An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

Reading images : the book club in the art gallery

This paper seeks to document and understand one instance of community-university engagement: that of an on-going book club organised in conjunction with public art exhibitions. The curator of the Queensland University of Technology (QUT) Art Museum invited the authors, three postgraduate research students in the faculty of Creative Writing and Literary Studies at QUT, to facilitate an informal book club. The purpose of the book club was to generate discussion, through engagement with fiction, around the themes and ideas explored in the Art Museum’s exhibitions. For example, during the William Robinson exhibition, which presented evocative images of the environment around Brisbane, Queensland, the book club explored texts that symbolically represented aspects of the Australian landscape in a variety of modes and guises. This paper emerges as a result of the authors’ observations during, and reflections on, their experiences facilitating the book club. It responds to the research question, how can we create a best practice model to engage readers through open-ended, reciprocal discussion of fiction, while at the same time encouraging interactions in the gallery space? To provide an overview of reading practices in book clubs, we rely on Jenny Hartley’s seminal text on the subject, The Reading Groups Book (2002). Although the book club was open to all members of the community, the participants were generally women. Elizabeth Long, in Book Clubs: Woman and the Uses of Reading in the Everyday (2003), offers a comprehensive account of women’s interactions as they engage in a reading community. Long (2003, 2) observes that an image of the solitary reader governs our understanding of reading. Long challenges this notion, arguing that reading is profoundly social (ibid), and, as women read and talk in book clubs, ‘they are supporting each other in a collective working-out of their relationship to a particular historical movement and the particular social conditions that characterise it’ (Long 2003, 22). Despite the book club’s capacity to act as a forum for analytical discussion, DeNel Rehberg Sedo (2010, 2) argues that there are barriers to interaction in such a space, including that members require a level of cultural capital and literacy before they feel comfortable to participate. How then can we seek to make book clubs more inclusive, and encourage readers to discuss and question outside of their comfort zone? How can we support interactions with texts and images? In this paper, we draw on pragmatic and self-reflective practice methods to document and evaluate the development of the book club model designed to facilitate engagement. We discuss how we selected texts, negotiating the dual needs of relevance to the exhibition and engagement with, and appeal to, the community. We reflect on developing questions and material prior to the book club to encourage interaction, and describe how we developed a flexible approach to question-asking and facilitating discussion. We conclude by reflecting on the outcomes of and improvements to the model.

Real-time power line extraction from unmanned aerial system video images

In this paper a real-time vision based power line extraction solution is investigated for active UAV guidance. The line extraction algorithm starts from ridge points detected by steerable filters. A collinear line segments fitting algorithm is followed up by considering global and local information together with multiple collinear measurements. GPU boosted algorithm implementation is also investigated in the experiment. The experimental result shows that the proposed algorithm outperforms two baseline line detection algorithms and is able to fitting long collinear line segments. The low computational cost of the algorithm make suitable for real-time applications.

Integration of medical images to the teaching of systematic pathology : an evaluation of relevance

A sound knowledge of pathological disease processes is required for professional practice within health professions. The project described in this paper reviewed the resources currently available for the delivery of systematic pathology tutorials. Additional complementary resources were developed and the inclusion of these additional learning resources in practical tutorial sessions was evaluated for their impact on student learning. Student evaluation of the learning resources was undertaken across one semester with two different cohorts of health profession students using questionnaires and focus group discussion. Both cohorts reported an enhancement to their understanding of pathological disease processes through the use of the additional resources. Results indicate student perception of the value of the resources correlates with staff perception and is independent of prior experiences.

Static vertical displacement measurement of bridges using Fiber Bragg Grating (FBG) sensors

Vertical displacements are one of the most relevant parameters for structural health monitoring of bridges in both the short and long terms. Bridge managers around the globe are always looking for a simple way to measure vertical displacements of bridges. However, it is difficult to carry out such measurements. On the other hand, in recent years, with the advancement of fiber-optic technologies, fiber Bragg grating (FBG) sensors are more commonly used in structural health monitoring due to their outstanding advantages including multiplexing capability, immunity of electromagnetic interference as well as high resolution and accuracy. For these reasons, using FBG sensors is proposed to develop a simple, inexpensive and practical method to measure vertical displacements of bridges. A curvature approach for vertical displacement measurements using curvature measurements is proposed. In addition, with the successful development of FBG tilt sensors, an inclination approach is also proposed using inclination measurements. A series of simulation tests of a full- scale bridge was conducted. It shows that both of the approaches can be implemented to determine vertical displacements for bridges with various support conditions, varying stiffness (EI) along the spans and without any prior known loading. These approaches can thus measure vertical displacements for most of slab-on-girder and box-girder bridges. Besides, the approaches are feasible to implement for bridges under various loading. Moreover, with the advantages of FBG sensors, they can be implemented to monitor bridge behavior remotely and in real time. A beam loading test was conducted to determine vertical displacements using FBG strain sensors and tilt sensors. The discrepancies as compared with dial gauges reading using the curvature and inclination approaches are 0.14mm (1.1%) and 0.41mm (3.2%), respectively. Further recommendations of these approaches for developments will also be discussed at the end of the paper.

