Journal articles

1. The Effect of Drugs With Ion Channel-Blocking Activity on the Early Embryonic Rat Heart
   Authors: Dominique Abela(1), Helen Ritchie(2), Deena Ababneh(1), Caroline Gavin(1), Mats F. Nilsson(3), Muhammad Khalid Khan, Kristin Carlsson(1), and William S. Webster(1)
   (1) Dept. of Anatomy and Histology, Sydney Medical School, University of Sydney, Sydney, Australia
   (2) Discipline of Biomedical Sciences, Sydney Medical School, University of Sydney, Sydney, Australia
   (3) Dept. of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University
   Journal: Birth defects research. Part B. Developmental and reproductice toxicology 89(5), pp. 429-440
   Abstract: This study investigated the effects of a range of pharmaceutical drugs with ion channel-blocking activity on the heart of gestation day 13 rat embryos in vitro. The general hypothesis was that the blockade of the I-Kr/hERG channel, that is highly important for the normal functioning of the embryonic rat heart, would cause bradycardia and arrhythmia. Concomitant blockade of other channels was expected to modify the effects of hERG blockade. Fourteen drugs with varying degrees of specificity and affinity toward potassium, sodium, and calcium channels were tested over a range of concentrations. The rat embryos were maintained for 2 hr in culture, 1 hr to acclimatize, and 1 hr to test the effect of the drug. All the drugs caused a concentration-dependent bradycardia except nifedipine, which primarily caused a negative inotropic effect eventually stopping the heart. A number of drugs induced arrhythmias and these appeared to be related to either sodium channel blockade, which resulted in a double atrial beat for each ventricular beat, or IKr/hERG blockade, which caused irregular atrial and ventricular beats. However, it is difficult to make a precise prediction of the effect of a drug on the embryonic heart just by looking at the polypharmacological action on ion channels. The results indicate that the use of the tested drugs during pregnancy could potentially damage the embryo by causing periods of hypoxia. In general, the effects on the embryonic heart were only seen at concentrations greater than those likely to occur with normal therapeutic dosing.

2. Robust Signal Detection in 3D Fluorescence Microscopy
   Authors: Amin Allalou, Amalka Pinidiyaarachchi, Carolina Wählby
   Journal: Cytometry. Part A, 77A, pp. 86-96
   Abstract: Robust detection and localization of biomolecules inside cells is of great importance to better understand the functions related to them. Fluorescence microscopy and specific staining methods make biomolecules appear as point-like signals on image data, often acquired in 3D. Visual detection of such point-like signals can be time consuming and problematic if the 3D images are large, containing many, sometimes overlapping, signals. This sets a demand for robust automated methods for accurate detection of signals in 3D fluorescence microscopy. We propose a new 3D point-source signal detection method that is based on Fourier series. The method consists of two parts, a detector, which is a cosine filter to enhance the point-like signals, and a verifier, which is a sine filter to validate the result from the detector. Compared to conventional methods, our method shows better robustness to noise and good ability to resolve signals that are spatially close. Tests on image data show that the method has equivalent accuracy in signal detection in comparison to Visual detection by experts. The proposed method can be used as an efficient point-like signal detection tool for various types of biological 3D image data.

3. 3D pore structure characterisation of paper
   Authors: Maria Axelsson, Stina Svensson
   Journal: Pattern Analysis and Applications, 13(2), pp. 159-172
   Abstract: Pore structure characterisation of paper, using automated image analysis methods, has previously been performed in two-dimensional images. Three dimensional (3D) images have become available and thereby new representations and corresponding measurements are needed for 3D pore structure characterisation. In this article, we present a new pore structure representation, the individual pore-based skeleton, and new quantitative measurements for individual pores in 3D, such as surface area, orientation, anisotropy, and size distributions. We also present measurements for network relations, like tortuosity and connectivity. The data used to illustrate the pore structure representations and corresponding measurements are high resolution X-ray microtomography volume images of a layered duplex board imaged at the European Synchrotron Radiation Facility (ESRF). Quantification of the pore structure is exemplified and the results show that differences in pore structure between the layers in the cardboard can be characterised using the presented methods.

