A segmentation editing framework based on shape change statistics

Segmentation is a key task in medical image analysis because its accuracy significantly affects successive steps. Automatic segmentation methods often produce inadequate segmentations, which require the user to manually edit the produced segmentation slice by slice. Because editing is time-consuming, an editing tool that enables the user to produce accurate segmentations by only drawing a sparse set of contours would be needed. This paper describes such a framework as applied to a single object. Constrained by the additional information enabled by the manually segmented contours, the proposed framework utilizes object shape statistics to transform the failed automatic segmentation to a more accurate version. Instead of modeling the object shape, the proposed framework utilizes shape change statistics that were generated to capture the object deformation from the failed automatic segmentation to its corresponding correct segmentation. An optimization procedure was used to minimize an energy function that consists of two terms, an external contour match term and an internal shape change regularity term. The high accuracy of the proposed segmentation editing approach was confirmed by testing it on a simulated data set based on 10 in-vivo infant magnetic resonance brain data sets using four similarity metrics. Segmentation results indicated that our method can provide efficient and adequately accurate segmentations (Dice segmentation accuracy increase of 10%), with very sparse contours (only 10%), which is promising in greatly decreasing the work expected from the user

User Interaction in Semi-Automatic Segmentation of Organs at Risk: a Case Study in Radiotherapy

Accurate segmentation of organs at risk is an important step in radiotherapy planning. Manual segmentation being a tedious procedure and prone to inter- and intra-observer variability, there is a growing interest in automated segmentation methods. However, automatic methods frequently fail to provide satisfactory result, and post-processing corrections are often needed. Semi-automatic segmentation methods are designed to overcome these problems by combining physicians’ expertise and computers’ potential. This study evaluates two semi-automatic segmentation methods with different types of user interactions, named the “strokes” and the “contour”, to provide insights into the role and impact of human-computer interaction. Two physicians participated in the experiment. In total, 42 case studies were carried out on five different types of organs at risk. For each case study, both the human-computer interaction process and quality of the segmentation results were measured subjectively and objectively. Furthermore, different measures of the process and the results were correlated. A total of 36 quantifiable and ten non-quantifiable correlations were identified for each type of interaction. Among those pairs of measures, 20 of the contour method and 22 of the strokes method were strongly or moderately correlated, either directly or inversely. Based on those correlated measures, it is concluded that: (1) in the design of semi-automatic segmentation methods, user interactions need to be less cognitively challenging; (2) based on the observed workflows and preferences of physicians, there is a need for flexibility in the interface design; (3) the correlated measures provide insights that can be used in improving user interaction design

Interactive GPU active contours for segmenting inhomogeneous objects.

We present a segmentation software package primarily targeting medical and biological applications, with a high level of visual feedback and several usability enhancements over existing packages. Specifically, we provide a substantially faster GPU implementation of the local Gaussian distribution fitting energy model, which can segment inhomogeneous objects with poorly defined boundaries as often encountered in biomedical images. We also provide interactive brushes to guide the segmentation process in a semiautomated framework. The speed of our implementation allows us to visualize the active surface in real time with a built-in ray tracer, where users may halt evolution at any time step to correct implausible segmentation by painting new blocking regions or new seeds. Quantitative and qualitative validation is presented, demonstrating the practical efficacy of our interactive elements for a variety of real-world datasets

Study of medical image data transformation techniques and compatibility analysis for 3D printing

Various applications exist for additive manufacturing (AM) and reverse engineering (RE) within the medical sector. One of the significant challenges identified in the literature is the accuracy of 3D printed medical models compared to their original CAD models. Some studies have reported that 3D printed models are accurate, while others claim the opposite. This thesis aims to highlight the medical applications of AM and RE, study medical image reconstruction techniques into a 3D printable file format, and the deviations of a 3D printed model using RE. A case study on a human femur bone was conducted through medical imaging, 3D printing, and RE for comparative deviation analysis. In addition, another medical application of RE has been presented, which is for solid modelling. Segmentation was done using opensource software for trial and training purposes, while the experiment was done using commercial software. The femur model was 3D printed using an industrial FDM printer. Three different non-contact 3D scanners were investigated for the RE process. Post-processing of the point cloud was done in the VX Elements software environment, while mesh analysis was conducted in MeshLab. The scanning performance was measured using the VX Inspect environment and MeshLab. Both relative and absolute metrics were used to determine the deviation of the scanned models from the reference mesh. The scanners' range of deviations was approximately from -0.375 mm to 0.388 mm (range of about 0.763mm) with an average RMS of about 0.22 mm. The results showed that the mean deviation of the 3D printed model (based on 3D scanning) has an average range of about 0.46mm, with an average mean value of about 0.16 mm

ReSCon '09, Research Student Conference: Book of Abstracts

The second SED Research Student Conference (ReSCon2009) was hosted over three days, 22-24 June 2009, in the Lecture Centre at Brunel University. The conference consisted of technical presentations, a poster session and social events. The abstracts and presentations were the result of ongoing research by postgraduate research students from the School of Engineering and Design at Brunel University. The conference is held annually, and ReSCon plays a key role in contributing to research and innovations within the School