A Web-based system enabling the integration, analysis, and 3D sub-surface visualization of groundwater monitoring data and geological models

The 3D Water Chemistry Atlas is an intuitive, open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model (formation and aquifer strata). This paper firstly describes the results of evaluating existing virtual globe technologies, which led to the decision to use the Cesium open source WebGL Virtual Globe and Map Engine as the underlying platform. Next it describes the backend database and search, filtering, browse and analysis tools that were developed to enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about coal seam gas extraction, waste water extraction, and water reuse.

Use of 3D printed materials as tissue-equivalent phantoms

This study used the specific example of 3D printing with acrylonitrile butadiene styrene (ABS) as a means to investigate the potential usefulness of benchtop rapid prototyping as a technique for producing patient specific phantoms for radiotherapy dosimetry. Three small cylinders and one model of a human lung were produced via in-house 3D printing with ABS, using 90%, 50%, 30% and 10% ABS infill densities. These phantom samples were evaluated in terms of their geometric accuracy, tissue equivalence and radiation hardness, when irradiated using a range of clinical radiotherapy beams. The measured dimensions of the small cylindrical phantoms all matched their planned dimensions, within 1mm. The lung phantom was less accurately matched to the lung geometry on which it was based, due to simplifications introduced during the phantom design process. The mass densities, electron densities and linear attenuation coefficients identified using CT data, as well as the results of film measurements made using megavoltage photon and electron beams, indicated that phantoms printed with ABS, using infill densities of 30% or more, are potentially useful as lung- and tissue-equivalent phantoms for patient-specific radiotherapy dosimetry. All cylindrical 3D printed phantom samples were found to be unaffected by prolonged radiation and to accurately match their design specifications. However, care should be taken to avoid oversimplifying anatomical structures when printing more complex phantoms.

Creation and copyright law: The case of 3D printing

The Australian Law Reform Commission is conducting an inquiry into copyright law and the digital economy in 2012 and 2013.The President, Rosalind Croucher, stated: “While the Copyright Act has been amended on occasion over the past 12 years to account for digital developments, these changes occurred before the digital economy took off. The Australian Law Reform Commission will need to find reforms that are responsive to this new environment, and to future scenarios that are still in the realm of the imagination. It is a complex and important area of law and we are looking forward to some robust debate and discussion during the course of this very important Inquiry.”

Development of a method to assess the quality of ankle joint reduction in 3D

This project developed a quantitative method for determining the quality of the surgical alignment of the bone fragments after an ankle fracture. The research examined the feasibility of utilising MRI-based bone models versus the gold standard CT-based bone models in order to reduce the amount of ionising radiation the patient is exposed to. In doing so, the thesis reports that there is potential for MRI to be used instead of CT depending on the scanning parameters used to obtain the medical images, the distance of the implant relative to the joint surface, and the implant material.

A virtual radiation therapy workflow training simulation

Aim Simulation forms an increasingly vital component of clinical skills development in a wide range of professional disciplines. Simulation of clinical techniques and equipment is designed to better prepare students for placement by providing an opportunity to learn technical skills in a “safe” academic environment. In radiotherapy training over the last decade or so this has predominantly comprised treatment planning software and small ancillary equipment such as mould room apparatus. Recent virtual reality developments have dramatically changed this approach. Innovative new simulation applications and file processing and interrogation software have helped to fill in the gaps to provide a streamlined virtual workflow solution. This paper outlines the innovations that have enabled this, along with an evaluation of the impact on students and educators. Method Virtual reality software and workflow applications have been developed to enable the following steps of radiation therapy to be simulated in an academic environment: CT scanning using a 3D virtual CT scanner simulation; batch CT duplication; treatment planning; 3D plan evaluation using a virtual linear accelerator; quantitative plan assessment, patient setup with lasers; and image guided radiotherapy software. Results Evaluation of the impact of the virtual reality workflow system highlighted substantial time saving for academic staff as well as positive feedback from students relating to preparation for clinical placements. Students valued practice in the “safe” environment and the opportunity to understand the clinical workflow ahead of clinical department experience. Conclusion Simulation of most of the radiation therapy workflow and tasks is feasible using a raft of virtual reality simulation applications and supporting software. Benefits of this approach include time-saving, embedding of a case-study based approach, increased student confidence, and optimal use of the clinical environment. Ongoing work seeks to determine the impact of simulation on clinical skills.