4. Effects of Aging and Gender on the Spatial Organization of Nuclei in Single Human Skeletal Muscle Cells
   Authors: Alexander Cristea(1), Rizwan Qaisar(1), Patrick Karlsson Edlund, Joakim Lindblad, Ewert Bengtsson, Lars Larsson(1)
   (1) UU, Dept. of Clinical Neurophysiology
   Journal: Aging Cell, 9(5), pp. 685-697
   Abstract: The skeletal muscle fibre is a syncitium where each myonucleus regulates the gene products in a finite volume of the cytoplasm, i.e., the myonuclear domain (MND). We analysed aging- and gender-related effects on myonuclei organization and the MND size in single muscle fibres from six young (21-31 years) and nine old men (72-96 years), and from six young (24-32 years) and nine old women (65-96 years), using a novel image analysis algorithm applied to confocal images. Muscle fibres were classified according to myosin heavy chain (MyHC) isoform expression. Our image analysis algorithm was effective in determining the spatial organization of myonuclei and the distribution of individual MNDs along the single fibre segments. Significant linear relations were observed between MND size and fibre size, irrespective age, gender and MyHC isoform expression. The spatial organization of individual myonuclei, calculated as the distribution of nearest neighbour distances in 3D, and MND size were affected in old age, but changes were dependent on MyHC isoform expression. In type I muscle fibres, average NN-values were lower and showed an increased variability in old age, reflecting an aggregation of myonuclei in old age. Average MND size did not change in old age, but there was an increased MND size variability. In type IIa fibres, average NN-values and MND sizes were lower in old age, reflecting the smaller size of these muscle fibres in old age. It is suggested that these changes have a significant impact on protein synthesis and degradation during the aging process.

5. Signal Extraction and Separation in In Vivo Animal PET Studies with Masked Volumewise Principal-Component Analysis
   Authors: Fredrik Engbrant(1), Azita Monazzam(1), Per-Edvin Svensson(1), Johan Olsson(1), Ewert Bengtsson, Pasha Razifar(1)
   (1) Uppsala Applied Science Laboratory (UASL), GE Healthcare, Uppsala, Sweden
   Journal: Nuclear Medicine Technology, 38(2), pp. 53-60
   Abstract: The standardized uptake value is commonly used as a tool to supplement visual interpretation and to quantify the images acquired from static in vivo animal PET. The preferred approach for analyzing PET data is either to sum the images and calculate the standardized uptake value or to use kinetic modeling. The aim of this study was to investigate the performance of masked volumewise principal-component analysis (MVW-PCA) used in dynamic in vivo animal PET studies to extract and separate signals with different kinetic behaviors. Methods: PET data were acquired with a small-animal PET scanner and a fluorine tracer in a study of rats and mice. After acquisition, the data were reconstructed by use of 4 time protocols with different frame lengths. Data were analyzed by use of MVW-PCA with applied noise prenormalization and a new masking technique developed in this study. Results: The resulting principal-component images showed a clear separation of the activity in the spine into the first MVW-PCA component and the activity in the kidneys into the second MVW-PCA component. In addition, the different time protocols were shown to have little or no impact on the results obtained with MVW-PCA. Conclusion: MVW-PCA can efficiently separate different kinetic behaviors into different principal-component images. Moreover, MVW-PCA is a stable technique in the sense that the time protocol chosen has only a small impact on the resulting principal-component images.

