Image acquisition and manipulation protocols for CT-PET fusion to improve the accuracy of gross tumour volume localisation for 3D conformal radiotherapy for lung cancer

Aims: To develop clinical protocols for acquiring PET images, performing CT-PET registration and tumour volume definition based on the PET image data, for radiotherapy for lung cancer patients and then to test these protocols with respect to levels of accuracy and reproducibility. Method: A phantom-based quality assurance study of the processes associated with using registered CT and PET scans for tumour volume definition was conducted to: (1) investigate image acquisition and manipulation techniques for registering and contouring CT and PET images in a radiotherapy treatment planning system, and (2) determine technology-based errors in the registration and contouring processes. The outcomes of the phantom image based quality assurance study were used to determine clinical protocols. Protocols were developed for (1) acquiring patient PET image data for incorporation into the 3DCRT process, particularly for ensuring that the patient is positioned in their treatment position; (2) CT-PET image registration techniques and (3) GTV definition using the PET image data. The developed clinical protocols were tested using retrospective clinical trials to assess levels of inter-user variability which may be attributed to the use of these protocols. A Siemens Somatom Open Sensation 20 slice CT scanner and a Philips Allegro stand-alone PET scanner were used to acquire the images for this research. The Philips Pinnacle3 treatment planning system was used to perform the image registration and contouring of the CT and PET images. Results: Both the attenuation-corrected and transmission images obtained from standard whole-body PET staging clinical scanning protocols were acquired and imported into the treatment planning system for the phantom-based quality assurance study. Protocols for manipulating the PET images in the treatment planning system, particularly for quantifying uptake in volumes of interest and window levels for accurate geometric visualisation were determined. The automatic registration algorithms were found to have sub-voxel levels of accuracy, with transmission scan-based CT-PET registration more accurate than emission scan-based registration of the phantom images. Respiration induced image artifacts were not found to influence registration accuracy while inadequate pre-registration over-lap of the CT and PET images was found to result in large registration errors. A threshold value based on a percentage of the maximum uptake within a volume of interest was found to accurately contour the different features of the phantom despite the lower spatial resolution of the PET images. Appropriate selection of the threshold value is dependant on target-to-background ratios and the presence of respiratory motion. The results from the phantom-based study were used to design, implement and test clinical CT-PET fusion protocols. The patient PET image acquisition protocols enabled patients to be successfully identified and positioned in their radiotherapy treatment position during the acquisition of their whole-body PET staging scan. While automatic registration techniques were found to reduce inter-user variation compared to manual techniques, there was no significant difference in the registration outcomes for transmission or emission scan-based registration of the patient images, using the protocol. Tumour volumes contoured on registered patient CT-PET images using the tested threshold values and viewing windows determined from the phantom study, demonstrated less inter-user variation for the primary tumour volume contours than those contoured using only the patient’s planning CT scans. Conclusions: The developed clinical protocols allow a patient’s whole-body PET staging scan to be incorporated, manipulated and quantified in the treatment planning process to improve the accuracy of gross tumour volume localisation in 3D conformal radiotherapy for lung cancer. Image registration protocols which factor in potential software-based errors combined with adequate user training are recommended to increase the accuracy and reproducibility of registration outcomes. A semi-automated adaptive threshold contouring technique incorporating a PET windowing protocol, accurately defines the geometric edge of a tumour volume using PET image data from a stand alone PET scanner, including 4D target volumes.

3D visualisation of groundwater/surface water systems as a planning and communication tool

Groundwater is increasingly recognised as an important yet vulnerable natural resource, and a key consideration in water cycle management. However, communication of sub-surface water system behaviour, as an important part of encouraging better water management, is visually difficult. Modern 3D visualisation techniques can be used to effectively communicate these complex behaviours to engage and inform community stakeholders. Most software developed for this purpose is expensive and requires specialist skills. The Groundwater Visualisation System (GVS) developed by QUT integrates a wide range of surface and sub-surface data, to produce a 3D visualisation of the behaviour, structure and connectivity of groundwater/surface water systems. Surface data (elevation, surface water, land use, vegetation and geology) and data collected from boreholes (bore locations and subsurface geology) are combined to visualise the nature, structure and connectivity of groundwater/surface water systems. Time-series data (water levels, groundwater quality, rainfall, stream flow and groundwater abstraction) is displayed as an animation within the 3D framework, or graphically, to show water system condition changes over time. GVS delivers an interactive, stand-alone 3D Visualisation product that can be used in a standard PC environment. No specialised training or modelling skills are required. The software has been used extensively in the SEQ region to inform and engage both water managers and the community alike. Examples will be given of GVS visualisations developed in areas where there have been community concerns around groundwater over-use and contamination.

