Refereed conference proceedings

Authors affiliated with CBA are in bold.

1. Calving events detection and quantification from time-lapse images in Tunabreen glacier
   Authors: Sigit Adinugroh(1), Dorothée Vallot(2), Pontus Westrin(2), Robin Strand
   (1) Dept. of Information Technology, UU, Uppsala, Sweden
   (2) Dept. of Earth Science, UU, Uppsala, Sweden
   In Proceedings: Proceedings of 2015 International Conference on Information & Communication Technology and Systems (ICTS), pages 61-66
   Abstract: An automatic observation method for calving activity is an absolute necessity for researchers to collect statistical data for deeper understanding of the activity that is well known as a contributing factor for sea level rise. In this paper a new framework for calving event detection and area estimation is presented. First, a set of time-lapse images are registered where the first image in sequence acts as a reference for others. Registration process exploits M-estimator Sample Consensus (MSAC)to build transformation model based on matched Speeded-UpRobust Features (SURF) features. After that, terminus of glacier is extracted by a semi-automatic Chan-vese segmentation. Then, calving regions in a terminus are recognized as textural difference of two consecutive images. Since the difference forms a clustered points, -shape reconstruction is applied to form polygons representing changed areas. Finally, the areas of changed regions are estimated by referring to a Global Digital Elevation Map(GDEM) data. Experimental result on noise-free images confirms the effectiveness of the proposed framework.

2. Blur detection and visualization in histological whole slide images
   Authors: Christophe Avenel, Ingrid Carlbom
   In Proceedings: Proceedings 10th International Conference on Mass Data Analysis of Images and Signals, Leipzig, Germany: IBaI
   Abstract: Digital pathology holds the promise of improved workflow and also of the use of image analysis to extract features from tissue samples for quantitative analysis to improve current subjective analysis of, for example, cancer tissue. But this requires fast and reliable image digitization. In this paper we address image blurriness, which is a particular problem with very large images or tissue micro arrays scanned with whole slide scanners, since autofocus methods may fail when there is a large variation in image content. We introduce a method to detect, quantify and dis-play blurriness from whole slide images (WSI) in real-time. We describe a blurriness measurement based on an ideal high pass filter in the frequency domain. In contrast with other method our method does not require any prior knowledge of the image content, and it produces a continuous blurriness map over the entire WSI. This map can be displayed as an overlay of the original data and viewed at different levels of magnification with zoom and pan features. The computation time for an entire WSI is around 5 minutes on an average workstation, which is about 180 times faster than existing methods.

3. Adaptive hit or miss transform
   Authors: Vladimir Curic(1), Sébastien Lefèvre(2), Cris L. Luengo Hendriks
   (1) Dept. of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
   (2) IRISA, University of Bretagne-Sud, Vannes, France
   In Proceedings: Mathematical Morphology and Its Applications to Signal and Image Processing, LNCS vol. 9082, Springer, pages 741-752
   Editors: Atli Jón Benediktsson, Jocelyn Chanussot, Laurent Najman, Hugues Talbot
   Abstract: The Hit or Miss Transform is a fundamental morphological operator, and can be used for template matching. In this paper, we present a framework for adaptive Hit or Miss Transform, where structuring elements are adaptive with respect to the input image itself. We illustrate the difference between the new adaptive Hit or Miss Transform and the classical Hit or Miss Transform. As an example of its usefulness, we show how the new adaptive Hit or Miss Transform can detect particles in single molecule imaging.

4. LBP - a novel member of the Local Binary Pattern family based on -cutting
   Authors: Marija Delic(1), Joakim Lindblad(1), Nataša Sladoje(2)
   (1) Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia
   (2) Mathematical Institute, Serbian Academy of Sciences and Arts, Serbia
   In Proceedings: IEEE Proceedings 9th International Symposium on Image and Signal Processing and Analysis (ISPA), pages 13-18
   Abstract: Local binary pattern (LBP) descriptors have been popular in texture classification in recent years. They were introduced as descriptors of local image texture and their histograms are shown to be well performing texture features. In this paper we introduce two new LBP descriptors, LBP and its improved variant ILBP. We evaluate their performance in classification by comparing them with some of the existing LBP descriptors - LBP, ILBP, shift LBP (SLBP) and with one ternary descriptor - LTP. The texture descriptors are evaluated on three datasets - KTH-TIPS2b, UIUC and Virus texture dataset. The novel descriptor outperforms the other descriptors on two datasets, KTH-TIPS2b and Virus, and is tied for first place with ILBP on the UIUC dataset.

