Journal articles

1. Comparison of histomorphometrical data obtained with two different image analysis methods
   Authors: Ballerini, L.(1); Franke-Stenport, V.(2); Borgefors, G.; Johansson, C.(1)
   (1) Dept. of Clinical Medicine, Örebro University
   (2) Dept. of Biomaterials, Göteborg University
   Journal: Journal of Materials Science: Materials in Medicine 18(8):1471-1479, 2007
   Abstract: A common way to determine tissue acceptance of biomaterials is to perform histomorphometrical analysis on histologically stained sections from retrieved samples with surrounding tissue, using various methods. The time and money consuming methods and techniques used are often in house standards. We address light microscopic investigations of bone tissue reactions on un-decalcified cut and ground sections of threaded implants. In order to screen sections and generate results faster, the aim of this pilot project was to compare results generated with the in-house standard visual image analysis tool (i.e., quantifications and judgements done by the naked eye) with a custom made automatic image analysis program. The histomorphometrical bone area measurements revealed no significant differences between the methods but the results of the bony contacts varied significantly. The raw results were in relative agreement, i.e., the values from the two methods were proportional to each other: low bony contact values in the visual method corresponded to low values with the automatic method. With similar resolution images and further improvements of the automatic method this difference should become insignificant. A great advantage using the new automatic image analysis method is that it is time saving - analysis time can be significantly reduced.

2. Resolving the geometry of biomolecules imaged by cryo electron tomography
   Authors: Bongini, L.(1); Fanelli, D.(2); Svensson, S.; Gedda, M.; Piazza, F.(3), Skoglund, U.(4)
   (1) Dipartimento di Fisica, Università di Firenze, Florence, Italy
   (2) Theoretical Physics, School of Physics and Astronomy, University of Manchester, Manchester, U.K.
   (3) Laboratoire de Biophysique Statistique ITP/SB, Ecole Polytechnique Fédérale de Lausanne, Switzerland
   (4) Cell and Molecular Biology Department, Karolinska Institut, Stockholm
   Journal: Journal of Microscopy 228:174-184, 2007
   Abstract: In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immonoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.

3. Weighted distance transforms generalized to modules and their computation on point lattices
   Authors: Fouard, C.; Strand, R.; Borgefors, G.
   Journal: Pattern Recognition 40(9):2453-2474, 2007
   Abstract: This paper presents the generalization of weighted distances to modules and their computation through the chamfer algorithm on general point lattices. The first part is dedicated to formalization of definitions and properties (distance, metric, norm) of weighted distances on modules. It resumes tools found in literature to express the weighted distance of any point of a module and to compute optimal weights in the general case to get rotation invariant distances. The second part of this paper proves that, for any point lattice, the sequential two-scan chamfer algorithm produces correct distance maps. Finally, the definitions and computation of weighted distances are applied to the face-centered cubic (FCC) and body-centered cubic (BCC) grids.

4. Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis
   Authors: Jahangir Tafrechi, R.S.(1); van de Rijke, F.M.(1); Allalou, A.; Larsson, C.(1); Sloos, W.C.R.(1); van de Sande, M.(1); Wählby, Carolina; Janssen, G. M. C.(1); Raap, A. K.(1)
   (1) Dept. of Molecular Cell Biology and Dept. of Genetics and pathology, Leiden University Medical Center, Leiden, The Netherlands
   Journal: Journal of Histochemistry and Cytochemistry 55(11):1159-1166, 2007
   Abstract: Segregation of mitochondrial DNA (mtDNA) is an important underlying pathogenic factor in mtDNA mutation accumulation in mitochondrial diseases and aging, but the molecular mechanisms of mtDNA segregation are elusive. Lack of high-throughput single-cell mutation load assays lies at the root of the paucity of studies in which, at the single-cell level, mitotic mtDNA segregation patterns have been analyzed. Here we describe development of a novel fluorescence-based, non-gel PCR restriction fragment length polymorphism method for single-cell A3243G mtDNA mutation load measurement. Results correlated very well with a quantitative in situ Padlock/rolling circle amplification-based genotyping method. In view of the throughput and accuracy of both methods for single-cell A3243G mtDNA mutation load determination, we conclude that they are well suited for segregation analysis.