GVS : A flexible, low-end, 3D visualisation framework for enhancing conceptual groundwater models for community, management and simulations

In this paper we discuss an advanced, 3D groundwater visualisation and animation system that allows scientists, government agencies and community groups to better understand the groundwater processes that effect community planning and decision-making. The system is unique in that it has been designed to optimise community engagement. Although it incorporates a powerful visualisation engine, this open-source system can be freely distributed and boasts a simple user interface allowing individuals to run and investigate the models on their own PCs and gain intimate knowledge of the groundwater systems. The initial version of the Groundwater Visualisation System (GVS v1.0), was developed from a coastal delta setting (Bundaberg, QLD), and then applied to a basalt catchment area (Obi Obi Creek, Maleny, QLD). Several major enhancements have been developed to produce higher quality visualisations, including display of more types of data, support for larger models and improved user interaction. The graphics and animation capabilities have also been enhanced, notably the display of boreholes, depth logs and time-series water level surfaces. The GVS software remains under continual development and improvement

Digital modelling for sustainability

Digital modelling tools are the next generation of computer aided design (CAD) tools for the construction industry. They allow a designer to build a virtual model of the building project before the building is constructed. This supports a whole range of analysis, and the identification and resolution of problems before they arise on-site, in ways that were previously not feasible.

SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Computational approaches to the visual validation of 3D virtual environments

Virtual environments can provide, through digital games and online social interfaces, extremely exciting forms of interactive entertainment. Because of their capability in displaying and manipulating information in natural and intuitive ways, such environments have found extensive applications in decision support, education and training in the health and science domains amongst others. Currently, the burden of validating both the interactive functionality and visual consistency of a virtual environment content is entirely carried out by developers and play-testers. While considerable research has been conducted in assisting the design of virtual world content and mechanics, to date, only limited contributions have been made regarding the automatic testing of the underpinning graphics software and hardware. The aim of this thesis is to determine whether the correctness of the images generated by a virtual environment can be quantitatively defined, and automatically measured, in order to facilitate the validation of the content. In an attempt to provide an environment-independent definition of visual consistency, a number of classification approaches were developed. First, a novel model-based object description was proposed in order to enable reasoning about the color and geometry change of virtual entities during a play-session. From such an analysis, two view-based connectionist approaches were developed to map from geometry and color spaces to a single, environment-independent, geometric transformation space; we used such a mapping to predict the correct visualization of the scene. Finally, an appearance-based aliasing detector was developed to show how incorrectness too, can be quantified for debugging purposes. Since computer games heavily rely on the use of highly complex and interactive virtual worlds, they provide an excellent test bed against which to develop, calibrate and validate our techniques. Experiments were conducted on a game engine and other virtual worlds prototypes to determine the applicability and effectiveness of our algorithms. The results show that quantifying visual correctness in virtual scenes is a feasible enterprise, and that effective automatic bug detection can be performed through the techniques we have developed. We expect these techniques to find application in large 3D games and virtual world studios that require a scalable solution to testing their virtual world software and digital content.

