| 1. |
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| 2. |
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| 3. |
- Van den Bulcke, Jan, et al.
(författare)
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3D tree-ring analysis using helical X-ray tomography
- 2014
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Ingår i: Dendrochronologia. - : Elsevier BV. - 1125-7865 .- 1612-0051. ; 32:1, s. 39-46
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Tidskriftsartikel (refereegranskat)abstract
- The current state-of-the-art of tree-ring analysis and densitometry is still mainly limited to two dimensions and mostly requires proper treatment of the surface of the samples. In this paper we elaborate on the potential of helical X-ray computed tomography for 3D tree-ring analysis. Microdensitometrical profiles are obtained by processing of the reconstructed volumes. Correction of the structure direction, taking into account the angle of growth rings and grain, results in very accurate microdensity and precise ring width measurements. Both a manual as well as an automated methodology is proposed here, of which the MATLAB (c) code is available. Examples are given for pine (Pinus sylvestris L), oak (Quercus robur L) and teak (Tectona grandis L.). In all, the methodologies applied here on the 3D volumes are useful for growth related studies, enabling a fast and non-destructive analysis.
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| 4. |
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| 5. |
- Wernersson, Erik L. G., et al.
(författare)
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Postprocessing method for reducing phase effects in reconstructed microcomputed-tomography data
- 2013
-
Ingår i: Optical Society of America. Journal A. - 1084-7529 .- 1520-8532. ; 30:3, s. 455-461
-
Tidskriftsartikel (refereegranskat)abstract
- With increased resolution in x-ray computed tomography, refraction adds increasingly to the attenuation signal. Though potentially beneficial, the artifacts caused by refraction often need to be removed from the image. In this paper, we propose a postprocessing method, based on deconvolution, that is able to remove these artifacts after conventional reconstruction. This method poses two advantages over existing projection-based (preprocessing) phase-retrieval or phase-removal algorithms. First, evaluation of the parameters can be done very quickly, improving the overall speed of the method. Second, postprocessing methods can be applied when projection data is not available, which occurs in several commercial systems with closed software or when projection data has been deleted. It is shown that the proposed method performs comparably to state-of-the-art methods in terms of image quality.
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| 6. |
- Asplund, Teo, et al.
(författare)
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A Faster, Unbiased Path Opening by Upper Skeletonization and Weighted Adjacency Graphs
- 2016
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Ingår i: IEEE Transactions on Image Processing. - 1057-7149 .- 1941-0042. ; 25:12, s. 5589-5600
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Tidskriftsartikel (refereegranskat)abstract
- The path opening is a filter that preserves bright regions in the image in which a path of a certain length L fits. A path is a (not necessarily straight) line defined by a specific adjacency relation. The most efficient implementation known scales as O(min(L, d, Q)N) with the length of the path, L, the maximum possible path length, d, the number of graylevels, Q, and the image size, N. An approximation exists (parsimonious path opening) that has an execution time independent of path length. This is achieved by preselecting paths, and applying 1D openings along these paths. However, the preselected paths can miss important structures, as described by its authors. Here, we propose a different approximation, in which we preselect paths using a grayvalue skeleton. The skeleton follows all ridges in the image, meaning that no important line structures will be missed. An H-minima transform simplifies the image to reduce the number of branches in the skeleton. A graph-based version of the traditional path opening operates only on the pixels in the skeleton, yielding speedups up to one order of magnitude, depending on image size and filter parameters. The edges of the graph are weighted in order to minimize bias. Experiments show that the proposed algorithm scales linearly with image size, and that it is often slightly faster for longer paths than for shorter paths. The algorithm also yields the most accurate results- as compared with a number of path opening variants-when measuring length distributions.
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| 7. |
- Asplund, Teo, et al.
(författare)
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Adaptive Mathematical Morphology on Irregularly Sampled Signals in Two Dimensions
- 2020
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Ingår i: Mathematical Morphology : Theory and Applications. - : Walter de Gruyter. - 2353-3390. ; 4:1, s. 108-126
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Tidskriftsartikel (refereegranskat)abstract
- This paper proposes a way of better approximating continuous, two-dimensional morphologyin the discrete domain, by allowing for irregularly sampled input and output signals. We generalizeprevious work to allow for a greater variety of structuring elements, both flat and non-flat. Experimentallywe show improved results over regular, discrete morphology with respect to the approximation ofcontinuous morphology. It is also worth noting that the number of output samples can often be reducedwithout sacrificing the quality of the approximation, since the morphological operators usually generateoutput signals with many plateaus, which, intuitively do not need a large number of samples to be correctlyrepresented. Finally, the paper presents some results showing adaptive morphology on irregularlysampled signals.
