other state-of-the-art approaches.

Automated Detection of Brain Abnormalities in Neonatal Hypoxiaischemic Injury

Symmetry integrated region growing (SIRG) based lesion detection. We compared the efficacy of three automated brain injury detection methods: SIRG, HRS, and MWS in human and animal MRI datasets for the detection of hypoxic ischemic injuries (HIIs). Sensitivity, specificity, and similarity were used as performance metrics based on manual ("gold standard") injury detection to quantify comparisons. When compared to the gold standard results SIRG performed the best in 62% of the data, while results from HRS performed best in 29% of the data, and results for MWS performed the best in 9% of the data. Injury severity detection revealed that SIRG performed the best in 67% of the cases, while HRS performed the best in only 33% of the cases. Among these methods, SIRG performs the best in detecting lesion volumes; HRS is the most robust, while MWS is inferior in both respects.

Visual and Contextual Modeling for the Detection of Repeated m-TBI

Example of fusion between visual model and contextual model on a contralaterally injured rat. Currently, there is a lack of computational methods for the evaluation of mild traumatic brain injury (mTBI). Furthermore, the development of automated analyses has been hindered by the subtle nature of mTBI abnormalities. This research proposes an approach that is able to detect mTBI lesions by combining both the high-level context and low-level visual information. The visual model utilizes texture features in MRI along with a probabilistic support vector machine. Clinically, our approach has the potential to benefit both clinicians by speeding diagnosis and patients by improving clinical care.

Detecting Mild Traumatic Brain Injury using Dynamic Low Level Context

Mild traumatic brain injury is difficult to detect in standard magnetic resonance (MR) images due to the low contrast appearance of lesions. In this research a discriminative approach is presented using a classifier to directly estimate the posterior probability of lesion at every voxel using low-level context learned from previous classifiers. Both visual features including multiple texture measures, and context features, which include novel features such as proximity, directional distance, and posterior marginal edge distance, are used. The context is also taken from previous time points, so the system automatically captures the dynamics of the injury progression. The approach is tested on an mTBI rat model using MR imaging at multiple time points. Our results show an improved performance in both the dice score and convergence rate compared to other approaches.

Computational Analysis Reveals Increased Blood Deposition

3D reconstruction of injury volume Mild traumatic brain injury (mTBI) has become an increasing public health concern. This study investigated the temporal development of cortical lesions. Examination of lesion volume 1d post last injury revealed increased tissue abnormalities within animals compared to other groups. Histological measurements revealed spatial overlap of regions containing blood deposition and microglial activation within the cortices of all animals. Our findings suggest that there is a window of tissue vulnerability where a second distant mTBI, induced 7d after an initial injury, exacerbates tissue abnormalities consistent with hemorrhagic progression.

Contextual and Visual Modeling for Detection of Mild Traumatic Brain Injury in MRI

Mild traumatic brain injury (mTBI) is difficult to detect as the current tools are qualitative, which can lead to poor diagnosis and treatment. The low contrast appearance of mTBI abnormalities on magnetic resonance (MR) images makes quantification problematic for image processing and analysis techniques. To overcome these difficulties, an algorithm is proposed that takes advantage of subject information and texture information from MR images. A contextual model is developed to simulate the progression of the disease using multiple inputs, such as the time postinjury and the location of injury. Textural features are used along with feature selection for a single MR modality. Results from a probabilistic support vector machine using textural features are fused with the contextual model to obtain a robust estimation of abnormal tissue. A novel rat temporal dataset demonstrates the ability of our approach to outperform other state of the art approaches.

Automated Ischemic Lesion Detection in a NeonatalModel of Hypoxic Ischemic Injury

Here we introduce and compare an automated detection system for ischemic lesions in a neonatal model of BCAO-H from T2 weighted MRI (T2WI) to the currently used "gold standard" of manual segmentation. Forty-three, P10 BCAO-H rat pups and 8 controls underwent T2WI for 1 day and for 28 days. A computational imaging method - Hierarchical Region Splitting (HRS) - was developed to automatically and rapidly detect and quantify 3D lesion and normal appearing brain matter (NABM) volumes. HRS quantified lesions and NABM volumes within 15 seconds in comparison to 3 hours for its manual counterpart.

Semi-Automated Segmentation of ADC Maps Reliably Defines Ischemic Perinatal Stroke Injury

Ischemic brain tissue has a signature hypointensity on ADC maps that indicates a net reduction in water diffusion relative to normal unaffected tissue. The ischemic lesions induced by embolic arterial stroke are prominent within the first 72 hrs of injury and can be defined by identifying and segmenting the hypointense region. Assessment of these ischemic lesions soon after injury would help clinicians make timely, informative treatment decisions. Manual volumetric injury quantification is not used clinically because it is a labor intensive process. Observer (inter-/intra-) variability can also be problematic; however, it remains the gold standard. We used a multi-disciplinary approach to develop two semi-automated methods of ischemic injury segmentation: ADC thresholding and hierarchical region splitting, and compared them with manual segmentation results. We believe that this multi-disciplinary approach will provide a fundamental basis for the development of novel and clinically relevant automated segmentation software for rapid and unbiased ischemic injury discrimination.

Symmetry-Integrated Injury Detection for Brain MRI

We present a new brain injury detection approach in images acquired by magnetic resonance imaging (MRI). The proposed approach is based on the fact that the anatomical structure of a 2D brain is highly symmetric, while most of the injury in the brain generally indicates asymmetry. The approach starts from symmetry integrated region growing segmentation of the brain images using the symmetry affinity matrix, and candidate asymmetric regions are initially extracted using kurtosis and skewness of symmetry affinity matrix. An Expectation Maximum classifier with Gaussian mixture model is used explicitly to classify asymmetric regions into two sections: injury and non-injury. Experimental results are carried out to demonstrate the efficacy of the approach for injury detection.