3D anthropometry : from the ergonomist's perspective

Since the availability of 3D full body scanners and the associated software systems for operations with large point clouds, 3D anthropometry has been marketed as a breakthrough and milestone in ergonomic design. The assumptions made by the representatives of the 3D paradigm need to be critically reviewed though. 3D anthropometry has advantages as well as shortfalls, which need to be carefully considered. While it is apparent that the measurement of a full body point cloud allows for easier storage of raw data and improves quality control, the difficulties in calculation of standardized measurements from the point cloud are widely underestimated. Early studies that made use of 3D point clouds to derive anthropometric dimensions have shown unacceptable deviations from the standardized results measured manually. While 3D human point clouds provide a valuable tool to replicate specific single persons for further virtual studies, or personalize garment, their use in ergonomic design must be critically assessed. Ergonomic, volumetric problems are defined by their 2-dimensional boundary or one dimensional sections. A 1D/2D approach is therefore sufficient to solve an ergonomic design problem. As a consequence, all modern 3D human manikins are defined by the underlying anthropometric girths (2D) and lengths/widths (1D), which can be measured efficiently using manual techniques. Traditionally, Ergonomists have taken a statistical approach to design for generalized percentiles of the population rather than for a single user. The underlying method is based on the distribution function of meaningful single and two-dimensional anthropometric variables. Compared to these variables, the distribution of human volume has no ergonomic relevance. On the other hand, if volume is to be seen as a two-dimensional integral or distribution function of length and girth, the calculation of combined percentiles – a common ergonomic requirement - is undefined. Consequently, we suggest to critically review the cost and use of 3D anthropometry. We also recommend making proper use of widely available single and 2-dimensional anthropometric data in ergonomic design.

Assessment of flood-related recharge to alluvial aquifers of an irrigated catchment following extended drought conditions using 3D visualisation and environmental tracers, Lockyer Valley, southeast Queensland, Australia.

The Lockyer Valley in southeast Queensland, Australia, hosts an economically significant alluvial aquifer system which has been impacted by prolonged drought conditions (~1997 to ~ 2009). Throughout this time, the system was under continued groundwater extraction, resulting in severe aquifer depletion. By 2008, much of the aquifer was at <30% of storage but some relief occurred with rains in early 2009. However, between December 2010 and January 2011, most of southeast Queensland experienced unprecedented flooding, which generated significant aquifer recharge. In order to understand the spatial and temporal controls of groundwater recharge in the alluvium, a detailed 3D lithological property model of gravels, sands and clays was developed using GOCAD software. The spatial distribution of recharge throughout the catchment was assessed using hydrograph data from about 400 groundwater observation wells screened at the base of the alluvium. Water levels from these bores were integrated into a catchment-wide 3D geological model using the 3D geological modelling software GOCAD; the model highlights the complexity of recharge mechanisms. To support this analysis, groundwater tracers (e.g. major and minor ions, stable isotopes, 3H and 14C) were used as independent verification. The use of these complementary methods has allowed the identification of zones where alluvial recharge primarily occurs from stream water during episodic flood events. However, the study also demonstrates that in some sections of the alluvium, rainfall recharge and discharge from the underlying basement into the alluvium are the primary recharge mechanisms of the alluvium. This is indicated by the absence of any response to the flood, as well as the observed old radiocarbon ages and distinct basement water chemistry signatures at these locations. Within the 3D geological model, integration of water chemistry and time-series displays of water level surfaces before and after the flood suggests that the spatial variations of the flood response in the alluvium are primarily controlled by the valley morphology and lithological variations within the alluvium. The integration of time-series of groundwater level surfaces in the 3D geological model also enables the quantification of the volumetric change of groundwater stored in the unconfined sections of this alluvial aquifer during drought and following flood events. The 3D representation and analysis of hydraulic and recharge information has considerable advantages over the traditional 2D approach. For example, while many studies focus on singular aspects of catchment dynamics and groundwater-surface water interactions, the 3D approach is capable of integrating multiple types of information (topography, geological, hydraulic, water chemistry and spatial) into a single representation which provides valuable insights into the major factors controlling aquifer processes.

Assessment of interactions between alluvial, Great Artesian Basin (GAB) and volcanic aquifers using 3D visualisation and environmental tracers, Lockyer Valley, southeast Queensland, Australia