The vertebral venous system in healthy and scoliotic adolescent spines - a 3D MRI investigation

Introduction. The venous drainage system within vertebral bodies (VBs) has been well documented previously in cadaveric specimens. Advances in 3D imaging and image processing now allow for in vivo quantification of larger venous vessels, such as the basivertebral vein. Differences between healthy and scoliotic VB veins can therefore be investigated. Methods. 20 healthy adolescent controls and 21 AIS patients were recruited (with ethics approval) to undergo 3D MRI, using a 3 Tesla, T1-weighted 3D gradient echo sequence, resulting in 512 slices across the thoraco-lumbar spine, with a voxel size of 0.5x0.5x0.5mm. Using Amira Filament Editor, five transverse slices through the VB were examined simultaneously and the resulting observable vascular network traced. Each VB was assessed, and a vascular network recorded when observable. A local coordinate system was created in the centre of each VB and the vascular networks aligned to this. The length of the vascular network on the left and right sides (with a small central region) of the VB was calculated, and the spatial patterning of the networks assessed level-by-level within each subject. Results. An average of 6 (range 4-10) vascular networks, consistent with descriptions of the basivertebral vein, were identifiable within each subject, most commonly between T10-L1. Differences were seen in the left/right distribution of vessels in the control and AIS subjects. Healthy controls saw a percentage distribution of 29:18:53 across the left:centre:right regions respectively, whereas the AIS subjects had a slightly shifted distribution of 33:25:42. The control group showed consistent spatial patterning of the vascular networks across most levels, but this was not seen in the AIS group. Conclusion. Observation and quantification of the basivertebral vein in vivo is possible using 3D MRI. The AIS group lacked the spatial pattern repetition seen in the control group and minor differences were seen in the left/right distribution of vessels.

Automated fit assessment of intramedullary nail designs during insertion

Modern intramedullary nails, which are utilised for the treatment of bone fractures, need to be designed to fit the anatomy of the patient population. Traditional and recent semi-automated approaches for quantifying the anatomical fit between bones and nail designs suffer from various drawbacks. This thesis proposed an automated comprehensive nail design validation method. The developed software tool was utilised to quantify the anatomical fit of four commercial nail designs. Furthermore, the thesis demonstrated the existence of a bone-nail specific nail entry point. The developed method is of great benefit for the implant manufacturing industry as a nail design validation tool.

Single molecule microscopy in 3D cell cultures and tissues

From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Separable spatiotemporal priors for convex reconstruction of time-varying 3D point clouds

Reconstructing 3D motion data is highly under-constrained due to several common sources of data loss during measurement, such as projection, occlusion, or miscorrespondence. We present a statistical model of 3D motion data, based on the Kronecker structure of the spatiotemporal covariance of natural motion, as a prior on 3D motion. This prior is expressed as a matrix normal distribution, composed of separable and compact row and column covariances. We relate the marginals of the distribution to the shape, trajectory, and shape-trajectory models of prior art. When the marginal shape distribution is not available from training data, we show how placing a hierarchical prior over shapes results in a convex MAP solution in terms of the trace-norm. The matrix normal distribution, fit to a single sequence, outperforms state-of-the-art methods at reconstructing 3D motion data in the presence of significant data loss, while providing covariance estimates of the imputed points.

LiDAR Augmented Optimal Path Planning for Unmanned Aerial Vehicle during Remote Sensing at Low Altitude and Network Sensor Data Acquisition

This technical report describes a Light Detection and Ranging (LiDAR) augmented optimal path planning at low level flight methodology for remote sensing and sampling Unmanned Aerial Vehicles (UAV). The UAV is used to perform remote air sampling and data acquisition from a network of sensors on the ground. The data that contains information on the terrain is in the form of a 3D point clouds maps is processed by the algorithms to find an optimal path. The results show that the method and algorithm are able to use the LiDAR data to avoid obstacles when planning a path from a start to a target point. The report compares the performance of the method as the resolution of the LIDAR map is increased and when a Digital Elevation Model (DEM) is included. From a practical point of view, the optimal path plan is loaded and works seemingly with the UAV ground station and also shows the UAV ground station software augmented with more accurate LIDAR data.

Leveraging of software as a service by small and medium enterprises: Information systems capabilities and organisational complementarities

This research explored how small and medium enterprises can achieve success with software as a service (SaaS) applications from cloud. Based upon an empirical investigation of six growth oriented and early technology adopting small and medium enterprises, this study proposes a SaaS for small and medium enterprise success model with two approaches: one for basic and one for advanced benefits. The basic model explains the effective use of SaaS for achieving informational and transactional benefits. The advanced model explains the enhanced use of software as a service for achieving strategic and transformational benefits. Both models explicate the information systems capabilities and organizational complementarities needed for achieving success with SaaS.

Supramolecular assembly of heterocirculenes in 2D and 3D

The results of a high-resolution ambient STM study of ‘sulflower’ (octathio[8]circulene) and ‘selenosulflower’ (sym-tetraselena-tetrathio[8]circulene) molecules, immobilized in a hydrogen-bonded matrix of trimesic acid (TMA) at the solid–liquid interface, are compared with the STM and X-ray structure of separate host and guest 2D and 3D crystals, respectively.

Understanding the use of a bug tracking system in a global software development setup

Bug fixing is a highly cooperative work activity where developers, testers, product managers and other stake-holders collaborate using a bug tracking system. In the context of Global Software Development (GSD), where software development is distributed across different geographical locations, we focus on understanding the role of bug trackers in supporting software bug fixing activities. We carried out a small-scale ethnographic fieldwork in a software product team distributed between Finland and India at a multinational engineering company. Using semi-structured interviews and in-situ observations of 16 bug cases, we show that the bug tracker 1) supported information needs of different stake holder, 2) established common-ground, and 3) reinforced issues related to ownership, performance and power. Consequently, we provide implications for design around these findings.