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| 8. |
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| 9. |
- Asplund, Teo, et al.
(författare)
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Mathematical Morphology on Irregularly Sampled Data Applied to Segmentation of 3D Point Clouds of Urban Scenes
- 2019
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Ingår i: International Symposium on Mathematical Morphology and Its Applications to Signal and Image Processing. - Cham : Springer Nature. - 9783030208660 - 9783030208677
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Konferensbidrag (refereegranskat)abstract
- This paper proposes an extension of mathematical morphology on irregularly sampled signals to 3D point clouds. The proposed method is applied to the segmentation of urban scenes to show its applicability to the analysis of point cloud data. Applying the proposed operators has the desirable side-effect of homogenizing signals that are sampled heterogeneously. In experiments we show that the proposed segmentation algorithm yields good results on the Paris-rue-Madame database and is robust in terms of sampling density, i.e. yielding similar labelings for more sparse samplings of the same scene.
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| 10. |
- Asplund, Teo, et al.
(författare)
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Mathematical Morphology on Irregularly Sampled Signals
- 2017
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Ingår i: Computer Vision – ACCV 2016 Workshops. - Cham : Springer. - 9783319544267 - 9783319544274 ; , s. 506-520
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Konferensbidrag (refereegranskat)abstract
- This paper introduces a new operator that can be used to ap-proximate continuous-domain mathematical morphology on irregularly sampled surfaces. We define a new way of approximating the continuous domain dilation by duplicating and shifting samples according to a flat continuous structuring element. We show that the proposed algorithm can better approximate continuous dilation, and that dilations may be sampled irregularly to achieve a smaller sampling without greatly com-promising the accuracy of the result.
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| 11. |
- Asplund, Teo
(författare)
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Precise Image-Based Measurements through Irregular Sampling
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mathematical morphology is a theory that is applicable broadly in signal processing, but in this thesis we focus mainly on image data. Fundamental concepts of morphology include the structuring element and the four operators: dilation, erosion, closing, and opening. One way of thinking about the role of the structuring element is as a probe, which traverses the signal (e.g. the image) systematically and inspects how well it "fits" in a certain sense that depends on the operator.Although morphology is defined in the discrete as well as in the continuous domain, often only the discrete case is considered in practice. However, commonly digital images are a representation of continuous reality and thus it is of interest to maintain a correspondence between mathematical morphology operating in the discrete and in the continuous domain. Therefore, much of this thesis investigates how to better approximate continuous morphology in the discrete domain. We present a number of issues relating to this goal when applying morphology in the regular, discrete case, and show that allowing for irregularly sampled signals can improve this approximation, since moving to irregularly sampled signals frees us from constraints (namely those imposed by the sampling lattice) that harm the correspondence in the regular case. The thesis develops a framework for applying morphology in the irregular case, using a wide range of structuring elements, including non-flat structuring elements (or structuring functions) and adaptive morphology. This proposed framework is then shown to better approximate continuous morphology than its regular, discrete counterpart.Additionally, the thesis contains work dealing with regularly sampled images using regular, discrete morphology and weighting to improve results. However, these cases can be interpreted as specific instances of irregularly sampled signals, thus naturally connecting them to the overarching theme of irregular sampling, precise measurements, and mathematical morphology.
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| 12. |
- Bernander, Karl B., et al.
(författare)
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Improving the stochastic watershed
- 2013
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Ingår i: Pattern Recognition Letters. - : Elsevier BV. - 0167-8655 .- 1872-7344. ; 34:9, s. 993-1000
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Tidskriftsartikel (refereegranskat)abstract
- The stochastic watershed is an unsupervised segmentation tool recently proposed by Angulo and Jeulin. By repeated application of the seeded watershed with randomly placed markers, a probability density function for object boundaries is created. In a second step, the algorithm then generates a meaningful segmentation of the image using this probability density function. The method performs best when the image contains regions of similar size, since it tends to break up larger regions and merge smaller ones. We propose two simple modifications that greatly improve the properties of the stochastic watershed: (1) add noise to the input image at every iteration, and (2) distribute the markers using a randomly placed grid. The noise strength is a new parameter to be set, but the output of the algorithm is not very sensitive to this value. In return, the output becomes less sensitive to the two parameters of the standard algorithm. The improved algorithm does not break up larger regions, effectively making the algorithm useful for a larger class of segmentation problems.