5. Recreating with photogrammetric techniques a submerged megalithic landscape: the case of the salas reservoir
   Authors: Benito V. Estévez(1), Miguel C. Pazos(2), José María E. Franco(3), Anders Hast
   (1) University of Wales Trinity Saint David, Cultural Astronomy and Astrology, Lampeter Campus, UK
   (2) Geography and History Faculty, University of Santiago de Compostela, Santiago de Compostela, Spain
   (3) Archeology section of the municipality of Ourense, Ourense, Spain
   In Proceedings: 3 Encontro Internacional de Arqueoloxia de Vilalba, pages 9-16 Abstract: The objective of this study is to try to reconstruct the megalithic landscape located at Val do Sala, that nowadays is situated under the water due to the construction of a dam at the seventies from the last century. The choice of this area is due to the several allusions that makes reference to the big amount of tumulus at this area. Though the employment of different photogrammetric techniques over historical photographs, it was possible to reconstruct this megalithic landscape. We also think that the methodology proposed might be a new step in the study of lost monuments, or that are beginning to disappear.

6. Mathematics + computer science = true
   Authors: Anders Hast
   In Proceedings: The Fifth International Scientific Colloquium Mathematics and Children, pages 85-93
   Abstract: Mathematics is a fundamental tool for many sciences. Even so, they are often taught as completely separate topics in higher education. Sometimes math problems are taken from sciences like physics or from real life examples and even if some parts of the mathematics needed is briefly explained when teaching sciences, it is often assumed that the knowledge and understanding of mathematics has already been acquired to a sufficient level before the course starts. However, it is easy to see that a deeper understanding of the mathematics behind the problem in question, also helps in acquiring a better and most of all a deeper understanding of the problem itself. So, the question therefore is how this can be done in computer science in higher education? In other words, how can computer science benefit from including some teaching of mathematics and vice versa? Examples from a mixed course in mathematics and computer graphics will be given and experiences from teaching graphics and mathematics will be discussed. Moreover, experiences from other levels of education will be given and also an overview of how Uppsala University in Sweden supports teachers with a variety of pedagogical and didactic courses as well as other initiatives.

7. Interest point detection based on the extended structure tensor with a scale space parameter
   Authors: Anders Hast
   In Proceedings: International Conference on Computer Vision Theory and Applications, electronic publication, 8 pages
   Abstract: Feature extraction is generally based on some kind of interest point detector, such as Harris, the determinant of the Hessian or difference of Gaussians, just to mention a few. The first two are based on tensors, while the latter computes the difference of two images in scale space. It is proposed herein to combine the structure tensor with a scale space parameter, yielding a structure tensor. The determinant of this tensor can be simplified and it will be shown how two rather different detectors can be obtained from this new formulation. It is shown under what conditions they will be less invariant to scale and rotations than previous approaches. It will also be shown that they find different points and why this could be useful for making the matching faster and also how the subsequent RANSAC could be implemented in parallel, working on different sets of matches.

8. Swedish eScience Education - a graduate school in eScience
   Authors: Anders Hast, Michael Hanke(1), Hans O. Karlsson(2)
   (1) Dept. of Mathematics School of Engineering Sciences, KTH, Royal Institute of Technology Stockholm, Sweden
   (2) Dept. of Chemistry - Ångström Laboratory, Theoretical Chemistry and UPPMAX - Uppsala Multidisciplinary Centre for Advanced Computational Science, Uppsala University, Uppsala, Sweden
   In Proceedings: IEEE Proceedings, 11th International Conference on e-Science, pages 31-35
   Abstract: Swedish eScience Education (SeSE) is a national graduate school in eScience in Sweden. It comes from the collaboration between two major research initiatives in eScience and the school has turned out to be very successful. It has made it possible for students at different universities to get access to education that is not normally available at their home universities. With SeSE they get access to education by the top experts within their respective field. We argue why such graduate school is important and how it is different from training offered by many HPC centres in Europe. Furthermore, examples of courses and their structure is discussed as well as lessons learned from SeSE and its two predecessors in Sweden.

9. Stereo visualisation of historical aerial photos - a valuable digital heritage research tool
   Authors: Anders Hast, Andrea Marchetti(1)
   (1) Istituto di Informatica e Telematica Consiglio Nazionale delle Ricerche, Pisa, Italy
   In Proceedings: Digital Heritage, electronic publication, 4 pages
   Abstract: We demonstrate with several examples how historical aerial photos can benefit from being viewed in stereo and how this can be useful as tool in digital heritage research. The main reason why stereo images are important is that they give a much better understanding of what is actually in the scene than single photos can. The important factor is the depth cue that helps understanding the content and adds the ability to distinguish between objects such as houses and trees and the ground as well as estimating heights of objects. There are however still challenges but also possibilities that will be discussed.