A comparison of calculated and experimental HRTEM images of twinned boron carbide

High resolution TEM images of boron carbide (B13C2) have been recorded and compared with images calculated using the multislice method as implemented by M. A. O'Keefe in the SHRLI programs. Images calculated for the [010] zone, using machine parameters for the JEOL 2000FX AEM operating at 200 keV, indicate that for the structure model of Will et al., the optimum defocus image can be interpreted such that white spots correspond to B12 icosahedra for thin specimens and to low density channels through the structure adjacent to the direct inter-icosahedral bonds for specimens of intermediate thickness (-40 > t > -100 nm). With this information, and from the symmetry observed in the TEM images, it is likely that the (101) twin plane passes through the center of icosahedron located at the origin. This model was tested using the method of periodic continuation. Resulting images compare favorably with experimental images, thus supporting the structural model. The introduction of a (101) twin plane through the origin creates distortions to the icosahedral linkages as well as to the intra-icosahedral bonding. This increases the inequivalence of adjacent icosahedral sites along the twin plane, and thereby increases the likelihood of bipolaron hopping.

An optimal under-frequency load shedding strategy considering distributed generators and load static characteristics

The well-established under-frequency load shedding (UFLS) is deemed to be the last of effective remedial measures against a severe frequency decline of a power system. With the ever-increasing size of power systems and the extensive penetration of distributed generators (DGs) in power systems, the problem of developing an optimal UFLS strategy is facing some new challenges. Given this background, an optimal UFLS strategy for a distribution system with DGs and load static characteristics taken into consideration is developed. Based on the frequency and the rate of change of frequency, the presented strategy consists of several basic rounds and a special round. In the basic round, the frequency emergency can be alleviated by quickly shedding some loads. In the special round, the frequency security can be maintained, and the operating parameters of the distribution system can be optimized by adjusting the output powers of DGs and some loads. The modified IEEE 37-node test feeder is employed to demonstrate the essential features of the developed optimal UFLS strategy in the MATLAB/SIMULINK environment.

Static analysis of executables for collaborative malware detection on Android

Smartphones are getting increasingly popular and several malwares appeared targeting these devices. General countermeasures to smartphone malwares are currently limited to signature-based antivirus scanners which efficiently detect known malwares, but they have serious shortcomings with new and unknown malwares creating a window of opportunity for attackers. As smartphones become host for sensitive data and applications, extended malware detection mechanisms are necessary complying with the corresponding resource constraints. The contribution of this paper is twofold. First, we perform static analysis on the executables to extract their function calls in Android environment using the command readelf. Function call lists are compared with malware executables for classifying them with PART, Prism and Nearest Neighbor Algorithms. Second, we present a collaborative malware detection approach to extend these results. Corresponding simulation results are presented.

Detecting Symbian OS malware through static function call analysis

Smartphones become very critical part of our lives as they offer advanced capabilities with PC-like functionalities. They are getting widely deployed while not only being used for classical voice-centric communication. New smartphone malwares keep emerging where most of them still target Symbian OS. In the case of Symbian OS, application signing seemed to be an appropriate measure for slowing down malware appearance. Unfortunately, latest examples showed that signing can be bypassed resulting in new malware outbreak. In this paper, we present a novel approach to static malware detection in resource-limited mobile environments. This approach can be used to extend currently used third-party application signing mechanisms for increasing malware detection capabilities. In our work, we extract function calls from binaries in order to apply our clustering mechanism, called centroid. This method is capable of detecting unknown malwares. Our results are promising where the employed mechanism might find application at distribution channels, like online application stores. Additionally, it seems suitable for directly being used on smartphones for (pre-)checking installed applications.

Using static analysis for automatic assessment and mitigation of unwanted and malicious activities within Android applications

In the last decade, smartphones have gained widespread usage. Since the advent of online application stores, hundreds of thousands of applications have become instantly available to millions of smart-phone users. Within the Android ecosystem, application security is governed by digital signatures and a list of coarse-grained permissions. However, this mechanism is not fine-grained enough to provide the user with a sufficient means of control of the applications' activities. Abuse of highly sensible private information such as phone numbers without users' notice is the result. We show that there is a high frequency of privacy leaks even among widely popular applications. Together with the fact that the majority of the users are not proficient in computer security, this presents a challenge to the engineers developing security solutions for the platform. Our contribution is twofold: first, we propose a service which is able to assess Android Market applications via static analysis and provide detailed, but readable reports to the user. Second, we describe a means to mitigate security and privacy threats by automated reverse-engineering and refactoring binary application packages according to the users' security preferences.