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| 13. |
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| 14. |
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| 15. |
- Curic, Vladimir, et al.
(författare)
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Adaptive hit or miss transform
- 2015
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Ingår i: Mathematical Morphology and Its Applications to Signal and Image Processing. - Cham : Springer. - 9783319187198 ; , s. 741-752
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Konferensbidrag (refereegranskat)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.
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| 16. |
- Curic, Vladimir, et al.
(författare)
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Adaptive structuring elements based on salience distance transform
- 2012
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Ingår i: In Proceedings of Swedish Society for Image Analysis, SSBA 2012. - KTH, Stockholm.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Spatially adaptive structuring elements adjust their shape to the local structures in the image, and are often defined by a ball in a geodesic distance or gray-weighted distance metric space. This paper introduces salience adaptive structuring elements as spatially variant structuring elements that modify not only their shape, but also their size according to the salience of the edges in the image. Consequently they have good properties for filtering.
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| 17. |
- Ćurić, Vladimir, 1981-
(författare)
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Distance Functions and Their Use in Adaptive Mathematical Morphology
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One of the main problems in image analysis is a comparison of different shapes in images. It is often desirable to determine the extent to which one shape differs from another. This is usually a difficult task because shapes vary in size, length, contrast, texture, orientation, etc. Shapes can be described using sets of points, crisp of fuzzy. Hence, distance functions between sets have been used for comparing different shapes.Mathematical morphology is a non-linear theory related to the shape or morphology of features in the image, and morphological operators are defined by the interaction between an image and a small set called a structuring element. Although morphological operators have been extensively used to differentiate shapes by their size, it is not an easy task to differentiate shapes with respect to other features such as contrast or orientation. One approach for differentiation on these type of features is to use data-dependent structuring elements.In this thesis, we investigate the usefulness of various distance functions for: (i) shape registration and recognition; and (ii) construction of adaptive structuring elements and functions.We examine existing distance functions between sets, and propose a new one, called the Complement weighted sum of minimal distances, where the contribution of each point to the distance function is determined by the position of the point within the set. The usefulness of the new distance function is shown for different image registration and shape recognition problems. Furthermore, we extend the new distance function to fuzzy sets and show its applicability to classification of fuzzy objects.We propose two different types of adaptive structuring elements from the salience map of the edge strength: (i) the shape of a structuring element is predefined, and its size is determined from the salience map; (ii) the shape and size of a structuring element are dependent on the salience map. Using this salience map, we also define adaptive structuring functions. We also present the applicability of adaptive mathematical morphology to image regularization. The connection between adaptive mathematical morphology and Lasry-Lions regularization of non-smooth functions provides an elegant tool for image regularization.
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| 18. |
- Curic, Vladimir, et al.
(författare)
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Salience adaptive structuring elements
- 2012
-
Ingår i: IEEE Journal on Selected Topics in Signal Processing. - 1932-4553 .- 1941-0484. ; 6:7, s. 809-819
-
Tidskriftsartikel (refereegranskat)abstract
- Spatially adaptive structuring elements adjust their shape to the local structures in the image, and are often defined by a ball in a geodesic distance or gray-weighted distance metric space. This paper introduces salience adaptive structuring elements as spatially variant structuring elements that modify not only their shape, but also their size according to the salience of the edges in the image. Morphological operators with salience adaptive structuring elements shift edges with high salience to a less extent than those with low salience. Salience adaptive structuring elements are less flexible than morphological amoebas and their shape is less affected by noise in the image. Consequently, morphological operators using salience adaptive structuring elements have better properties.
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| 19. |
- Curic, Vladimir, et al.
(författare)
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Salience-Based Parabolic Structuring Functions
- 2013
-
Ingår i: Mathematical Morphology and Its Applications to Signal and Image Processing. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783642382932 ; 7883, s. 183-194
-
Konferensbidrag (refereegranskat)abstract
- It has been shown that the use of the salience map based on the salience distance transform can be useful for the construction of spatially adaptive structuring elements. In this paper, we propose salience-based parabolic structuring functions that are defined for a fixed, predefined spatial support, and have low computational complexity. In addition, we discuss how to properly define adjunct morphological operators using the new spatially adaptive structuring functions. It is also possible to obtain flat adaptive structuring elements by thresholding the salience-based parabolic structuring functions.
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| 20. |
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| 21. |
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| 22. |
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| 23. |
- Fakhrzadeh, Azadeh, et al.
