Identifying weak linear features with the "coalescing shortest path image transform"

The detection of line-like features in images finds many applications in microanalysis. Actin fibers, microtubules, neurites, pilis, DNA, and other biological structures all come up as tenuous curved lines in microscopy images. A reliable tracing method that preserves the integrity and details of these structures is particularly important for quantitative analyses. We have developed a new image transform called the "Coalescing Shortest Path Image Transform" with very encouraging properties. Our scheme efficiently combines information from an extensive collection of shortest paths in the image to delineate even very weak linear features. © Copyright Microscopy Society of America 2011.

DroplIT, an improved image analysis method for droplet identification in high-throughput crystallization trials

The application of robotics to protein crystallization trials has resulted in the production of millions of images. Manual inspection of these images to find crystals and other interesting outcomes is a major rate-limiting step. As a result there has been intense activity in developing automated algorithms to analyse these images. The very first step for most systems that have been described in the literature is to delineate each droplet. Here, a novel approach that reaches over 97% success rate and subsecond processing times is presented. This will form the seed of a new high-throughput system to scrutinize massive crystallization campaigns automatically. © 2010 International Union of Crystallography Printed in Singapore-all rights reserved.

Multi-modal deformable medical image registration

Non-rigid image registration is an essential tool required for overcoming the inherent local anatomical variations that exist between images acquired from different individuals or atlases. Furthermore, certain applications require this type of registration to operate across images acquired from different imaging modalities. One popular local approach for estimating this registration is a block matching procedure utilising the mutual information criterion. However, previous block matching procedures generate a sparse deformation field containing displacement estimates at uniformly spaced locations. This neglects to make use of the evidence that block matching results are dependent on the amount of local information content. This paper presents a solution to this drawback by proposing the use of a Reversible Jump Markov Chain Monte Carlo statistical procedure to optimally select grid points of interest. Three different methods are then compared to propagate the estimated sparse deformation field to the entire image including a thin-plate spline warp, Gaussian convolution, and a hybrid fluid technique. Results show that non-rigid registration can be improved by using the proposed algorithm to optimally select grid points of interest.

A Likelihood-Maximizing Framework for Enhanced In-Car Speech Recognition Based on Speech Dialog System Interaction

Speech recognition in car environments has been identified as a valuable means for reducing driver distraction when operating noncritical in-car systems. Under such conditions, however, speech recognition accuracy degrades significantly, and techniques such as speech enhancement are required to improve these accuracies. Likelihood-maximizing (LIMA) frameworks optimize speech enhancement algorithms based on recognized state sequences rather than traditional signal-level criteria such as maximizing signal-to-noise ratio. LIMA frameworks typically require calibration utterances to generate optimized enhancement parameters that are used for all subsequent utterances. Under such a scheme, suboptimal recognition performance occurs in noise conditions that are significantly different from that present during the calibration session – a serious problem in rapidly changing noise environments out on the open road. In this chapter, we propose a dialog-based design that allows regular optimization iterations in order to track the ever-changing noise conditions. Experiments using Mel-filterbank noise subtraction (MFNS) are performed to determine the optimization requirements for vehicular environments and show that minimal optimization is required to improve speech recognition, avoid over-optimization, and ultimately assist with semireal-time operation. It is also shown that the proposed design is able to provide improved recognition performance over frameworks incorporating a calibration session only.

A survey of radiographers' confidence and self-perceived accuracy in frontline image interpretation and their continuing educational preferences

