Refereed conference proceedings

1. Image based measurements of single cell mtDNA mutation load
   Authors: Allalou, A.; van de Rijke, M.F.(1); Jahangir Tafrechi, R.(1); Raap, A.K.(1); Wählby, C.
   (1) Dept. of Molecular Cell Biology, Leiden University Medical Center, The Netherlands
   Conference: 15th Scandinavian Conference on Image Analysis (SCIA 2007), Aalborg, Denmark. LNCS vol. 4522, pp. 631-640
   Editors: Ersbøll, B.K.; Pedersen, K.S.
   Abstract: Cell cultures as well as cells in tissue always display a certain degree of variability, and measurements based on cell averages will miss important information contained in a heterogeneous population. This paper presents automated methods for image based measurements of mitochondiral DNA (mtDNA) mutations in individual cells. The mitochondria are present in the cell2019s cytoplasm, and each cytoplasm has to be delineated. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.

2. 3D tracking of cellulose fibres in volume images
   Authors: Axelsson, M.
   Conference: IEEE International Conference on Image Processing (ICIP 2007), San Antonio, TX, volume 4, pp. 309-312.
   Abstract: Segmentation of individual fibres in volume images is important when analysing the three dimensional (3D) fibre structure in paper and cellulose based composite materials. This paper presents a novel method for 3D tracking of individual fibres which can be used as a pre-segmentation step to a full cell wall segmentation or be used to estimate the fibre orientation. The tracking starts in one seed in each fibre and automatically extracts the local fibre orientation and the fibre centre point in each step using 3D information. Good results are obtained for cellulose fibres that are partially collapsed, cracked or irregularly shaped. The proposed method can also be used in other applications where tracking of tubular structures is of interest.

3. Flexibility description of the MET protein stalk based on the use of non-uniform B-splines
   Authors: Gedda, M.; Svensson, S.
   Conference: 12th International Conference on Computer Analysis of Images and Patterns (CAIP 2007), Vienna, Austria. LNCS vol. 4673, pp. 173-180
   Editors: Kropatsch, W.G.; Kampel, M.; Hanbury, A.
   Abstract: The MET protein controls growth, invasion, and metastasis in cancer cells and is thereby of interest to study, for example from a structural point of view. For individual particle imaging by Cryo-Electron Tomography of the MET protein, or other proteins, dedicated image analysis methods are required to extract information in a robust way as the images have low contrast and resolution (with respect to the size of the imaged structure). We present a method to identify the two parts of the MET protein, 003b2-propeller and stalk, using a fuzzy framework. Furthermore, we describe how a representation of the MET stalk, denoted stalk curve, can be identified based on the use of non-uniform B-splines. The stalk curve is used to extract relevant geometrical information about the stalk, e.g., to facilitate curvature and length measurements.