A detailed 3D lithological model framework was developed using GOCAD software to understand interactions between alluvial, volcanic and GAB aquifers and the spatial and temporal distribution of groundwater recharge to the alluvium of the Lockyer Valley. Groundwater chemistry, isotope data (H20-δ2H and δ18O , 87Sr/86Sr, 3H and 14C) and groundwater level time-series data from approximately 550 observation wells were integrated into the catchment-wide 3D model to assess the recharge processes involved. This approach enabled the identification of zones where recharge to the alluvium primarily occurs from stream water during episodic flood events. Importantly, the study also demonstrates that in some sections of the alluvium recharge is also from storm rainfall and seepage discharge from the underlying GAB aquifers. These other sources of recharge are indicated by (a) the absence of a response of groundwater levels to flooding in some areas, (b) old radiocarbon ages, and (c) distinct bedrock water chemistry and δ2H and δ18O signatures in alluvial groundwater at these locations. Integration of isotopes, water chemistry and time-series displays of groundwater levels before and after the 2010/2011 flood into the 3D model suggest that the spatial variations in the alluvial groundwater response are mostly controlled by valley morphology and lithological (i.e. permeability) variations within the alluvium. Examination of the groundwater level variations in the 3D model also enabled quantification of the volumetric change of groundwater stored in the unconfined alluvial aquifer prior to and post-flood events.

A CAD interface for GEANT4

Often CAD models already exist for parts of a geometry being simulated using GEANT4. Direct import of these CAD models into GEANT4 however,may not be possible and complex components may be diffcult to define via other means. Solutions that allow for users to work around the limited support in the GEANT4 toolkit for loading predefined CAD geometries have been presented by others, however these solutions require intermediate file format conversion using commercial software. Here within we describe a technique that allows for CAD models to be directly loaded as geometry without the need for commercial software and intermediate file format conversion. Robustness of the interface was tested using a set of CAD models of various complexity; for the models used in testing, no import errors were reported and all geometry was found to be navigable by GEANT4. Funding source: Cancer Australia (Department of Health and Ageing) Research Grant 614217

Groundwater visualisation system (GVS) : a software framework for integrated display and interrogation of conceptual hydrogeological models, data and time-series animation

Management of groundwater systems requires realistic conceptual hydrogeological models as a framework for numerical simulation modelling, but also for system understanding and communicating this to stakeholders and the broader community. To help overcome these challenges we developed GVS (Groundwater Visualisation System), a stand-alone desktop software package that uses interactive 3D visualisation and animation techniques. The goal was a user-friendly groundwater management tool that could support a range of existing real-world and pre-processed data, both surface and subsurface, including geology and various types of temporal hydrological information. GVS allows these data to be integrated into a single conceptual hydrogeological model. In addition, 3D geological models produced externally using other software packages, can readily be imported into GVS models, as can outputs of simulations (e.g. piezometric surfaces) produced by software such as MODFLOW or FEFLOW. Boreholes can be integrated, showing any down-hole data and properties, including screen information, intersected geology, water level data and water chemistry. Animation is used to display spatial and temporal changes, with time-series data such as rainfall, standing water levels and electrical conductivity, displaying dynamic processes. Time and space variations can be presented using a range of contouring and colour mapping techniques, in addition to interactive plots of time-series parameters. Other types of data, for example, demographics and cultural information, can also be readily incorporated. The GVS software can execute on a standard Windows or Linux-based PC with a minimum of 2 GB RAM, and the model output is easy and inexpensive to distribute, by download or via USB/DVD/CD. Example models are described here for three groundwater systems in Queensland, northeastern Australia: two unconfined alluvial groundwater systems with intensive irrigation, the Lockyer Valley and the upper Condamine Valley, and the Surat Basin, a large sedimentary basin of confined artesian aquifers. This latter example required more detail in the hydrostratigraphy, correlation of formations with drillholes and visualisation of simulation piezometric surfaces. Both alluvial system GVS models were developed during drought conditions to support government strategies to implement groundwater management. The Surat Basin model was industry sponsored research, for coal seam gas groundwater management and community information and consultation. The “virtual” groundwater systems in these 3D GVS models can be interactively interrogated by standard functions, plus production of 2D cross-sections, data selection from the 3D scene, rear end database and plot displays. A unique feature is that GVS allows investigation of time-series data across different display modes, both 2D and 3D. GVS has been used successfully as a tool to enhance community/stakeholder understanding and knowledge of groundwater systems and is of value for training and educational purposes. Projects completed confirm that GVS provides a powerful support to management and decision making, and as a tool for interpretation of groundwater system hydrological processes. A highly effective visualisation output is the production of short videos (e.g. 2–5 min) based on sequences of camera ‘fly-throughs’ and screen images. Further work involves developing support for multi-screen displays and touch-screen technologies, distributed rendering, gestural interaction systems. To highlight the visualisation and animation capability of the GVS software, links to related multimedia hosted online sites are included in the references.

