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.

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.

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.

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.

Reconstructing 3D x-ray CT images of polymer gel dosimeters using the zero-scan method

In this study x-ray CT has been used to produce a 3D image of an irradiated PAGAT gel sample, with noise-reduction achieved using the ‘zero-scan’ method. The gel was repeatedly CT scanned and a linear fit to the varying Hounsfield unit of each pixel in the 3D volume was evaluated across the repeated scans, allowing a zero-scan extrapolation of the image to be obtained. To minimise heating of the CT scanner’s x-ray tube, this study used a large slice thickness (1 cm), to provide image slices across the irradiated region of the gel, and a relatively small number of CT scans (63), to extrapolate the zero-scan image. The resulting set of transverse images shows reduced noise compared to images from the initial CT scan of the gel, without being degraded by the additional radiation dose delivered to the gel during the repeated scanning. The full, 3D image of the gel has a low spatial resolution in the longitudinal direction, due to the selected scan parameters. Nonetheless, important features of the dose distribution are apparent in the 3D x-ray CT scan of the gel. The results of this study demonstrate that the zero-scan extrapolation method can be applied to the reconstruction of multiple x-ray CT slices, to provide useful 2D and 3D images of irradiated dosimetry gels.

Using images to communicate the hidden struggles of life on dialysis

Background: Nurse-patient communication in the hemodialysis context is unique given the amount of time spent together in a confined clinical room. Poor communication may lead to low quality nursing care and undesirable patient outcomes. Aim: To explore the use of images as a visual communication technique for nurses and patients in the hemodialysis context. Methods: Descriptive qualitative design. Fifty two cards containing specific photos, illustrations and words were used in conversations between patients (n = 9) and one of two nurse interviewers about being on hemodialysis. Interview transcripts were thematically analysed. Findings: An overall theme titled ‘revealing the hidden struggles of living on dialysis’ conceptually captured three sub-themes: (1) the increased importance of relationships; (2) the struggle with money; and (3) quality over quantity of life. The cards assisted in uncovering these often covert (to nurses) aspects of dialysis patients’ lives. Conclusion: Nurses may need to be aware of the dialysis patients’ hidden struggles which include the importance of relationships, financial issues and the importance of quality aspects such as travel. The use of images may assist in revealing the important issues for each patient struggling with the restrictive life that is imposed by dialysis.

Voltammetric monitoring of gold nanoparticle formation facilitated by glycyl-L-tyrosine : relation to electronic spectra and transmission electron microscopy images

Voltammetric techniques have been introduced to monitor the formation of gold nanoparticles produced via the reaction of the amino acid glycyl-L-tyrosine with Au(III) (bromoaurate) in 0.05 M KOH conditions. The alkaline conditions facilitate amino acid binding to Au(III), inhibit the rate of reduction to Au(0), and provide an excellent supporting electrolyte for voltammetric studies. Data obtained revealed that a range of time-dependent gold solution species are involved in gold nanoparticle formation and that the order in which reagents are mixed is critical to the outcome. Concomitantly with voltammetric measurements, the properties of gold nanoparticles formed are probed by examination of electronic spectra in order to understand how the solution environment present during nanoparticle growth affects the final distribution of the nanoparticles. Images obtained by the ex situ transmission electron microscopy (TEM) technique enable the physical properties of the nanoparticles isolated in the solid state to be assessed. Use of this combination of in situ and ex situ techniques provides a versatile framework for elucidating the details of nanoparticle formation.

A Human identification technique using images of the iris and wavelet transform

A new approach for recognizing the iris of the human eye is presented. Zero-crossings of the wavelet transform at various resolution levels are calculated over concentric circles on the iris, and the resulting one-dimensional (1-D) signals are compared with model features using different dissimilarity functions.

Sensationalizing death? Graphic disaster images in the tabloid and broadsheet press

Debates over the extent of graphic imagery of death in newspapers often suffer from generalized assertions that are based on inadequate or incomplete empirical evidence. Newspapers are believed to display death in very graphic ways, with particularly the tabloid press assumedly leading a race to the bottom. This article reports the results of a study of tabloid and broadsheet images of death from the 2010 Haiti earthquake in eight Western European and North American countries. It shows that, far from omnipresent, graphic images of death are relatively rare. While tabloids overall display a larger percentage of graphic images, this was not the case everywhere, with particularly the UK, Canada and the US displaying strong similarities between tabloids and broadsheets. In Austria, Germany, Norway and Switzerland, on the other hand, there were distinct differences between the two types. The article argues that different extents of tabloidization may account for these differences.

Detecting and Analyzing Linear Structures in Biomedical Images : A Case Study Using Corneal Nerve Fibers

Diabetic peripheral neuropathy (DPN) is one of the most common long-term complications of diabetes. The accurate detection and quantification of DPN are important for defining at-risk patients, anticipating deterioration, and assessing new therapies. Current methods of detecting and quantifying DPN, such as neurophysiology, lack sensitivity, require expert assessment and focus primarily on large nerve fibers. However, the earliest damage to nerve fibers in diabetic neuropathy is to the small nerve fibers. At present, small nerve fiber damage is currently assessed using skin/nerve biopsy; both are invasive technique and are not suitable for repeated investigations.

The visibility of disaster deaths in news images : a comparison of newspapers from 15 countries

The extent to which newspapers display graphic images of death has rarely been studied in relation to the degree of the visibility of bodies, nor do many comparative analyses exist. This has led to a narrow understanding of how and why audiences are exposed to human suffering around the world. In examining newspaper images of the dead from the 2010 Haiti earthquake across 15 countries, this study develops a graphic image content scale to measure such visualizations. It finds significant differences in graphic images across the studied sample, both in terms of the amount of images and the degree of visibility of death. The study argues that major sociocultural influences, such as different religious traditions and societal levels of violence are part of the reason for the differences.