4. The spatial distribution of nuclei in single skeletal muscle cells as visualised by 3-D images: the differences in organisation between species and between healthy cells and cells affected by disease
   Authors: Höglund, A.-S.(1); Liu, J.(1); Karlsson, P.; Lindblad, J.; Borgefors, G.; Bengtsson, E.; Larsson, L.(1)
   (1) Dept. of Neuroscience, UU Hospital
   Conference: Biophysical Society, 51st annual meeting, Baltimore ML. Biophysical Journal : 637A Suppl. S. - 2007
   Abstract: This project is directed towards detailed image analyses of nuclear organization in single skeletal muscle cells. The object is to identify structural parameters which can be used for diagnosis of different muscle diseases. Skeletal muscle fibers are multinucleated cells, each nucleus determines the protein expression in a finite volume of the fiber, i.e. the myonuclear domain. Thus, it is important to characterize the spatial organization of muscle cell nuclei and understand the basic mechanism behind their distribution in order to reach insights about the importance of distorted nuclear organizations during various muscle diseases. However, the spatial organization of nuclei in human muscle cells is poorly understood, partly due to insufficient methods for 3D visualization. Simply counting the number of nuclei in cross-sections, which is a common technique, is accompanied by a number of technical limitations. We use a procedure where single fibres are fluorescently labelled for actin and nuclei and attached between micromanipulators. This allows us to adjust the sarcomeres to an appropriate length and acquire confocal images through the entire muscle cell. We are now employing this technique to: 1) Analyze nuclei organization in confocal images of single muscle cells from seven different mammalian species representing a 100,000-fold difference in body size; 2) Determine the variability in nuclear size, nuclear domain, and 3D organization in segments of single fibers of both the fast- and slow-twitch types; 3) Determine the spatial organization of transcriptionally active/inactive nuclei in single muscle fibers; 4) Characterize the 3D organization of transcriptionally active, inactive and apoptotic nuclei in muscle cells in critically ill, intensive care unit patients (ICU) with severe muscle wasting and during recovery.
5. Defuzzification by feature distance minimization based on DC programming
   Authors: Lindblad, J.; Lukic, T.(1); Sladoje, N.(1)
   (1) Faculty of Engineering, University of Novi Sad, Serbia
   Conference: 5th International Symposium on Image and Signal Processing and Analysis (ISPA 2007), pp. 373-378 (IEEE proceedings)
   Editors: Petrou, M.; Saramäki, T.; Loncaric, S
   Abstract: We introduce the use of DC programming, in combination with convex-concave regularization, as a deterministic approach for solving the optimization problem imposed by defuzzification by feature distance minimization. We provide a DC based algorithm for finding a solution to the defuzzification problem by expressing the objective function as a difference of two convex functions and iteratively solving a family of DC programs. We compare the performance with the previously recommended method, simulated annealing, on a number of test images. Encouraging results, together with several advantages of the DC based method, approve use of this approach, and motivate its further exploration.

6. Assessment of GIS DATA interoperability in Uganda
   Authors: Musinguzi, M.; Tickodri-Togboa, S.(1); Bax, G.
   (1) Faculty of Technology, Makere University, Uganda
   Conference: Conference on Collaborative Research for Technological Development, Kampala, Uganda
   Abstract: In this paper, we present and discuss the data interoperability issues that are considered to place the greatest limitation to the utilization of GIS Technology in Uganda and other similar Developing Countries. Semantic Similarity Assessment and Geometrical Integration Assessment are applied to spatial datasets from the major providers of spatial data in Uganda. The major semantic issues are identified as either those originating from different approaches to spatial feature development by institutions, or using 'equivalent' spatial data in models that were designed for other environments. Geometrical Integration issues are identified as variations in scale, projections and local adjustments, to generic spatial reference systems and variations in approaches to seamless mapping for UTM projection in Uganda. Documentation of data and legislation on SDI are recommended as solutions to the interoperability issues in Uganda.

7. Analysis of the IMAPCT of GIS/ICT On wetland ASSESSMENT
   Authors: Musinguzi, M.; Bax, G.; Tickodri-Togboa, S.(1)
   (1) Faculty of Technology, Makere University, Uganda
   Conference: Conference on Collaborative Research for Technological Development, Kampala, Uganda
   Abstract: In this paper, we trace the origin and development of wetland assessment techniques from early 1970s up to the current age. We present the bottlenecks to wetland assessment and relate them to the levels of development in ICT, GIS and other spatial technologies. In order to address the current limitations to wetland assessment, which are mainly emanating from cost of data collection, use of GIS and ICT are justified as supporting technologies.

8. Grey weighted polar distance transform for outlining circular and approximately circular objects
   Authors: Norell, K.; Lindblad, J.; Svensson, S.
   Conference: 14th International Conference on Image Analysis and Processing (ICIAP 2007), Modena, Italy, pp.647-652 (IEEE proceedings)
   Editors: Cucchiara, R.
   Abstract: We introduce the polar distance transform and the grey weighted polar distance transform for computation of minimum cost paths preferring circular shape, as well as give algorithms for implementations in a digital setting. An alternative to the polar distance transform is to transform the image to polar coordinates, and then apply a Cartesian distance transform. By using the polar distance transform, resampling of the image and interpolation of new pixel values are avoided. We also handle the case of grey weighted distance transform in a neighbourhood, which, to our knowledge, is new. Initial results of using the grey weighted polar distance transform to outline annual rings in images of log end faces are presented.