Prostate gland and extra-capsular tissue 3D reconstruction and measurement

Currently there are little objective parameters that can quantify the success of one form of prostate surgical removal over another. Accordingly, at Old Dominion University (ODU) we have been developing a process resulting in the use of software algorithms to assess the coverage and depth of extra-capsular soft tissue removed with the prostate by the various surgical approaches. Parameters such as the percent of capsule that is bare of soft tissue and where present the depth and extent of coverage have been assessed. First, visualization methods and tools are developed for images of prostate slices that are provided to ODU by the Pathology Department at Eastern Virginia Medical School (EVMS). The visualization tools interpolate and present 3D models of the prostates. Measurement algorithms are then applied to determine statistics about extra-capsular tissue coverage. This paper addresses the modeling, visualization, and analysis of prostate gland tissue to aid in quantifying prostate surgery success. Particular attention is directed towards the accuracy of these measurements and is addressed in the analysis discussions.

A 3D virtual medical imaging suite : bridging the academic-clinical training boundary

Aims The Medical Imaging Training Immersive Environment (MITIE) system is a recently developed virtual reality (VR) platform that allows students to practice a range of medical imaging techniques. The aim of this pilot study was to harvest user feedback about the educational value of the application and inform future pedagogical development. This presentation explores the use of this technology for skills training and blurring the boundaries between academic learning and clinical skills training. Background MITIE is a 3D VR environment that allows students to manipulate a patient and radiographic equipment in order to produce a VR-generated image for comparison with a gold standard. As with VR initiatives in other health disciplines (1-6) the software mimics clinical practice as much as possible and uses 3D technology to enhance immersion and realism. The software was developed by the Medical Imaging Course Team at a provider University with funding from a Health Workforce Australia “Simulated Learning Environments” grant. Methods Over 80 students undertaking the Bachelor of Medical Imaging Course were randomised to receive practical experience with either MITIE or radiographic equipment in the medical radiation laboratory. Student feedback about the educational value of the software was collected and performance with an assessed setup was measured for both groups for comparison. Ethical approval for the project was provided by the university ethics panel. Results This presentation provides qualitative analysis of student perceptions relating to satisfaction, usability and educational value as well as comparative quantitative performance data. Students reported high levels of satisfaction and both feedback and assessment results confirmed the application’s significance as a pre-clinical training tool. There was a clear emerging theme that MITIE could be a useful learning tool that students could access to consolidate their clinical learning, either during their academic timetables or their clinical placement. Conclusion Student feedback and performance data indicate that MITIE has a valuable role to play in the clinical skills training for medical imaging students both in the academic and the clinical environment. Future work will establish a framework for an appropriate supporting pedagogy that can cross the boundary between the two environments. This project was possible due to funding made available by Health Workforce Australia.

HeatWave : a handheld 3D thermography system for energy auditing

Energy auditing is an effective but costly approach for reducing the long-term energy consumption of buildings. When well-executed, energy loss can be quickly identified in the building structure and its subsystems. This then presents opportunities for improving energy efficiency. We present a low-cost, portable technology called "HeatWave" which allows non-experts to generate detailed 3D surface temperature models for energy auditing. This handheld 3D thermography system consists of two commercially available imaging sensors and a set of software algorithms which can be run on a laptop. The 3D model can be visualized in real-time by the operator so that they can monitor their degree of coverage as the sensors are used to capture data. In addition, results can be analyzed offline using the proposed "Spectra" multispectral visualization toolbox. The presence of surface temperature data in the generated 3D model enables the operator to easily identify and measure thermal irregularities such as thermal bridges, insulation leaks, moisture build-up and HVAC faults. Moreover, 3D models generated from subsequent audits of the same environment can be automatically compared to detect temporal changes in conditions and energy use over time.

Towards quantitative 3D broadband ultrasound characterisation of breast lesions

This thesis describes the development and scientific validation of a real-time quantitative 3D flat-bed ultrasound scanner. Novel short-time Fourier transform software facilitated broadband ultrasound attenuation maps of a breast phantom, enabling detection and identification of both cystic and solid lesions.