Refereed conference proceedings

1. Estimating 3D fibre orientation in volume images
   Author: Maria Axelsson
   Conference: 19th International Conference on Pattern Recognition
   Abstract: Fibre orientation is an important structural property of fibre-based materials. For example, in paper the orientation of the fibres influences the dimensional strength of the sheet and the tendency of the sheet to curl and twist at moisture changes. Here, we present a threedimensional image analysis method for estimating the fibre orientation and the orientation anisotropy. The proposed method can be applied directly to greyscale volume images and is based on local orientation estimates using quadrature filters and structure tensors. From the tensor field the fibre orientation can be estimated together with a corresponding certainty measurement. Good results are obtained for both synthetic fibre data sets and fibre based materials imaged using X-ray microtomography.

2. Design and implementation of a stereoscopic display in a lecture-room
   Authors: Martin Ericsson (1), Anders Hast, Ingela Nyström
   (1) Dept. of Information Technology, UU
   Conference: SIGRAD 2008: The Annual SIGRAD Conference Special Theme: Interaction, Stockholm, pp. 79-80
   Editors: Kai-Mikael Jää-Aro, Lars Kjelldahl
   Abstract: This paper describes the master thesis project 3DIS4U: Design and implementation of a distributed visualization system with a stereoscopic display carried out at Uppsala University. The main contributions of the thesis are the installation and evaluation of a wallsized stereoscopic display in a class room-like environment and improvement of the quality, interactivity and usability of visualizations at Uppsala University by connecting the system to one of UPPMAX high-performance computing (HPC) clusters. The project involved modifications to open source softwares, mainly the Visualization ToolKit (VTK) and ParaView. Furthermore, software was developed to aid users in creating interactive stereoscopic simulations. Software was installed and modified for better usability. The option of using HPC resources for larger interactive visualizations also exists. As a final step, evaluations of the display and of the software were carried out together with background research on distributed rendering techniques to be able to produce a proposal for further development of the project. The result of this work is a class room environment which in a few minutes can be turned into a visualization studio with a stereoscopic display with the ability to create interactive visualizations. The lecture room retains its function as a class room and can support up to 30 simultaneous viewers.

3. Non-uniform 3D distance transform for anisotropic signal correction in confocal image volumes of skeletal muscle cell nuclei
   Authors: Patrick Karlsson Edlund, Joakim Lindblad
   Conference: 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp. 1363-1366
   Abstract: Detailed description of the three dimensional organization of nuclei in confocal microscope image volumes of skeletal muscle fibers needs accurate identification of the nuclei centroids. We propose a model based method, applied as a weighted distance transform that take into consideration the diffuse, attenuated, anisotropic, and non-symmetric behavior of the nuclei signals, to provide a transformed image volume where the individual nuclei are better separated, and where the correct nuclei centroids are easily attained.

4. Interactive visualization of new electromagnetic quantities
   Authors: Siavoush M. Mohammadi (1), Anders Hast, Lars K.S. Daldorff (3), Martin Ericsson (2), Jan, E.S. Bergman (1), Bo Thidè (1)
   (1) Swedish Institute of Space Physics
   (2) Dept. of Information Technology, UU
   (3) Dept. of Astronomy and Space Physics, UU
   Conference: SIGRAD 2008: The Annual SIGRAD Conference Special Theme: Interaction, Stockholm, pp. 71-4
   Editors: Kai-Mikael Jää-Aro, Lars Kjelldahl
   Abstract: Recent development in classical electrodynamics has demonstrated the usefulness of different rotational and topological modes in the electromagnetic fields (angular momentum, polarization, vorticity etc.). Unfortunately, the visualization tools available to illustrate these electrodynamic quantities have hitherto been inadequate. Therefore we have developed a VTK and Python based interactive visualization tool, with working name EMVT (ElectroMagnetic VisualizationTool), targeted at visualizing precisely these modes.In the near future, EMVT will be further developed to visualize and control live antenna systems, where electromagnetic field data is instantly received, calculated, and visualized from an antenna or a system of antennas. It will then be possible to see how the antenna properties change through direct user interaction in real time.

5. Fully automatic heart beat rate determination in digital video recordings of rat embryos
   Authors: Muhammad Khalid Khan Niazi, Mats F Nilsson (1), Bengt R. Danielsson (1), Ewert Bengtsson
   (1) Dept. of Pharmaceutical Biosciences, UU
   Conference: Third International Conference on Advances in Mass Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry and Food Industry, pp. 27-37
   Editors: Petra Perner, Ovidio Salvetti
   Abstract: Embryo cultures of rodents is an established technique for monitoring adverse effects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of rat embryos. First it detects the heart location, and then it counts the number of heart beats for a predetermined period of time. Using this automated method many more embryos can be evaluated at reasonable cost.