10. A simple and efficient feature descriptor for fast matching
    Authors: Anders Hast, Victoria Sablina(1), Gustav Kylberg(2), Ida-Maria Sintorn(2)
    (1) Dept. of Electronic Computers, Ryazan State Radio Engineering University RSREU, Ryazan, Russia
    (2) Vironova AB, Stockholm, Sweden
    In Proceedings: WSCG, pages 135-142
    Editors: V. Skala
    Abstract: A very simple but efficient feature descriptor is proposed for image matching/registration applications where invariance is not important. The descriptor length is only three times the height of the local region in which the descriptor is calculated, and experiments were conducted to compare it to the SURF descriptor. In addition, it is shown, how the sampling can be modified in order to obtain a rotation invariant descriptor, while still keeping it simple and efficient. Examples from stitching in microscopy and stereo processing of pairs of photographs are given to prove the concept.

11. Multimodal histological image registration using locally rigid transforms
    Authors: Andreas Kårsnäs, Robin Strand
    In Proceedings: Proceedings Interactive Medical Image Computing (IMIC) Workshop, MICCAI, electronic publication
    Abstract: Evaluating multimodal histological images is an important task within cancer diagnosis. Using aligned consecutive sections is still the most straight-forward approach for combining multimodal data.

    To overcome the difficulties in aligning the sections, we present an interactive registration approach and show its usage for aligning TMA core images from consecutive sections stained for different biomarkers. In order to reduce distortion of local structures, a global deformable transform is approximated with locally more or less rigid transformations. This gives a trade-off between registration quality and distortion of local structures. The method divides the registration in an offline (global registration) and online step, where the local approximation is done in real-time within current field of view. This approach gives the viewer the ability to quickly adjust the rigidity from a deformable, well-aligned transformation to a rigid where structures "look right''.

12. Coverage segmentation of 3D thin structures
    Authors: Kristína Lidayová, Joakim Lindblad(1), Nataša Sladoje(2), Hans Frimmel(3), Chunliang Wang(4), Örjan Smedby(4)
    (1) Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia
    (2) Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbia
    (3) Division of Scientific Computing, Dept. of Information Technology, Uppsala University, Sweden
    (4) School of Technology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
    In Proceedings: IEEE Proceedings, 5th International Conference on Image Processing Theory, Tools and Applications (IPTA), Orléans, France, pages 23-28
    Abstract: We present a coverage segmentation method for extracting thin structures in three-dimensional images. The proposed method is an improved extension of our coverage segmentation method for 2D thin structures. We suggest implementation that enables low memory consumption and processing time, and by that applicability of the method on real CTA data. The method needs a reliable crisp segmentation as an input and uses information from linear unmixing and the crisp segmentation to create a high-resolution crisp reconstruction of the object, which can then be used as a final result, or down-sampled to a coverage segmentation at the starting image resolution. Performed quantitative and qualitative analysis confirm excellent performance of the proposed method, both on synthetic and on real data, in particular in terms of robustness to noise.

13. Microscopy image enhancement for cost-effective cervical cancer screening
    Authors: Joakim Lindblad(1), Ewert Bengtsson, Nataša Sladoje(2)
    (1) Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia
    (2) Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbia
    In Proceedings: Proceedings, 19th Scandinavian Conference on Image Analysis, LNCS vol. 9127, Springer, pages 440-451
    Editors: Rasmus R. Paulsen, Kim S. Pedersen
    Abstract: We propose a simple and fast method for microscopy image enhancement and quantitatively evaluate its performance on a database containing cell images obtained from microscope setups of several levels of quality. The method utilizes an efficiently and accurately estimated relative modulation transfer function to generate images of higher quality,starting from those of lower quality, by filtering in the Fourier domain.We evaluate the method visually and based on correlation coefficient and normalized mutual information. We conclude that enhanced images exhibit high similarity, both visually and in terms of information content, with acquired high quality images. This is an important result for the development of a cost-effective screening system for cervical cancer.