Performance characterization of VGCF/epoxy nanocomposite sensors under static load cycles and in static structural health monitoring

Compared to conventional metal-foil strain gauges, nanocomposite piezoresistive strain sensors have demonstrated high strain sensitivity and have been attracting increasing attention in recent years. To fulfil their ultimate success, the performance of vapor growth carbon fiber (VGCF)/epoxy nanocomposite strain sensors subjected to static cyclic loads was evaluated in this work. A strain-equivalent quantity (resistance change ratio) in cantilever beams with intentionally induced notches in bending was evaluated using the conventional metal-foil strain gauges and the VGCF/epoxy nanocomposite sensors. Compared to the metal-foil strain gauges, the nanocomposite sensors are much more sensitive to even slight structural damage. Therefore, it was confirmed that the signal stability, reproducibility, and durability of these nanocomposite sensors are very promising, leading to the present endeavor to apply them for static structural health monitoring.

Static smartphone malware detection

Static anaylsis represents an approach of checking source code or compiled code of applications before it gets executed. Chess and McGraw state that static anaylsis promises to identify common coding problems automatically. While manual code checking is also a form of static analysis, software tools are used in most cases in order to perform the checks. Chess and McGraw additionaly claim that good static checkers can help to spot and eradicate common security bugs.

Breast cancer detection from thermal images using bispectral invariant features

Highly sensitive infrared (IR) cameras provide high-resolution diagnostic images of the temperature and vascular changes of breasts. These images can be processed to emphasize hot spots that exhibit early and subtle changes owing to pathology. The resulting images show clusters that appear random in shape and spatial distribution but carry class dependent information in shape and texture. Automated pattern recognition techniques are challenged because of changes in location, size and orientation of these clusters. Higher order spectral invariant features provide robustness to such transformations and are suited for texture and shape dependent information extraction from noisy images. In this work, the effectiveness of bispectral invariant features in diagnostic classification of breast thermal images into malignant, benign and normal classes is evaluated and a phase-only variant of these features is proposed. High resolution IR images of breasts, captured with measuring accuracy of ±0.4% (full scale) and temperature resolution of 0.1 °C black body, depicting malignant, benign and normal pathologies are used in this study. Breast images are registered using their lower boundaries, automatically extracted using landmark points whose locations are learned during training. Boundaries are extracted using Canny edge detection and elimination of inner edges. Breast images are then segmented using fuzzy c-means clustering and the hottest regions are selected for feature extraction. Bispectral invariant features are extracted from Radon projections of these images. An Adaboost classifier is used to select and fuse the best features during training and then classify unseen test images into malignant, benign and normal classes. A data set comprising 9 malignant, 12 benign and 11 normal cases is used for evaluation of performance. Malignant cases are detected with 95% accuracy. A variant of the features using the normalized bispectrum, which discards all magnitude information, is shown to perform better for classification between benign and normal cases, with 83% accuracy compared to 66% for the original.

Static and dynamic performance of lightweight hybrid composite floor plate system

In the modern built environment, building construction and demolition consume a large amount of energy and emits greenhouse gasses due to widely used conventional construction materials such as reinforced and composite concrete. These materials consume high amount of natural resources and possess high embodied energy. More energy is required to recycle or reuse such materials at the cessation of use. Therefore, it is very important to use recyclable or reusable new materials in building construction in order to conserve natural resources and reduce the energy and emissions associated with conventional materials. Advancements in materials technology have resulted in the introduction of new composite and hybrid materials in infrastructure construction as alternatives to the conventional materials. This research project has developed a lightweight and prefabricatable Hybrid Composite Floor Plate System (HCFPS) as an alternative to conventional floor system, with desirable properties, easy to construct, economical, demountable, recyclable and reusable. Component materials of HCFPS include a central Polyurethane (PU) core, outer layers of Glass-fiber Reinforced Cement (GRC) and steel laminates at tensile regions. This research work explored the structural adequacy and performance characteristics of hybridised GRC, PU and steel laminate for the development of HCFPS. Performance characteristics of HCFPS were investigated using Finite Element (FE) method simulations supported by experimental testing. Parametric studies were conducted to develop the HCFPS to satisfy static performance using sectional configurations, spans, loading and material properties as the parameters. Dynamic response of HCFPS floors was investigated by conducting parametric studies using material properties, walking frequency and damping as the parameters. Research findings show that HCFPS can be used in office and residential buildings to provide acceptable static and dynamic performance. Design guidelines were developed for this new floor system. HCFPS is easy to construct and economical compared to conventional floor systems as it is lightweight and prefabricatable floor system. This floor system can also be demounted and reused or recycled at the cessation of use due to its component materials.

The appearance and effects of metallic implants in CT images

Contemporary 3D radiotherapy treatment planning relies upon the use of 3D electron density maps derived from computed tomography (CT) scans of patient anatomy, to evaluate the effects of that anatomy on radiation dose distributions. Production of these electron density maps requires that the CT numbers (Hounsfield units) that quantify the attenuation of the x-ray beam by the patient’s anatomy must be reliably converted into electron densities, using a stable calibration relationship. This study investigates the fidelity of electron density assignment in the presence of metallic prostheses and implants.