6. Deterministic defuzzification based on spectral projected gradient optimization
   Authors: Tibor Lukic (1), Nataša Sladoje (1), Joakim Lindblad
   (1) Faculty of Engineering, University of Novi Sad, Serbia
   Conference: 30th Symposium of the German Association for Pattern Recognition (DAGM), pp. 576-485
   Editor: Gerhard Rigoll
   Abstract: We apply deterministic optimization based on Spectral Projected Gradient method in combination with concave regularization to solve the minimization problem imposed by defuzzification by feature distance minimization. We compare the performance of the proposed algorithm with the methods previously recommended for the same task, (non-deterministic) simulated annealing and (deterministic) DC based algorithm. The evaluation, including numerical tests performed on synthetic and real images, shows advantages of the new method in terms of speed and flexibility regarding inclusion of additional features in defuzzification. Its relatively low memory requirements allow the application of the suggested method for defuzzification of 3D objects.
7. Spatially-variant morphological operations on binary images based on the polar distance transform
   Authors: Kristin Norell, Joakim Lindblad
   Conference: Proceedings of 19th International Conference on Pattern Recognition (ICPR 2008), Tampa, Florida, December 2008
   Abstract: Binary mathematical morphology can be computed by thresholding a distance transform, provided that the distance transform is a metric. Here we show that the polar distance transform is a metric and use it for morphological operations. The polar distance transform varies with the spatial coordinates of the image, resulting in spatially-variant morphology. In this distance transform each pixel is related to an image origin. We prefer angular propagation over radial, thus we construct structuring elements that are elongated in the angular direction, which is useful when circular segments are handled. We show an example where segments of annual rings on a log end face are connected using mathematical morphology based on the polar distance transform.

8. Enabling bio-feedback using real-time fMRI
   Authors: Henrik Ohlsson (1), Joakim Rydell (2), Anders Brun, Jacob Roll (1), Mats Andersson (2), Anders Ynnerman (3), Hans Knutsson (2)
   (1) Dept. of Electrical Engineering, Linköping university
   (2) Dept. of Medical Engineering, Linköping university
   (3) Dept. of Science and Technology, Linköping university
   Conference: Proceedings of the 47th IEEE Conference on Decision and Control, pp. 3336-3341
   Abstract: Despite the enormous complexity of the human mind, fMRI techniques are able to partially observe the state of a brain in action. In this paper we describe an experimental setup for real-time fMRI in a bio-feedback loop. One of the main challenges in the project is to reach a detection speed, accuracy and spatial resolution necessary to attain sufficient bandwidth of communication to close the bio-feedback loop. To this end we have banked on our previous work on real-time filtering for fMRI and system identification, which has been tailored for use in the experiment setup.

9. Direct weight optimization applied to discontinuous functions
   Authors: Henrik Ohlsson (1), Jacob Roll (1), Anders Brun, Hans Knutsson (2), Mats Andersson (2), Lennart Ljung (1)
   (1) Dept. of Electrical Engineering, Linköping University
   (2) Dept. of Medical Engineering, Linköping University
   Conference: Proceedings of the 47th IEEE Conference on Decision and Control, pp. 117-122
   Abstract: The Direct Weight Optimization (DWO) approach is a nonparametric estimation approach that has appeared in recent years within the field of nonlinear system identification. In previous work, all function classes for which DWO has been studied have included only continuous functions. However, in many applications it would be desirable also to be able to handle discontinuous functions. Inspired by the bilateral filter method from image processing, such an extension of the DWO framework is proposed for the smoothing problem. Examples show that the properties of the new approach regarding the handling of discontinuities are similar to the bilateral filter, while at the same time DWO offers a greater flexibility with respect to different function classes handled.

10. Registration of 2D histological images of bone implants with 3D SRµCT volumes
    Authors: Hamid Sarve, Joakim Lindblad, Carina B. Johansson (1)
    (1) Dept. of Clinical Medicine, Örebro University
    Conference: ISVC 2008, pp. 1071-1080
    Editors: George Bebis, Richard Boyle, Bahram Parvin, Darko Koracin, Paolo Remagnino, Fatih Porikli, Jörg Peters, James Klosowski, Laura Arns, Yu Ka Chun, Theresa-Marie Rhyne, Laura Monroe
    Abstract: To provide better insight in bone modeling and remodeling around implants, information is extracted using different imaging techniques. Two types of data used in this project are 2D histological images and 3D SRuCT (synchrotron radiation-based computed microtomography) volumes. To enable a direct comparison between the two modalities and to bypass the time consuming and difficult task of manual annotation of the volumes, registration of these data types is desired.

    In this paper, we present two 2D-3D intermodal rigid-body registration methods for the mentioned purpose. One approach is based on Simulated Annealing (SA) while the other uses Chamfer Matching (CM). Both methods use Normalized Mutual Information for measuring the correspondence between an extracted 2D-slice from the volume and the 2D histological image whereas the latter approach also takes the edge distance into account for matching the implant boundary. To speed up the process, part of the computations are done on the Graphic Processing Unit.

    The results show that the CM-approach provides a more reliable registration than the SA-approach. The registered slices with the CM-approach correspond visually well to the histological sections, except for cases where the implant has been damaged.