6. Image Processing System for Localising Macromolecules in Cryo-Electron Tomography
   Authors: Magnus Gedda, L.-G. Öfverstedt(1), U. Skoglund(1), Stina Svensson
   (1) Okinawa Institute of Science and Technology, Japan
   Journal: Machine Graphics & Vision, 19(2), pp. 159-184
   Abstract: A major challenge in today's molecular biology research is to understand the interaction between proteins at the molecular level. Cryo-electron tomography (ET) has come to play an important role in facilitating objective qualitative experiments on protein structures and their interaction. Various protein conformation structures can be qualitatively analysed as complete galleries of proteins are captured by ET. To facilitate fast and objective macromolecular structure analysis procedures, image processing has become a crucial tool. This paper presents an image processing system for localising individual proteins from in vitro samples imaged by ET. We have evaluated the system using simulated data as well as experimental data.

7. Velocity and Pressure-based Partitions of Horizontal and Vertical Trajectories for On-line Signature Verification
   Authors: Muhammad Talal Ibrahim(1), M. Aurangzeb Khan(2), Khurram Saleem Alimgeer(2), Muhammad Khalid Khan, Imtiaz A. Taj(3), Ling Guan(1)
   (1) Ryerson Multimedia Research Lab, Ryerson University, Toronto, Canada
   (2) Dept. of Electrical Engineering, COMSATS Institute of Information Technology, Islamabad, Pakistan
   (3) Dept. of Electronics Engineering, Mohammad Ali Jinnah University, Islamabad, Pakistan
   Journal: Pattern Recognition 43(8), pp. 2817-2832
   Abstract: In general, shape of an on-line signature is used as a single discriminating feature. Sometimes shape of signature is used alone for verification purposes and sometimes it is used in combination with some other dynamic features such as velocity, pressure and acceleration. The shape of an on-line signature is basically formed due to the wrist and fingers movements where the wrist movement is represented by the horizontal trajectory and the movement of the fingers is represented by vertical trajectory. As the on-line signature is formed due to the combination of two movements that are essentially independent of each other, it will be more effective to use them as two separate discriminating features. Based on this observation, we propose to use these trajectories in isolation by first decomposing the pressure and velocity profiles into two partitions and then extracting the underlying horizontal and vertical trajectories. So the overall process can be thought as the process which exploits the inter-feature dependencies by decomposing signature trajectories depending upon pressure and velocity information and performs verification on each partition separately. As a result, we are able to extract eight discriminating features and among them the most stable discriminating feature is used in verification process. Further Principal Component Analysis (PCA) has been proposed to make the signatures rotation invariant. Experimental results demonstrate superiority of our approach in on-line signature verification in comparison with other techniques.

8. Three-dimensional Texture Analysis of Renal Cell Carcinoma Cell Nuclei for Computerized Automatic Grading
   Authors: Tae-Yun Kim(1), Hyun-Ju Choi, Hae-Gil Hwang(1), Heung-Kook Choi(2)
   (1) School of computer engineering, Inje University, Korea
   (2) Ubiquitous Healthcare Research Center, Inje University, Korea
   Journal: Journal of medical systems, 34(4), pp. 709-716
   Abstract: The extraction of important features in cancer cell image analysis is a key process in grading renal cell carcinoma. In this study, we analyzed the three-dimensional chromatin texture of cell nuclei based on digital image cytometry. Individual images of 2,423 cell nuclei were extracted from 80 renal cell carcinomas (RCCs) using confocal laser scanning microscopy (CLSM). First, we applied the 3D texture mapping method to render the volume of entire tissue sections. Then, we determined the chromatin texture quantitatively by calculating 3D gray level co-occurrence matrices and 3D run length matrices. Finally, to demonstrate the suitability of 3D texture features for classification, we performed a discriminant analysis. In addition, we conducted a principal component analysis to obtain optimized texture features. Automatic grading of cell nuclei using 3D texture features had an accuracy of 78.30%. Combining 3D textural and 3D morphological features improved the accuracy to 82.19%.

