Digitisation and 3D reconstruction of 30 year old microscopic sections of human embryo, foetus and orbit

A collection of 2200 microscopic sections was recently recovered at the Netherlands Ophthalmic Research Institute and the Department of Anatomy and Embryology of the Academic Medical Centre in Amsterdam. The sections were created thirty years ago and constitute the largest and most detailed study of human orbital anatomy to date. In order to preserve the collection, it was digitised. This paper documents a practical approach to the automatic reconstruction of a 3- D representation of the original objects from the digitised sections. To illustrate the results of our approach, we show a multi-planar reconstruction and a 3-D direct volume rendering of a reconstructed foetal head

Techniques and software architectures for medical visualisation and image processing

This thesis presents a flexible software platform for medical visualisation and image processing, a technique for the segmentation of the shoulder skeleton from CT data and three techniques that make contributions to the field of direct volume rendering. Our primary goal was to investigate the use of visualisation techniques to assist the shoulder replacement process. This motivated the need for a flexible environment within which to test and develop new visualisation and also image processing techniques with a medical focus. The Delft Visualisation and Image processing Development Environment, or DeVIDE, was created to answer this need. DeVIDE is a graphical data-flow application builder that combines visualisation and image processing techniques, supports the rapid creation of new functional components and facilitates a level of interaction with algorithm code and parameters that differentiates it from similar platforms. For visualisation, measurement and pre-operative planning, an accurate segmentation from CT data of the bony structures of the shoulder is required. Due to the complexity of the shoulder joint and the fact that a method was required that could deal with diseased shoulders, existing techniques could not be applied. In this thesis we present a suite of techniques for the segmentation of the skeletal structures from CT data, especially designed to cope with diseased shoulders. Direct volume rendering, or DVR, is a useful visualisation technique that is often applied as part of medical visualisation solutions. A crucial component of an effective DVR visualisation is a suitable transfer function that assigns optical characteristics to the data. Finding a suitable transfer function is a challenging task. We present two highly interactive methods that facilitate this process. We also present a method for interactive direct volume rendering on ubiquitous low-end graphics hardware. This method, called ShellSplatting, is optimised for the rendering of bony structures from CT data and supports the hardware-assisted blending of traditional surface rendering and direct volume rendering. This characteristic is useful in surgical simulation applications. ShellSplatting is based on the object-order splatting of discrete voxels. As such, maintaining a correct back-to-front or front-to-back ordering during rendering is crucial for correct images. All existing real-time perspective projection visibility orderings show artefacts when splatting discrete voxels. We present a new ordering for perspective projection that remedies these artefacts without a noticeable performance penalty.Electrical Engineering, Mathematics and Computer Scienc

Voxel classification and graph cuts for automated segmentation of pathological periprosthetic hip anatomy

Imaging- and therapeutic targets in neoplastic and musculoskeletal inflammatory diseas

Integrated Support for Medical Image Analysis Methods: from Development to Clinical Application

Computer-aided image analysis is becoming increasingly important to efficiently and safely handle large amounts of high-resolution images generated by advanced medical imaging devices. The development of medical image analysis (MIA) software with the required properties for clinical application, however, is difficult and labor-intensive. Such development should be supported by systems providing scalable computational capacity and storage space, as well as information management facilities. This paper describes the properties of distributed systems to support and facilitate the development, evaluation, and clinical application of MIA methods. First, the main characteristics of existing systems are presented. Then, the phases in a method's lifecycle are analyzed (development, parameter optimization, evaluation, clinical routine), identifying the types of users, tasks, and related computational issues. A scenario is described where all tasks are performed with the aid of computational tools integrated into an ideal supporting environment. The requirements for this environment are described, proposing a grid-oriented paradigm that emphasizes virtual collaboration among users, pieces of software, and devices distributed among geographically dispersed healthcare, research, and development enterprises. Finally, the characteristics of the existing systems are analyzed according to these requirements. The proposed requirements offer a useful framework to evaluate, compare, and improve the existing systems that support MIA developmen

Practical system for realtime on-plant flotation froth visual parameter extraction

In plants where froth flotation is utilized to extract minerals from mined ore, the visual interpretation of the froth surface can be used to optimize the flotation process, thus yielding a more efficient extraction. We present a computer-based system that is able to extract a wide range of on-line static and dynamic visual parameters from the froth surface. The system has been installed in several refineries and performs well in both laboratory and industrial environments.Articl

Voxel classification and graph cuts for automated segmentation of pathological periprosthetic hip anatomy