14. Exact linear time Euclidean distance transforms of grid line sampled shapes
    Authors: Joakim Lindblad(1), Nataša Sladoje(2)
    (1) University of Novi Sad, Faculty of Technical Sciences, Novi Sad, Serbia
    (2) Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbia
    In Proceedings: Proceedings, 12th International Symposium on Mathematical Morphology and Its Applications to Signal and Image Processing (ISMM), Reykjavik, Iceland, LNCS vol. 9082, Springer, pages 645-656
    Editors: Atli Jón Benediktsson, Jocelyn Chanussot, Laurent Najman, Hugues Talbot
    Abstract: We propose a method for computing, in linear time, the exact Euclidean distance transform of sets of points s.t. one coordinate of a point can be assigned any real value, whereas other coordinates are restricted to discrete sets of values. The proposed distance transform is applicable to objects represented by grid line sampling, and readily provides sub-pixel precise distance values. The algorithm is easy to implement; we present complete pseudo code. The method is easy to parallelize and extend to higher dimensional data. We present two ways of obtaining approximate grid line sampled representations, and evaluate the proposed EDT on synthetic examples. The method is competitive w.r.t. state-of-the-art methods for sub-pixel precise distance evaluation.

15. High-resolution reconstruction by feature distance minimization from multiple views of an object
    Authors: Joakim Lindblad(1), Nataša Sladoje(2), Amit Suveer, Anca Dragomir(3), Ida-Maria Sintorn
    (1) Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia
    (2) Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbia
    (3) Surgical Pathology, Uppsala University Hospital, Sweden
    In Proceedings: IEEE Proceedings, 5th International Conference on Image Processing Theory, Tools and Applications (IPTA), Orléans, France, pages 29-34
    Abstract: We present a method which utilizes advantages of fuzzy object representations and image processing techniques adjusted to them, to further increase efficient utilization of image information. Starting from a number of low-resolution images of affine transformations of an object, we create its suitably defuzzified high-resolution reconstruction. We evaluate the proposed method on synthetic data, observing its performance w.r.t. noise sensitivity, influence of the number of used low-resolution images, sensitivity to object variation and to inaccurate registration. Our aim is to explore applicability of the method to real image data acquired by Transmission Electron Microscopy, in a biomedical application we are currently working on.
    
16. Automatic 3DS conversion of historical aerial photographs
    Authors: Francesco Malapelle(1), Anders Hast, Andrea Fusiello(1), B. Rossi(2), P. Fragneto(2), Andrea Marchetti(3)
    (1) University of Udine, Dept. of Electrical Engineering, Mechanical Engineering and Management, DIEGM, Udine, Italy
    (2) STMicroelectronics, AST Lab, Agrate Brianza, Italy
    (3) Consiglio Nazionale delle Ricerche, IIT, Pisa, Italy
    In Proceedings: IEEE proceedings, International Conference on 3D Imaging (IC3D), electronic publication, 6 pages
    Abstract: In this paper we present a method for the generation of 3D stereo (3DS) pairs from sequences of historical aerial photographs. The goal of our work is to provide a stereoscopic display when the existing exposures are in a monocular sequence. Each input image is processed using its neighbours and a synthetic image is rendered, which, together with the original one, form a stereo pair. Promising results on real images taken from a historical photo archive are shown, that corroborate the viability of generating 3DS data from monocular footage.

    
    

17. Interactive deformation of volume images for image registration
    Authors: Filip Malmberg(1), Robin Strand(1), Joel Kullberg(1)
    (1) Section of Radiology, Dept. of Surgical Sciences, Uppsala University, Uppsala, Sweden
    In Proceedings: Proceedings, Interactive Medical Image Computing (IMIC) Workshop, MICCAI, electronic publication
    Abstract: Deformable image registration, the task of finding a spatial transformation that aligns two or more images with each other, is an important task in medical image analysis. To a large extent, research on image registration has been focused on automatic methods. This is in contrast to, e.g., image segmentation, where interactive semi-automatic methods are common. Here, we propose a method for interactive editing of a deformation eld aligning two volume images. The method has been implemented in a software that allows the user to click and drag points in the deformed image to a new location, while smoothly deforming surrounding points. The method is fast enough to allow real-time display of the deformed volume image during user interaction, on standard hardware. The resulting tool is useful for initializing automatic methods, and to correct errors in automatically generated registrations.
    
18. Teaching OpenGL and computer graphics with programmable shaders
    Authors: Johan Nysjö, Anders Hast
    In Proceedings: SIGRAD, 3 pages
    Abstract: This paper presents our approach and experiences of transferring an introductory computer graphics course from the fixed-function OpenGL pipeline to modern shader-based OpenGL. We provide an overview of the selected course structure and the C++-based programming environment that we use for assignments and projects, and discuss some of the technical and pedagogical challenges, e.g., multiplatform support and shader debugging, that we ran into. Based on course evaluations and the outcome of programming assignments, we conclude that introducing shaders early and skipping the fixed-function pipeline completely is a sound and viable approach. It requires more initial effort from teachers and students because of the added complexity of setting up and using shaders and vertex buffers, but offers a more interactive and powerful programming environment, which we believe helps promoting the creativity of students.

