Jane Courtney

A Monocular Marker-Free Gait Measurement System

This paper presents a new, user-friendly, portable motion capture and gait analysis system for capturing and analyzing human gait, designed as a telemedicine tool to monitor remotely the progress of patients through treatment. The system requires minimal user input and simple single-camera filming (which can be acquired from a basic webcam) making it very accessible to nontechnical, nonclinical personnel. This system can allow gait studies to acquire a much larger data set and allow trained gait analysts to focus their skills on the interpretation phase of gait analysis. The design uses a novel motion capture method derived from spatiotemporal segmentation and model-based tracking. Testing is performed on four monocular, sagittal-view, sample gait videos. Results of modeling, tracking, and analysis stages are presented with standard gait graphs and parameters compared to manually acquired data.

Tracking protein dynamics with photoconvertible Dendra2 on spinning disk confocal systems

Understanding the dynamic properties of cellular proteins in live cells and in real time is essential to delineate their function. In this context, we introduce the Fluorescence Recovery After Photobleaching‐Photoactivation unit (Andor) combined with the Nikon Eclipse Ti E Spinning Disk (Andor) confocal microscope as an advantageous and robust platform to exploit the properties of the Dendra2 photoconvertible fluorescent protein (Evrogen) and analyse protein subcellular trafficking in living cells. A major advantage of the spinning disk confocal is the rapid acquisition speed, enabling high temporal resolution of cellular processes. Furthermore, photoconversion and imaging are less invasive on the spinning disk confocal as the cell exposition to illumination power is reduced, thereby minimizing photobleaching and increasing cell viability. We have tested this commercially available platform using experimental settings adapted to track the migration of fast trafficking proteins such as UBC9, Fibrillarin and have successfully characterized their differential motion between subnuclear structures. We describe here step‐by‐step procedures, with emphasis on cellular imaging parameters, to successfully perform the dynamic imaging and photoconversion of Dendra2‐fused proteins at high spatial and temporal resolutions necessary to characterize the trafficking pathways of proteins.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

Tracking transverse 2D ultrasound images of the carotid artery

This paper focuses on tracking transverse 2D ultrasound images as a means to produce a 3D representation of a bifurcating blood vessel in order to provide a foundation for autonomous aneurysm detection and classification, and atherosclerosis/atherosclerotic narrowing detection. In any healthcare system, a means to achieve the goal of automating point of care testing is desirable, especially given that a NHS study shows that 1.5% of men aged 65 studied had aortic diameters of greater than three centimeters [1]. In this paper, a method for creating a 3D representation of the carotid artery, determining and modeling the bifurcation region, and determining a subjects heart rate based on vascular distension in order to provide a foundation for autonomous point of care testing is presented.

Dynamics of HIV-1 Rev sub-nuclear trafficking reveal new insight into the role of RNA in the regulation of Rev nucleolar accumulation

Background The Nucleolus is a sub-nuclear compartment controlling key cellular processes, including ribosome biogenesis, transcriptional regulation, RNA trafficking and cell cycle control. Nucleolar structure is maintained through accumulation and release of retained proteins, which are selectively immobilised by RNA-protein, and/or proteinprotein interactions. As part of their replicative strategy, viruses can target the nucleolus. Specifically, the essential HIV-1 regulatory protein, Rev, selectively hijacks the Importin b/ Transportin and CRM-1 transport pathways in order to shuttle between the nucleolus and the cytoplasm, facilitating the nuclear export of singly and unspliced HIV-1 mRNA. In this context, the nucleolar trafficking of HIV-1 Rev and viral transcripts could be crucial in controlling HIV-1 gene expression & replication. However, the nature of this association remains to be investigated in living cells. To better understand the molecular determinants of Rev nucleolar accumulation, we monitored HIV-1 Rev intra-nuclear movements in real time & under distinct physiological conditions using photo-convertible Dendra2 (Evrogen), and compared it the nucleolar trafficking of HIV-1 Tat, the orchestrator of HIV-1 transcription.

Blood Vessel Diameter Estimation System Using Active Contours

The study and analysis of blood vessel geometry has become the basis of medical applications related to early diagnosis and effective monitoring of therapies in vascular diseases. This paper presents a new method to trace the outline of blood vessels from imperfect images and extract useful information about their dimensions in an automated manner.The system consists of a segmentation procedure that uses two Active Contours to detect blood vessel boundaries and a novel approach to measure blood vessel diameters directly as the distance between two points. We have succeeded in designing and implementing an automated, robust, measurement method that is not only accurate (it takes away human error) but also user-friendly and requires very little image pre-processing. The system is tested with a set of grey scale images of blood vessels.Results of all the aspects of the design and implementation are presented along with graphs and images.