9. Quantification of bone remodeling in the proximity of implants
   Authors: Sarve, H.; Johansson, C.B.(1); Lindblad, J.; Borgefors, G.; Franke-Stenport, V.(2)
   (1) Dept. of Clinical Medicine, Örebro University
   (2) Biomaterials Research Center, Göteborg University
   Conference: 12th International Conference on Computer Analysis of Images and Patterns (CAIP 2007), Vienna, Austria. LNCS vol. 4673, pp. 253-260
   Editors: Kropatsch, W.G.; Kampel, M.; Hanbury, A.
   Abstract: In histomorphometrical investigations of bone tissue modeling around screw-shaped implants, the manual measurements of bone area and bone-implant contact length around the implant are time consuming and subjective. In this paper we propose an automatic image analysis method for such measurements. We evaluate different discriminant analysis methods and compare the automatic method with the manual one. The results show that the principal difference between the two methods occurs in length estimation, whereas the area measurement does not differ significantly. A major factor behind the dissimilarities in the results is believed to be misclassification of staining artifacts by the automatic method.

10. Real-time rendering of ice
    Authors: Seipel, S.; Nivfors, A.
    Conference: 9th IASTED International Conference: Computer Graphics and Imaging, pp. 60-66
    Editors: Gobbetti, E.
    Abstract: We present a method for implementing visual appearance of ice and its most important characteristics in real-time. The proposed method is capable of filling a given convex geometry with air particles and bubbles as well as adding an arbitrary amount of cracks. Techniques are presented for creating a bumpy and irregular surface that multiply reflects and refracts the environment. An improved image space technique for clipping a geometry using the Boolean difference of two geometries is presented as well. This technique is used on the cracks to clip them against the ices geometry. The reflection and refraction effects on the ice are implemented by using environment mapping. Two-sided refraction is accomplished by combining the normal vectors of the front and back side of the ice object. The result is ice with convincing visual appearance rendered in real-time using modern graphics hardware.

11. Volumetric normal mapping in rendering of multivariate volume data
    Authors: Seipel, S.
    Conference: EUROGRAPHICS 2007, Eurographics - Shortpapers and Medical Prices, pp. 49-52
    Editors: Cignoni, P.; Sochor, J.
    Abstract: The work presented in this paper introduces volumetric normal maps for producing visual structure in direct volume rendering (DVR) of 3D data for the purpose of visualizing multiple attributes in a 3D volume. We use volumetric normal maps to represent normal vector glyphs that are subsequently applied to warp the gradients in the primary volume data. This method is intended to visualize some secondary attribute in DVR. We demonstrate that our method can render visual structures in DVR without the need of explicit surface reconstruction and texturing.

12. Minimal cost-path for path-based distances
    Authors: Strand, R.; Malmberg, F.; Svensson, S.
    Conference: 5th International Symposium on Image and Signal Processing and Analysis (ISPA 2007), pp. 379-384 (IEEE proceedings)
    Editors: Petrou, M.; Saramäki, T.; Loncaric, S
    Abstract: Distance functions defined by the minimal cost-path using weights and neighbourhood sequences (n.s.) are considered for the constrained distance transform (CDT). The CDT is then used to find one minimal cost-path between two points. The behaviour of some path-based distance functions is analyzed and a new error function is introduced. It is concluded that the weighted n.s.-distance with two weights (3 3 neighbourhood) and the weighted distance with three weights (5 5 neighbourhood) have similar properties in terms of minimal cost-path computation, while the former is more efficient to compute.

13. Shape representation with maximal path-points for path-based distances
    Authors: Strand, R.
    Conference: 5th International Symposium on Image and Signal Processing and Analysis (ISPA 2007), pp. 397-402 (IEEE proceedings)
    Editors: Petrou, M.; Saramäki, T.; Loncaric, S
    Abstract: A general framework explaining the extraction of maximal path-points (related to the set of centres of maximal balls) for path-based distances is presented. The traditional weigthed distance and distance based on neighbourhood sequences are considered and compared with the recently developed weighted distance based on neighbourhood sequences.