19. Visuohaptic bone saw simulator: combining vibrotactile and kinesthetic feedback
    Authors: Pontus Olsson, Fredrik Nysjö, Neeru Singh(1), Andreas Thor(2), Ingrid Carlbom
    (1) Mount Sinai Beth Israel Medical Center, New York, USA
    (2) Faculty of Medicine, Dept. of Surgical Sciences, Oral and Maxillofacial Surgery, Uppsala University, Uppsala, Sweden
    In Proceedings: Proceedings, 8th ACM SIGGRAPH Asia Technical Briefs, ACM, New York, NY, USA, Article 10, electronic publication, 4 pages
    Abstract: The combination of stereo visualization and haptics provides a natural interface for surgical training simulators, an application which is inherently both highly visual and highly tactile. However, most off-the-shelf kinesthetic haptic devices, such as the popular Phantom devices, are not well-suited to display high-fidelity vibrotactile feedback for the high frequency force components in surgical tools such as a reciprocating bone saw. In these haptic devices, forces are mediated from the actuators to the user through a mechanical linkage, in which inertia, friction, and backlash may distort the feedback. In addition, sustained display of vibrations may cause undue wear of the device. We propose a hybrid solution combining kinesthetic feedback from an off-the-shelf haptic device with high-fidelity vibration feedback from a vibrotactile actuator, and show that the hybrid is able to reproduce vibrations of an actual surgical reciprocating saw within the full perceptible frequency range.

20. Triangulation painting
    Authors: Max Pihlström(1), Anders Hast, Anders Brun
    (1) Dept. of Information Technology, Uppsala University, Sweden
    In Proceedings: SIGRAD, electronic publication, 4 pages
    Abstract: In this paper a dynamic image representation is proposed by combining advantages of both raster and vector graphics in the triangulation. In order for a dynamic mesh to remain a triangulation, a method which maintains integrity of representation is devised. Together with techniques for synthesizing paint, the end result is a configurable scheme demonstrating potential as a viable alternative for digital painting and imaging in general.

21. Fast evaluation of the robust stochastic watershed
    Authors: Bettina Selig, Filip Malmberg, Cris L. Luengo Hendriks
    In Proceedings: Mathematical Morphology and Its Applications to Signal and Image Processing, LNCS vol. 9082, Springer, pages 705-716
    Editors: Atli Jón Benediktsson, Jocelyn Chanussot, Laurent Najman, Hugues Talbot
    Abstract: The stochastic watershed is a segmentation algorithm that estimates the importance of each boundary by repeatedly segmenting the image using a watershed with randomly placed seeds. Recently, this algorithm was further developed in two directions: (1) The exact evaluation algorithm efficiently produces the result of the stochastic watershed with an infinite number of repetitions. This algorithm computes the probability for each boundary to be found by a watershed with random seeds, making the result deterministic and much faster. (2) The robust stochastic watershed improves the usefulness of the segmentation result by avoiding false edges in large regions of uniform intensity. This algorithm simply adds noise to the input image for each repetition of the watershed with random seeds. In this paper, we combine these two algorithms into a method that produces a segmentation result comparable to the robust stochastic watershed, with a considerably reduced computation time. We propose to run the exact evaluation algorithm three times, with uniform noise added to the input image, to produce three different estimates of probabilities for the edges. We combine these three estimates with the geometric mean. In a relatively simple segmentation problem, F-measures averaged over the results on 46 images were identical to those of the robust stochastic watershed, but the computation times were an order of magnitude shorter.

22. Large scale style based dating of medieval manuscripts
    Authors: Fredrik Wahlberg, Lasse Mårtensson(1), Anders Brun
    (1) University of Gävle, Faculty of Education and Business Studies, Dept. of Humanities
    In Proceedings: Proceedings, 3rd International Workshop on Historical Document Imaging and Processing, ACM Digital Library
    Abstract: In this paper we propose a novel approach for manuscript dating based on shape statistics. Our goal was to develop a strategy well suited for a large scale dating effort where heterogeneous collections of thousands of manuscripts could be automatically processed. The proposed method takes the gray scale image as input, then uses the stroke width transform and a statistical model of the gradient image to find ink boundaries. Finally, a distribution over common shapes, quantified using shape context descriptors, is produced for each manuscript image. The proposed method is binarization-free, rotational invariant and requires minimal segmentation. We evaluate our work on the 10000+ manuscripts collection ``Svenskt diplomatariums huvudkartotek'', consisting of charters from the medieval period of todays Sweden. The images, originally intended for web viewing, were of low quality and had compression artifacts. Due to unsupervised feature learning and regression, the collection could be dated with a median absolute error below 19 years even though we only used 5