9. Evaluating 2D and 3D Visualizations of Spatiotemporal Information
   Authors: Andreas Kjellin(1), Lars Winkler Pettersson(1), Stefan Seipel, Mats Lind(1)
   (1) UU Human-Computer Interaction
   Journal: ACM Transactions on Applied Perception 7(3), pp. 1-23
   Abstract: Time-varying geospatial data presents some specific challenges for visualization. Here, we report the results of three experiments aiming at evaluating the relative efficiency of three existing visualization techniques for a class of such data. The class chosen was that of object movement, especially the movements of vehicles in a fictitious landscape. Two different tasks were also chosen. One was to predict where three vehicles will meet in the future given a visualization of their past movement history. The second task was to estimate the order in which four vehicles arrived at a specific place. Our results reveal that previous findings had generalized human perception in these situations and that large differences in user efficiency exist for a given task between different types of visualizations depicting the same data. Furthermore, our results are in line with earlier general findings on the nature of human perception of both object shape and scene changes. Finally, the need for new taxonomies of data and tasks based on results from perception research is discussed.

10. Different Levels of 3D: An Evaluation of Visualized Discrete Spatiotemporal Data in Space-time Cubes
    Authors: Andreas Kjellin(1), Lars Winkler Pettersson(1), Stefan Seipel, Mats Lind(1)
    (1) UU Human-Computer Interaction
    Journal: Information Visualization, 9(2), pp. 152-164
    Abstract: New technologies and techniques allow novel kinds of visualizations and different types of 3D visualizations are constantly developed. We propose a categorization of 3D visualizations and, based on this categorization, evaluate two versions of a space-time cube that show discrete spatiotemporal data. The two visualization techniques used are a head-tracked stereoscopic visualization ('strong 3D') and a static monocular visualization ('weak 3D'). In terms of effectiveness and efficiency the weak 3D visualization is as good as the strong 3D and thus the need for advanced 3D visualizations in these kinds of tasks may not be necessary.

11. Revisiting Priority Queues for Image Analysis
    Author: Cris L. Luengo Hendriks
    Journal: Pattern Recognition, 43(9), pp. 3003-3012
    Abstract: Many algorithms in image analysis require a priority queue, a data structure that holds pointers to pixels in the image, and which allows efficiently finding the pixel in the queue with the highest priority. However, very few articles describing such image analysis algorithms specify which implementation of the priority queue was used. Many assessments of priority queues can be found in the literature, but mostly in the context of numerical simulation rather than image analysis. Furthermore, due to the ever-changing characteristics of computing hardware, performance evaluated empirically 10 years ago is no longer relevant. In this paper I revisit priority queues as used in image analysis routines, evaluate their performance in a very general setting, and come to a very different conclusion than other authors: implicit heaps are the most efficient priority queues. At the same time, I propose a simple modification of the hierarchical queue (or bucket queue) that is more efficient than the implicit heap for extremely large queues.

12. Constrained and Dimensionality-Independent Path Opening
    Author: Cris L. Luengo Hendriks
    Journal: IEEE Transactions on Image Processing 19(6), pp. 1587-1595
    Abstract: Path openings and closings are morphological operations with flexible line segments as structuring elements. These line segments have the ability to adapt to local image structures, and can be used to detect lines that are not perfectly straight. They also are a convenient and efficient alternative to straight line segments as structuring elements when the exact orientation of lines in the image is not known. These path operations are defined by an adjacency relation, which typically allows for lines that are approximately horizontal, vertical or diagonal. However, because this definition allows zig-zag lines, diagonal paths can be much shorter than the corresponding horizontal or vertical paths. This undoubtedly causes problems when attempting to use path operations for length measurements. This paper 1) introduces a dimensionality-independent implementation of the path opening and closing algorithm by Appleton and Talbot, 2) proposes a constraint on the path operations to improve their ability to perform length measurements, and 3) shows how to use path openings and closings in a granulometry to obtain the length distribution of elongated structures directly from a gray-value image, without a need for binarizing the image and identifying individual objects.