Purpose Automated patient-specific image-based segmentation of tissues surrounding aseptically loose hip prostheses is desired. For this we present an automated segmentation pipeline that labels periprosthetic tissues in computed tomography (CT). The intended application of this pipeline is in pre-operative planning. Methods Individual voxels were classified based on a set of automatically extracted image features. Minimum-cost graph cuts were computed on the classification results. The graph-cut step enabled us to enforce geometrical containment constraints, such as cortical bone sheathing the femur’s interior. The solution’s novelty lies in the combination of voxel classification with multilabel graph cuts and in the way label costs were defined to enforce containment constraints. Results The segmentation pipeline was tested on a set of twelve manually segmented clinical CT volumes. The distribution of healthy tissue and bone cement was automatically determined with sensitivities greater than 82% and pathological fibrous interface tissue with a sensitivity exceeding 73%. Specificity exceeded 96% for all tissues. Conclusions The addition of a graph-cut step improved segmentation compared to voxel classification alone. The pipeline described in this paper represents a practical approach to segmenting multitissue regions from CT.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc

Extensions of Parallel Coordinates for Interactive Exploration of Large Multi-Timepoint Data Sets

Parallel coordinate plots (PCPs) are commonly used in information visualization to provide insight into multi-variate data. These plots help to spot correlations between variables. PCPs have been successfully applied to unstructured datasets up to a few millions of points. In this paper, we present techniques to enhance the usability of PCPs for the exploration of large, multi-timepoint volumetric data sets, containing tens of millions of points per timestep. The main difficulties that arise when applying PCPs to large numbers of data points are visual clutter and slow performance, making interactive exploration infeasible. Moreover, the spatial context of the volumetric data is usually lost. We describe techniques for preprocessing using data quantization and compression, and for fast GPU-based rendering of PCPs using joint density distributions for each pair of consecutive variables, resulting in a smooth, continuous visualization. Also, fast brushing techniques are proposed for interactive data selection in multiple linked views, including a 3D spatial volume view. These techniques have been successfully applied to three large data sets: Hurricane Isabel (Vis’04 contest), the ionization front instability data set (Vis’08 design contest), and data from a large-eddy simulation of cumulus clouds. With these data, we show how PCPs can be extended to successfully visualize and interactively explore multi-timepoint volumetric datasets with an order of magnitude more data points.MediamaticsElectrical Engineering, Mathematics and Computer Scienc

Combined surface and volume processing for fused joint segmentation

Purpose Segmentation of rheumatoid joints from CT images is a complicated task. The pathological state of the joint results in a non-uniform density of the bone tissue, with holes and irregularities complicating the segmentation process. For the specific case of the shoulder joint, existing segmentation techniques often fail and lead to poor results. This paper describes a novel method for the segmentation of these joints. Methods Given a rough surface model of the shoulder, a loop that encircles the joint is extracted by calculating the minimum curvature of the surface model. The intersection points of this loop with the separate CT-slices are connected by means of a path search algorithm. Inaccurate sections are corrected by iteratively applying a Hough transform to the segmentation result. Results As a qualitative measure we calculated the Dice coefficient and Hausdorff distances of the automatic segmentations and expert manual segmentations of CT-scans of ten severely deteriorated shoulder joints. For the humerus and scapula the median Dice coefficient was 98.9% with an interquartile range (IQR) of 95.8-99.4 and 98.5% (IQR 98.3-99.2%), respectively. The median Hausdorff distances were 3.06 mm (IQR 2.30-4.14) and 3.92 mm (IQR 1.96 5.92 mm), respectively. Conclusion The routine satisfies the criterion of our particular application to accurately segment the shoulder joint in under 2 min. We conclude that combining surface curvature, limited user interaction and iterative refinement via a Hough transform forms a satisfactory approach for the segmentation of severely damaged arthritic shoulder joints.Optimising joint reconstruction management in arthritis and bone tumour patient

Visualization of Sliding and Deformation of Orbital Fat During Eye Rotation

Neuro Imaging Researc

Piecewise Laplacian-based Projection for Interactive Data Exploration and Organization

Multidimensional projection has emerged as an important visualization tool in applications involving the visual analysis of high-dimensional data. However, high precision projection methods are either computationally expensive or not flexible enough to enable feedback from user interaction into the projection process. A built-in mechanism that dynamically adapts the projection based on direct user intervention would make the technique more useful for a larger range of applications and data sets. In this paper we propose the Piecewise Laplacian-based Projection (PLP), a novel multidimensional projection technique, that, due to the local nature of its formulation, enables a versatile mechanism to interact with projected data and to allow interactive changes to alter the projection map dynamically, a capability unique of this technique. We exploit the flexibility provided by PLP in two interactive projection-based applications, one designed to organize pictures visually and another to build music playlists. These applications illustrate the usefulness of PLP in handling high-dimensional data in a flexible and highly visual way. We also compare PLP with the currently most promising projections in terms of precision and speed, showing that it performs very well also according to these quality criteria.Radiolog