14. Topology preserving marching cubes-like algorithms on the face-centered cubic grid
    Authors: Strand, R.; Stelldinger, P.(1)
    (1) Cognitive Systems Group, University of Hamburg, Germany
    Conference: 14th International Conference on Image Analysis and Processing (ICIAP 2007), Modena, Italy, pp.781-788 (IEEE proceedings)
    Editors: Cucchiara, R.
    Abstract: The well-known marching cubes algorithm is modified to apply to the face-centered cubic (fcc) grid. Thus, the local configurations that are considered when extracting the local surface patches are not cubic anymore. This paper presents three different partitionings of the fcc grid to be used for the local configurations. The three candidates are evaluated theoretically and experimentally and compared with the original marching cubes algorithm. It is proved that the reconstructed surface is topologically equivalent to the surface of the original object when the surface of the original object that is digitized is smooth and a sufficiently dense fcc grid is used.

15. Weighted distances based on neighbourhood sequences in non-standard three-dimensional grids
    Authors: Strand, R.
    Conference: 15th Scandinavian Conference on Image Analysis (SCIA 2007), Aalborg, Denmark. LNCS vol. 4522, pp. 452-461
    Editors: Ersbøll, B.K.; Pedersen, K.S.
    Abstract: By combining weighted distances and distances based on neighbourhood sequences, a new family of distance functions with potentially low rotational dependency is obtained. The basic theory for these distance functions, including functional form of the distance between two points, is presented for the face-centered cubic grid and the body-centered cubic grid. By minimizing an error function, the optimal combination of weights and neighbourhood sequence is derived.

16. Centres of maximal balls extracted from a fuzzy distance transform
    Authors: Svensson, S.
    Conference: 8th International Symposium on Mathematical Morphology (ISMM 2007) volume 2, pp. 19-20
    Editors: Banon, G.J.F.; Barrera, J.; Braga-Neto, U.d.M.; Hirata, N.S.T.
    Comment: Extended abstract.

17. Hardware-accelerated volume visualization of parametrically mapped dynamic breast MRI data
    Authors: Vidholm, E.; Mehnert, A.(1); Bengtsson, E.; Wildermoth, M.(1); McMahon, K.(2); Wilson, S.(1); Crozier, S.(1)
    (1) School of ITEE, The University of Queensland, Brisbane, Australia
    (2) Queensland X-Ray, Greenslopes Private Hospital, Australia
    Conference: Workshop on Interaction in medical Image analysis and visualization at 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), pp. 33-40
    Abstract: We present a new approach to visualising parametric volumes obtained in voxel-wise model fitting of dynamic contrast-enhanced (DCE) MRI data of the breast. The visualisation makes use of hardware-accelerated rendering to obtain an interactive, 3D colour-correct maximum intensity projection (MIP). The method has been realised in software that permits the user to not only interactively visualise the parametric volume but also to delineate 3D regions of interest using a 2D slicewise interface. Experimental results, based on 14 DCE-MRI data sets from routine clinical practice, show that using the visualisation/tracing tool a medically qualified operator can achieve the same sensitivity for the detection of malignancy as a radiologist using conventional manual interpretation, but with better specificity. The results demonstrate that the visualisation methodology/software has potential as a tool for assisting the radiologist with the task of interpreting 4D DCE-MRI data in the routine clinical setting.

18. Haptic interaction with deformable models for 3D liver segmentation
    Authors: Vidholm, E.; Nyström, I.
    Conference: Workshop on Interaction in medical image analysis and visualization at 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), pp. 41-48
    Abstract: We present a tool for interactive 3D liver segmentation using deformable surface models represented by simplex meshes. The interaction is performed directly in 3D with a haptic device. We use volume haptics to convey information about the volumetric data used for external force computations. This helps us to better understand the data and adjust the deformation weights. It is also possible to interact directly with the mesh during deformation. By pointing the haptic probe like a "torch" at the mesh, vertices and faces in a user specified neighbourhood are selected and forces can be applied to the selected sub-mesh only. We performed an experiment where 10 segmentations of the liver from CT data was performed. The segmentation results show high sensitivity and specificity when compared to manual delineations made by a radiologist.