5. In situ detection of phosphorylated platelet-derived growth factor receptor beta using a generalized proximity ligation method
   Authors: Jarvius, M.(1); Paulsson, J.(2); Weibrecht, I.(1); Leuchowius, K.-J.(1); Andersson, A.-C.(3); Wählby, C.; Gullberg, M.(3); Botling, J.(1); Sjöblom, T.(1); Markova, B.(4); Ostman, A.(2); Landegren, U.(1); Söderberg, O.(1)
   (1) Dept. of Genetics and Pathology, Rudbeck Laboratory, UU
   (2) Dept. of Oncology-Pathology, Cancer Center, Karolinska Institut, Stockholm
   (3) Olink AB, Uppsala
   (4) 3rd Medical Department, Hematology-Oncology, Johannes Gutenberg University, Mainz, Germany
   Journal: Molecular and Cellular Proteomics 6:1500-1509, 2007
   Abstract: Improved methods are needed for in situ characterization of post-translational modifications in cell lines and tissues. For example, it is desirable to monitor the phosphorylation status of individual receptor tyrosine kinases in samples from human tumors treated with inhibitors to evaluate therapeutic responses. Unfortunately the leading methods for observing the dynamics of tissue post-translational modifications in situ, immunohistochemistry and immunofluorescence, exhibit limited sensitivity and selectivity. Proximity ligation assay is a novel method that offers improved selectivity through the requirement of dual recognition and increased sensitivity by including DNA amplification as a component of detection of the target molecule. Here we therefore established a generalized in situ proximity ligation assay to investigate phosphorylation of platelet-derived growth factor receptor ß (PDGFRß) in cells stimulated with platelet-derived growth factor BB. Antibodies specific for immunoglobulins from different species, modified by attachment of DNA strands, were used as secondary proximity probes together with a pair of primary antibodies from the corresponding species. Dual recognition of receptors and phosphorylated sites by the primary antibodies in combination with the secondary proximity probes was used to generate circular DNA strands; this was followed by signal amplification by replicating the DNA circles via rolling circle amplification. We detected tyrosine phosphorylated PDGFRß in human embryonic kidney cells stably overexpressing human influenza hemagglutinin-tagged human PDGFRß in porcine aortic endothelial cells transfected with the -receptor, but not in cells transfected with the alpha-receptor, and also in immortalized human foreskin fibroblasts, BJ hTert, endogenously expressing the PDGFRß. We furthermore visualized tyrosine phosphorylated PDGFRß in tissue sections from fresh frozen human scar tissue undergoing wound healing. The method should be of great value to study signal transduction, screen for effects of pharmacological agents, and enhance the diagnostic potential in histopathology.

6. Endothelial cell image enhancement using non-subsampled image pyramid
   Authors: Khan, M.A.U.(1); Khan, M.K.; Khan, M.A.(1); Ibrahim, M.T.(2)
   (1) Dept. of Electrical Engineering, COMSAT Institute of Information Technology, Abbottabad, Pakistan
   (2) Dept. of Computer Engineering, Center for Advanced Studies in Engineering, Islamabad, Pakistan
   Journal: Information Technology Journal 6(7):1057-1062, 2007
   Abstract: A corneal endothelial cell image provides vast amount of information about a human eye. The cell density and cell shape parameters of a given endothelial cell image help opthamologists in making many vital clinical decisions. The acquired endothelial image is poor in contrast where cell boundaries are masked in the background. Previously, most of the work was based on morphological operations in spatial domain. However, if we think of cell structure as texture hidden in noisy background, we can get help from texture segmentation, a well studied area. In this work, we propose a non-subsampled Gaussian pyramid decomposition of lowpass region. At certain level of the pyramid, we start observing cleaner cell boundary structure which greatly facilitates its segmentation. Once segmented automatic cell counting can be used and simulation results have shown improvement in cell density count.

7. Representation and reconstruction of fuzzy disks by moments
   Authors: Sladoje, N.; Lindblad, J.
   Journal: Fuzzy Sets and Systems 158(5):517-534, 2007
   Abstract: In this paper, we analyze the representation and reconstruction of fuzzy disks by using moments. Both continuous and digital fuzzy disks are considered. A fuzzy disk is a convex fuzzy spatial set, where the membership of a point to the fuzzy disk depends only on the distance of the point to the centre of the disk. We show that, for a certain class of membership functions defining a fuzzy disk, there exists a one-to-one correspondence between the set of fuzzy disks and the set of their generalized moment representations. Theoretical error bounds for the accuracy of the estimation of generalized moments of a continuous fuzzy disk from the generalized moments of its digitization and, in connection with that, the accuracy of an approximate reconstruction of a continuous fuzzy disk from the generalized moments of its digitization, are derived. Defuzzification (reduction of a continuous fuzzy disk to a crisp representative) is also considered. A statistical study of generated synthetic objects complements the theoretical results.