11. A connection between and generalized triangular grids
    Authors: Robin Strand, Benedek Nagy (1)
    (1) Dept. of Computer Science, Faculty of Informatics, University of Debrecen, Hungary
    Conference: International Symposium on Visual Computing (ISVC 2008), Las Vegas, Nevada, USA, pp. 1157-1166
    Editors: George Bebis, Richard Boyle, Bahram Parvin, Darko Koracin, Paolo Remagnino, Fatih Porikli, Jörg Peters, James Klosowski, Laura Arns, Yu Ka Chun, Theresa-Marie Rhyne, Laura Monroe
    Abstract: In this paper we show how non-standard three-dimensional grids, such as the face-centered cubic (fcc), the body-centered cubic (bcc), and the diamond grids can be embedded in . The fcc grid is a hyperplane in , the diamond grid is the union of two parallel hyperplanes. The union of four hyperplanes (in a circular way) gives the bcc grid. Based on these connections, several types of neighborhood structures are introduced on these grids. These structures span from the most natural ones (crystal bonds, Voronoi neighbors) to infinite families.

12. The polar distance transform by fast-marching
    Authors: Robin Strand, Kristin Norell
    Conference: 19th International Conference on Pattern Recognition (ICPR 2008), Tampa, Florida, USA
    Abstract: Image analysis tools that process the image using polar coordinates are needed to avoid the interpolation from polar to cartesian coordinates. We present a tool for analysing and processing circular objects -- the polar distance transform computed by fast-marching. The fast marching method can be used for computing the grey-weighted distance transform by numerically approximating the Eikonal differential equation. We modify the Eikonal equation using weights that depend on the radius and angle relative to a pre-defined coordinate system.

13. Weighted neighborhood sequences in non-standard three-dimensional grids - parameter optimization
    Authors: Robin Strand, Benedek Nagy (1)
    (1) Dept. of Computer Science, Faculty of Informatics, University of Debrecen, Hungary
    Conference: International Workshop on Combinatorial Image Analysis (IWCIA 2008), Buffalo, NY, USA, pp. 51-62
    Editors: Valentin E. Brimkov, Reneta P. Barneva, Herbert A. Hauptman
    Abstract: Recently, a distance function was defined on the face-centered cubic and body-centered cubic grids by combining weights and neighborhood sequences. These distances share many properties with traditional path-based distance functions, such as the city-block distance, but are less rotational dependent. We introduce four different error functions which are used to find the optimal weights and neighborhood sequences that can be used to define the distance functions with low rotational dependency.

14. Weighted neighbourhood sequences in non-standard three-dimensional grids -- metricity and algorithms
    Authors: Robin Strand, Benedek Nagy (1)
    (1) Dept. of Computer Science, Faculty of Informatics, University of Debrecen, Hungary
    Conference: International Conference on Discrete Geometry for Computer Imagery (DGCI 2008), Lyon, France, pp.201-212
    Editors: David Coeurjolly, Isabelle Sivignon, Laure Tougne, Florent Dupont
    Abstract: Recently, a distance function was defined on the face- centered cubic and body-centered cubic grids by combining weights and neighbourhood sequences. These distances share many properties with traditional path-based distance functions, such as the city-block distance, but are less rotational dependent. We present conditions for metricity and algorithms to compute the distances.
15. Accurate and reproducible semi-automatic liver segmentation using haptic interaction
    Authors: Erik Vidholm, Milan Golubovic (1), Sven Nilsson (1), Ingela Nyström
    (1) Dept. of Oncology, Radiology and Clinical Immunology, UU
    Conference: Medical Imaging 2008: Visualization, Image-Guided Procedures, and Modeling
    Editors: Michael I. Miga, Kevin R. Cleary
    Abstract: In this work, we describe and evaluate a semi-automatic method for liver segmentation in CT images using a 3D interface with haptic feedback and stereo graphics. Recently, we reported our fast semi-automatic method using fast marching segmentation. Four users performed initialization of the method for 52 datasets by manually drawing seed-regions directly in 3D using the haptic interface. Here, we evaluate our segmentation method by computing accuracy based on newly obtained manual delineations by two radiologists for 23 datasets. We also show that by performing subsequent segmentation with an interactive deformable model, we can increase segmentation accuracy. Our method shows high reproducibility compared to manual delineation. The mean precision for the manual delineation is 89%, while it is 97% for the fast marching method. With the subsequent deformable mesh segmentation, we obtain a mean precision of 98%. To assess accuracy, we construct a fuzzy ground truth by averaging the manual delineations. The mean sensitivity for the fast marching segmentation is 93% and the specificity is close to 100%. When we apply deformable model segmentation, we obtain a sensitivity increase of three percentage points while the high specificity is maintained. The mean interaction time for the deformable model segmentation is 1.5 minutes. We present a fully 3D liver segmentation method where high accuracy and precision is efficiently obtained via haptic interaction in a 3D user interface. Our method makes it possible to avoid time-consuming manual delineation, which otherwise is a common option prior to, e.g., hepatic surgery planning.