13. Improved Methodology for Identifying the Teratogenic Potential in Early Drug Development of hERG Channel Blocking Drugs
    Authors: M. F. Nilsson(1), C. Danielsson(2), A.-C. Sköld(3), A. Johansson (3), B. Blomgren(3), J. Wilson(3), K.M. Khan, E. Bengtsson, K. Kultima(1,4), W.S. Webster(5), B.R. Danielsson(1)
    (1) Dept. of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Sweden
    (2) Dept. of Medicine H7, Division of Cardiology, Karolinska University Hospital, Stockholm, Sweden
    (3) AstraZeneca R&D Södertälje, Safety Assessment, Södertälje, Sweden
    (4) Dept. on Medical Sciences, Cancer Pharmacology and Informatics, Uppsala University Hospital
    (5) Dept. of Anatomy and Histology, University of Sydney, NSW 2006, Australia
    Journal: Reproductive Toxicology 29(2), pp. 156-163
    Abstract: Drugs blocking the potassium current IKr of the heart (via hERG channel-inhibition) have the potential to cause hypoxia-related teratogenic effects. However, this activity may be missed in conventional teratology studies because repeat dosing may cause resorptions. The aim of the present study was to investigate an alternative protocol to reveal the teratogenic potential of IKr-blocking drugs. The IKr blocker astemizole, given as a single dose (80mg/kg) on gestation day (GD) 13 to pregnant rats caused digital defects. In whole rat embryo culture (2h) on GD 13, astemizole caused a decrease in embryonic heart rate at 20nM, and arrhythmias at 200-400nM. Cetirizine, without IKr-blocking properties, did not affect the rat embryonic heart in vitro. The present study shows that single dose testing on sensitive days of development, together with whole embryo culture, can be a useful methodology to better characterize the teratogenic potential of IKr-blocking drugs.

14. Integrating Data Clustering and Visualizationfor the Analysis of 3D Gene Expression Data
    Authors: Oliver Rbel(1), Gunther H. Weber(1), Min-YuHuang(2), E. Wes Bethel(1), Mark D. Biggin(1), Charless C. Fowlkes(3), Cris L. Luengo Hendriks, Soile V.E. Keränen(1), Michael B. Eisen(4), David W. Knowles(1), Jitendra Malik(4) and Bernd Hamann(2)
    (1) Lawrence Berkeley National Laboratory
    (2) University of California, Davis
    (3) University of California, Irvine
    (4) University of California, Berkeley
    Journal: IEEE/ACM Transactions on Computational Biology & Bioinformatics 7(1), pp. 64-69
    Abstract: The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex data sets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss 1) the integration of data clustering and visualization into one framework, 2) the application of data clustering to 3D gene expression data, 3) the evaluation of the number of clusters k in the context of 3D gene expression clustering, and 4) the improvement of overall analysis quality via dedicated postprocessing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.

15. Gradient Based Intensity Normalization
    Authors: Ida-Maria Sintorn, Leanne Bischof(1), Michael Buckley(1), Paul Jackway(1), Stephen Haggarty(2)
    (1) CSIRO Mathematical and Information Sciences
    (2) BROAD Institute of Harvard and MIT
    Journal: Journal of Microscopy, 3, pp. 249-258
    Abstract: Intensity normalization is important in quantitative image analysis, especially when extracting features based on intensity. In automated microscopy, particularly in large cellular screening experiments, each image contains objects of similar type (e.g. cells) but the object density (number and size of the objects) may vary markedly from image to image. Standard intensity normalization methods, such as matching the grey-value histogram of an image to a target histogram from, i.e. a reference image, only work well if both object type and object density are similar in the images to be matched. This is typically not the case in cellular screening and many other types of images where object type varies little from image to image, but object density may vary dramatically. In this paper, we propose an improved form of intensity normalization which uses grey-value as well as gradient information. This method is very robust to differences in object density. We compare and contrast our method with standard histogram normalization across a range of image types, and show that the modified procedure performs much better when object density varies between images.