(författare)
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Epithelial Cell Segmentation in Histological Images of Testicular Tissue Using Graph-Cut
- 2013
-
Ingår i: Image Analysis and Processing – ICIAP 2013. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783642411830 - 9783642411847 ; 8157, s. 201-208
-
Konferensbidrag (refereegranskat)abstract
- Computerized image processing has provided us with valuable tools for analyzing histology images. However, histology images are complex, and the algorithm which is developed for a data set may not work for a new and unseen data set. The preparation procedure of the tissue before imaging can significantly affect the resulting image. Even for the same staining method, factors like delayed fixation may alter the image quality. In this paper we face the challenging problem of designing a method that works on data sets with strongly varying quality. In environmental research, due to the distance between the site where the wild animals are caught and the laboratory, there is always a delay in fixation. Here we suggest a segmentation method based on the structural information of epithelium cell layer in testicular tissue. The cell nuclei are detected using the fast radial symmetry filter. A graph is constructed on top of the epithelial cells. Graph-cut optimization method is used to cut the links between cells of different tubules. The algorithm is tested on five different groups of animals. Group one is fixed immediately, three groups were left at room temperature for 18, 30 and 42 hours respectively, before fixation. Group five was frozen after 6 hours in room temperature and thawed. The suggested algorithm gives promising results for the whole data set.
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| 24. |
- Fakhrzadeh, Azadeh, et al.
(författare)
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New computerized staging method to analyze mink testicular tissue in environmental research
- 2017
-
Ingår i: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 36:1, s. 156-164
-
Tidskriftsartikel (refereegranskat)abstract
- Histopathology of testicular tissue is considered to be the most sensitive tool to detect adverse effects on male reproduction. When assessing tissue damage, seminiferous epithelium needs to be classified into different stages to detect certain cell damages; but stage identification is a demanding task. The authors present a method to identify the 12 stages in mink testicular tissue. The staging system uses Gata-4 immunohistochemistry to visualize acrosome development and proved to be both intraobserver-reproducible and interobserver-reproducible with a substantial agreement of 83.6% (kappa=0.81) and 70.5% (kappa=0.67), respectively. To further advance and objectify this method, they present a computerized staging system that identifies these 12 stages. This program has an agreement of 52.8% (kappa 0.47) with the consensus staging by 2 investigators. The authors propose a pooling of the stages into 5 groups based on morphology, stage transition, and toxicologically important endpoints. The computerized program then reached a substantial agreement of 76.7% (kappa=0.69). The computerized staging tool uses local ternary patterns to describe the texture of the tubules and a support vector machine classifier to learn which textures correspond to which stages. The results have the potential to modernize the tedious staging process required in toxicological evaluation of testicular tissue, especially if combined with whole-slide imaging and automated tubular segmentation. Environ Toxicol Chem 2017;36:156-164.
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| 25. |
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| 26. |
- Hall, Hardy, et al.
(författare)
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Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images
- 2016
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- While novel whole-plant phenotyping technologies have been successfully implemented into functional genomics and breeding programs, the potential of automated phenotyping with cellular resolution is largely unexploited. Laser scanning confocal microscopy has the potential to close this gap by providing spatially highly resolved images containing anatomic as well as chemical information on a subcellular basis. However, in the absence of automated methods, the assessment of the spatial patterns and abundance of fluorescent markers with subcellular resolution is still largely qualitative and time-consuming. Recent advances in image acquisition and analysis, coupled with improvements in microprocessor performance, have brought such automated methods within reach, so that information from thousands of cells per image for hundreds of images may be derived in an experimentally convenient time-frame. Here, we present a MATLAB-based analytical pipeline to (1) segment radial plant organs into individual cells, (2) classify cells into cell type categories based upon Random Forest classification, (3) divide each cell into sub-regions, and (4) quantify fluorescence intensity to a subcellular degree of precision for a separate fluorescence channel. In this research advance, we demonstrate the precision of this analytical process for the relatively complex tissues of Arabidopsis hypocotyls at various stages of development. High speed and robustness make our approach suitable for phenotyping of large collections of stem-like material and other tissue types.
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| 27. |
- Joffre, Thomas, 1987-, et al.