Introduction The provision of a written comment on traumatic abnormalities of the musculoskeletal system detected by radiographers can assist referrers and may improve patient management, but the practice has not been widely adopted outside the United Kingdom. The purpose of this study was to investigate Australian radiographers’ perceptions of their readiness for practice in a radiographer commenting system and their educational preferences in relation to two different delivery formats of image interpretation education, intensive and non-intensive. Methods A cross-sectional web-based questionnaire was implemented between August and September 2012. Participants included radiographers with experience working in emergency settings at four Australian metropolitan hospitals. Conventional descriptive statistics, frequency histograms, and thematic analysis were undertaken. A Wilcoxon signed-rank test examined whether a difference in preference ratings between intensive and non-intensive education delivery was evident. Results The questionnaire was completed by 73 radiographers (68% response rate). Radiographers reported higher confidence and self-perceived accuracy to detect traumatic abnormalities than to describe traumatic abnormalities of the musculoskeletal system. Radiographers frequently reported high desirability ratings for both the intensive and the non-intensive education delivery, no difference in desirability ratings for these two formats was evident (z = 1.66,P = 0.11). Conclusions Some Australian radiographers perceive they are not ready to practise in a frontline radiographer commenting system. Overall, radiographers indicated mixed preferences for image interpretation education delivered via intensive and non-intensive formats. Further research, preferably randomised trials, investigating the effectiveness of intensive and non-intensive education formats of image interpretation education for radiographers is warranted.

Detecting rare events using Kullback-Leibler divergence

One main challenge in developing a system for visual surveillance event detection is the annotation of target events in the training data. By making use of the assumption that events with security interest are often rare compared to regular behaviours, this paper presents a novel approach by using Kullback-Leibler (KL) divergence for rare event detection in a weakly supervised learning setting, where only clip-level annotation is available. It will be shown that this approach outperforms state-of-the-art methods on a popular real-world dataset, while preserving real time performance.

Integrating field survey data with satellite image data to improve shallow water seagrass maps : the role of AUV and snorkeller surveys

Repeatable and accurate seagrass mapping is required for understanding seagrass ecology and supporting management decisions. For shallow (< 5 m) seagrass habitats, these maps can be created by integrating high spatial resolution imagery with field survey data. Field survey data for seagrass is often collected via snorkelling or diving. However, these methods are limited by environmental and safety considerations. Autonomous Underwater Vehicles (AUVs) are used increasingly to collect field data for habitat mapping, albeit mostly in deeper waters (>20 m). Here we demonstrate and evaluate the use and potential advantages of AUV field data collection for calibration and validation of seagrass habitat mapping of shallow waters (< 5 m), from multispectral satellite imagery. The study was conducted in the seagrass habitats of the Eastern Banks (142 km2), Moreton Bay, Australia. In the field, georeferenced photos of the seagrass were collected along transects via snorkelling or an AUV. Photos from both collection methods were analysed manually for seagrass species composition and then used as calibration and validation data to map seagrass using an established semi-automated object based mapping routine. A comparison of the relative advantages and disadvantages of AUV and snorkeller collected field data sets and their influence on the mapping routine was conducted. AUV data collection was more consistent, repeatable and safer in comparison to snorkeller transects. Inclusion of deeper water AUV data resulted in mapping of a larger extent of seagrass (~7 km2, 5 % of study area) in the deeper waters of the site. Although overall map accuracies did not differ considerably, inclusion of the AUV data from deeper water transects corrected errors in seagrass mapped at depths to 5 m, but where the bottom is visible on satellite imagery. Our results demonstrate that further development of AUV technology is justified for the monitoring of seagrass habitats in ongoing management programs.

Investigation of fiducial marker and soft-tissue image guidance techniques in prostate radiation therapy

This thesis examines and compares imaging methods used during the radiotherapy treatment of prostate cancer. The studies found that radiation therapists were able to localise and target the prostate consistently with planar imaging techniques and that the use of small gold markers in the prostate reduced the variation in prostate localisation when using volumetric imaging. It was concluded that larger safety margins are required when using volumetric imaging without gold markers.

An external field prior for the hidden Potts model with application to cone-beam computed tomography

In images with low contrast-to-noise ratio (CNR), the information gain from the observed pixel values can be insufficient to distinguish foreground objects. A Bayesian approach to this problem is to incorporate prior information about the objects into a statistical model. A method for representing spatial prior information as an external field in a hidden Potts model is introduced. This prior distribution over the latent pixel labels is a mixture of Gaussian fields, centred on the positions of the objects at a previous point in time. It is particularly applicable in longitudinal imaging studies, where the manual segmentation of one image can be used as a prior for automatic segmentation of subsequent images. The method is demonstrated by application to cone-beam computed tomography (CT), an imaging modality that exhibits distortions in pixel values due to X-ray scatter. The external field prior results in a substantial improvement in segmentation accuracy, reducing the mean pixel misclassification rate for an electron density phantom from 87% to 6%. The method is also applied to radiotherapy patient data, demonstrating how to derive the external field prior in a clinical context.