16. On the Role of Visual References in Collaborative Visualization
    Authors: Lars Winkler Pettersson(1), Andreas Kjellin(1), Mats Lind(1), Stefan Seipel
    (1) Uppsala University, Human-Computer Interaction
    Journal: Information Visualization, 9(2), pp. 98-114
    Abstract: Multi-Viewer Display Environments (MVDE) provide unique opportunities to present personalized information to several users concurrently in the same physical display space. MVDEs can support correct 3D visualizations to multiple users, present correctly oriented text and symbols to all viewers and allow individually chosen subsets of information in a shared context. MVDEs aim at supporting collaborative visual analysis, and when used to visualize disjoint information in partitioned visualizations they even necessitate collaboration. When solving visual tasks collaboratively in a MVDE, overall performance is affected not only by the inherent effects of the graphical presentation but also by the interaction between the collaborating users. We present results from an empirical study where we compared views with lack of shared visual references in disjoint sets of information to views with mutually shared information. Potential benefits of 2D and 3D visualizations in a collaborative task were investigated and the effects of partitioning visualizations both in terms of task performance, interaction behavior and clutter reduction. In our study of a collaborative task that required only a minimum of information to be shared, we found that partitioned views with a lack of shared visual references were significantly less efficient than integrated views. However, the study showed that subjects were equally capable of solving the task at low error levels in partitioned and integrated views. An explorative analysis revealed that the amount of visual clutter was reduced heavily in partitioned visualization, whereas verbal and deictic communication between subjects increased. It also showed that the type of the visualization (2D/3D) affects interaction behavior strongly. An interesting result is that collaboration on complex geo-time visualizations is actually as efficient in 2D as in 3D.

17. Bright-Field Microscopy Visualization of Proteins and Protein Complexes by In Situ Proximity Ligation with Peroxidase Detection
    Authors: Agata Zieba(1), Carolina Wählby, Fredrik Hjelm(2), Lee Jordan(3), Jonathan Berg(3), Ulf Landegren(1), Katerina Pardali(1)
    (1) Dept. of Genetics and Pathology, UU
    (2) Olink Bioscience, Uppsala
    (3) Ninewells Hospital and Medical School, University of Dundee, Scotland, UK
    Journal: Clinical Chemistry, 56(1), pp. 99-110
    Abstract: BACKGROUND: The in situ proximity ligation assay (PLA) allows a protein or protein complex to be represented as an amplifiable DNA molecule. Recognition is mediated by proximity probes consisting of antibodies coupled with oligonucleotides. Upon dual binding of the proximity probes, the oligonucleotides direct the formation of a circular DNA molecule, which is then amplified by rolling-circle replication. The localized concatemeric product is then detected with fluorescent probes. The in situ PLA enables localized detection of individual native proteins or interacting protein pairs in fixed cells or tissue sections, thus providing an important tool for basic and clinical research.

    METHODS: We used horseradish peroxidase (HRP)conjugated oligonucleotides to couple in situ PLA with enzymatic visualization of the localized detection event.

    RESULTS: We demonstrate the detection of protein complexes, both in cells and in tissue sections, and show that we can quantify the complexes with image-analysis software specially developed for recognizing HRP signals in bright-field microscopy images. We show that fluorescence and HRP signals produce equivalent results, both ill cultured cells and in tissue samples.

    CONCLUSIONS: The combination of in situ PLA with bright-field detection and automated image analysis allows the signals present to be Counted in an automated fashion and thus provides a sensitive and specific method for quantification of proteins and protein complexes with bright-field microscopy. With this approach, in situ PLA can be used without the requirement for expensive fluorescence microscopes, thereby avoiding problems with nonspecific fluorescence while maintaining compatibility with conventional histologic staining.