8. Distances based on neighbourhood sequences in non-standard three-dimensional grids
   Authors: Strand, R.; Nagy, B.(1)
   (1) Dept. of Computer Science, Faculty of Informatics, University of Debrecen, Debrecen, Hungary
   Journal: Discrete Applied Mathematics 255(4):548-557
   Abstract: Properties for distances based on neighbourhood sequences on the face-centred cubic (fcc) and the body-centred cubic (bcc) grids are presented. Formulas to both compute the distances and assure that the distances satisfy the conditions for being metrics are presented and proved to be correct. The formulas are used to calculate the neighbourhood sequences that generates distances with lowest deviation from the Euclidean distance.

9. Weighted distances based on neighbourhood sequences
   Authors: Strand, R.
   Journal: Pattern Recognition Letters 28(15):2029-2036, 2007
   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. By minimizing an error function, the weights and neighbourhood sequence that give the distance function with the lowest rotational dependency are derived. To verify that the low rotational dependency of the proposed distance function is valid also in applications, the constrained distance transform on a binary image is computed and compared with some traditionally used distance functions.

10. A decomposition scheme for 3D fuzzy objects based on fuzzy distance information
    Authors: Svensson, S.
    Journal: Pattern Recognition Letters 28(2):224-232, 2007
    Abstract: A decomposition scheme for 3D fuzzy objects is presented. The decomposition is guided by a fuzzy distance transform (FDT) of the fuzzy object and aims to decompose the fuzzy object into simpler parts. Relevant voxels, corresponding to the "centres" of the parts, are detected on the FDT and suitably grouped, using a hierarchical clustering technique, into significant seeds for the decomposition. A region growing process is then applied to the seeds. The region growing process makes use of the reverse fuzzy distance transform, which is introduced in this manuscript. The decomposition scheme is illustrated using real data from different applications of which one, namely the identification of the three parts of the Immunoglobulin G antibody imaged using cryo electron tomography, is described more in detail.

11. Identification of the main arterial branches by whole-body contrast-enhanced MRA in elderly subjects using limited user interaction and fast marching
    Authors: Tizon, X.; Lin, Q. (1); Hansen, T.(2); Borgefors, G.; Johansson, L.(2); Ahlström, H.(2); Frimmel, H.(2)
    (1) Computer Vision Laboratory, Linköping University, Linköping
    (2) Dept. of Oncology, Radiology and Clinical Immunology, UU Hospital
    Journal: Journal of Magnetic Resonance Imaging 25(4):806-814, 2007
    Abstract: To extract a graph model corresponding to a predefined set of arterial branches from whole-body contrast-enhanced magnetic resonance angiography (CE-MRA) data sets in elderly asymptomatic subjects, a high-incidence group.Maximum intensity projections (MIPs) were used as an interface to place landmarks in the three-dimensional (3D) data sets. These landmarks were linked together using fast marching to form a graph model of the arterial tree. Only vessels of interest were identified.We tested our method on 10 subjects. We were able to build a graph model of the main arterial branches that performed well in the presence of vascular pathologies, such as stenosis and aneurysm. The results were rated by an experienced radiologist, with an overall success rate of 80%.We were able to extract chosen arterial branches in 3D whole-body CE-MRA images with a moderate amount of interaction using a single MIP projection.

12. Application of underwater hyperspectral data for color correction purposes
    Authors: Åhlén, J.; Sundgren, D.(1); Bengtsson, E.
    (1) Dept. of Computer and Systems Sciences, Royal Institute of Technology, Stockholm
    Journal: Pattern Recognition and Image Analysis 17(1):170-173, 2007
    Abstract: Color correction of underwater images has been considered a difficult task for a number of reasons. Those include severe absorption of the water column, the unpredictable behavior of light under the water surface, limited access to reliable data for correction purposes, and the fact that we are only able to process three spectral channels, which is insufficient for most color correction applications. Here, the authors present a method to estimate a hyperspectral image from an RGB image and pointwise hyperspectral data. This is then used to color correct the hyperspectral underwater image and transform it back into RGB color space.