Reflexive and automatic violence: A function of aberrant perceptual inhibition

It’s commonly assumed that psychiatric violence is motivated by delusions, but here the concept of a reversed impetus is explored, to understand whether delusions are formed as ad-hoc or post-hoc rationalizations of behaviour or in advance of the actus reus. The reflexive violence model proposes that perceptual stimuli has motivational power and this may trigger unwanted actions and hallucinations. The model is based on the theory of ecological perception, where opportunities enabled by an object are cues to act. As an apple triggers a desire to eat, a gun triggers a desire to shoot. These affordances (as they are called) are part of the perceptual apparatus, they allow the direct recognition of objects – and in emergencies they enable the fastest possible reactions. Even under normal circumstances, the presence of a weapon will trigger inhibited violent impulses. The presence of a victim will also, but under normal circumstances, these affordances don’t become violent because negative action impulses are totally inhibited, whereas in psychotic illness, negative action impulses are treated as emergencies and bypass frontal inhibitory circuits. What would have been object recognition becomes a blind automatic action. A range of mental illnesses can cause inhibition to be bypassed. At its most innocuous, this causes both simple hallucinations (where the motivational power of an object is misattributed). But ecological perception may have the power to trigger serious violence also –a kind that’s devoid of motives or planning and is often shrouded in amnesia or post-rational delusions.

Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data

Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data.

Content-independent embedding scheme for multi-modal medical image watermarking

Background As the increasing adoption of information technology continues to offer better distant medical services, the distribution of, and remote access to digital medical images over public networks continues to grow significantly. Such use of medical images raises serious concerns for their continuous security protection, which digital watermarking has shown great potential to address. Methods We present a content-independent embedding scheme for medical image watermarking. We observe that the perceptual content of medical images varies widely with their modalities. Recent medical image watermarking schemes are image-content dependent and thus they may suffer from inconsistent embedding capacity and visual artefacts. To attain the image content-independent embedding property, we generalise RONI (region of non-interest, to the medical professionals) selection process and use it for embedding by utilising RONI’s least significant bit-planes. The proposed scheme thus avoids the need for RONI segmentation that incurs capacity and computational overheads. Results Our experimental results demonstrate that the proposed embedding scheme performs consistently over a dataset of 370 medical images including their 7 different modalities. Experimental results also verify how the state-of-the-art reversible schemes can have an inconsistent performance for different modalities of medical images. Our scheme has MSSIM (Mean Structural SIMilarity) larger than 0.999 with a deterministically adaptable embedding capacity. Conclusions Our proposed image-content independent embedding scheme is modality-wise consistent, and maintains a good image quality of RONI while keeping all other pixels in the image untouched. Thus, with an appropriate watermarking framework (i.e., with the considerations of watermark generation, embedding and detection functions), our proposed scheme can be viable for the multi-modality medical image applications and distant medical services such as teleradiology and eHealth.

Semi-automated annotation of environmental acoustic recordings

Environmental sensors collect massive amounts of audio data. This thesis investigates computational methods to support human analysts in identifying faunal vocalisations from that audio. A series of experiments was conducted to trial the effectiveness of novel user interfaces. This research examines the rapid scanning of spectrograms, decision support tools for users, and cleaning methods for folksonomies. Together, these investigations demonstrate that providing computational support to human analysts increases their efficiency and accuracy; this allows bioacoustics projects to efficiently utilise their valuable human analysts.

Applications of real-time machine vision to the control of mining equipment

The mining industry presents us with a number of ideal applications for sensor based machine control because of the unstructured environment that exists within each mine. The aim of the research presented here is to increase the productivity of existing large compliant mining machines by retrofitting with enhanced sensing and control technology. The current research focusses on the automatic control of the swing motion cycle of a dragline and an automated roof bolting system. We have achieved: * closed-loop swing control of an one-tenth scale model dragline; * single degree of freedom closed-loop visual control of an electro-hydraulic manipulator in the lab developed from standard components.