(författare)
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Characterization of interfacial stress transfer ability in acetylation-treated wood fibre composites using X-ray microtomography
- 2017
-
Ingår i: Industrial crops and products (Print). - : Elsevier BV. - 0926-6690 .- 1872-633X. ; 95, s. 43-49
-
Tidskriftsartikel (refereegranskat)abstract
- The properties of the fibre/matrix interface contribute to stiffness, strength and fracture behaviour of fibre-reinforced composites. In cellulosic composites, the limited affinity between the hydrophilic fibres and the hydrophobic thermoplastic matrix remains a challenge, and the reinforcing capability of the fibres is hence not fully utilized. A direct characterisation of the stress transfer ability through pull-out tests on single fibres is extremely cumbersome due to the small dimension of the wood fibres. Here a novel approach is proposed: the length distribution of the fibres sticking out of the matrix at the fracture surface is approximated using X-ray microtomography and is used as an estimate of the adhesion between the fibres and the matrix. When a crack grows in the material, the fibres will either break or be pulled-out of the matrix depending on their adhesion to the matrix: good adhesion between the fibres and the matrix should result in more fibre breakage and less pull-out of the fibres than poor adhesion. The effect of acetylation on the adhesion between the wood fibres and the PLA matrix was evaluated at different moisture contents using the proposed method. By using an acetylation treatment of the fibres it was possible to improve the strength of the composite samples soaked in the water by more than 30%.
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| 28. |
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| 29. |
- Luengo Hendriks, Cris L.
(författare)
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Path openings and their applications
- 2010
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Ingår i: Proceedings SSBA 2010. - Uppsala : Centre for Image Analysis. ; , s. 79-82
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 30. |
- Luengo Hendriks, Cris L., 1974-
(författare)
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Revisiting priority queues for image analysis
- 2010
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Ingår i: Pattern Recognition. - : Elsevier BV. - 0031-3203 .- 1873-5142. ; 43:9, s. 3003-3012
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Tidskriftsartikel (refereegranskat)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.
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| 31. |
- Malmberg, Filip, et al.
(författare)
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An efficient algorithm for exact evaluation of stochastic watersheds
- 2014
-
Ingår i: Pattern Recognition Letters. - : Elsevier BV. - 0167-8655 .- 1872-7344. ; 47, s. 80-84
-
Tidskriftsartikel (refereegranskat)abstract
- The stochastic watershed is a method for unsupervised image segmentation proposed by Angulo and Jeulin (2007). The method first computes a probability density function (PDF), assigning to each piece of contour in the image the probability to appear as a segmentation boundary in seeded watershed segmentation with randomly selected seeds. Contours that appear with high probability are assumed to be more important. This PDF is then post-processed to obtain a final segmentation. The main computational hurdle with the stochastic watershed method is the calculation of the PDF. In the original publication by Angulo and Jeulin, the PDF was estimated by Monte Carlo simulation, i.e., repeatedly selecting random markers and performing seeded watershed segmentation. Meyer and Stawiaski (2010) showed that the PDF can be calculated exactly, without performing any Monte Carlo simulations, but do not provide any implementation details. In a naive implementation, the computational cost of their method is too high to make it useful in practice. Here, we extend the work of Meyer and Stawiaski by presenting an efficient (quasi-linear) algorithm for exact computation of the PDF. We demonstrate that in practice, the proposed method is faster than any previously reported method by more than two orders of magnitude. The algorithm is formulated for general undirected graphs, and thus trivially generalizes to images with any number of dimensions.
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| 32. |
- Malmberg, Filip, et al.
(författare)
-
Exact evaluation of stochastic watersheds : From trees to general graphs
- 2014
-
Ingår i: Discrete Geometry for Computer Imagery. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783319099545 ; 8668, s. 309-319
-
Konferensbidrag (refereegranskat)abstract
- The stochastic watershed is a method for identifying salient contours in an image, with applications to image segmentation. The method computes a probability density function (PDF), assigning to each piece of contour in the image the probability to appear as a segmentation boundary in seeded watershed segmentation with randomly selected seedpoints. Contours that appear with high probability are assumed to be more important. This paper concerns an efficient method for computing the stochastic watershed PDF exactly, without performing any actual seeded watershed computations. A method for exact evaluation of stochastic watersheds was proposed by Meyer and Stawiaski (2010). Their method does not operate directly on the image, but on a compact tree representation where each edge in the tree corresponds to a watershed partition of the image elements. The output of the exact evaluation algorithm is thus a PDF defined over the edges of the tree. While the compact tree representation is useful in its own right, it is in many cases desirable to convert the results from this abstract representation back to the image, e. g, for further processing. Here, we present an efficient linear time algorithm for performing this conversion.
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| 33. |
- Malmberg, Filip, 1980-, et al.
(författare)
-
Exact Evaluation of Targeted Stochastic Watershed Cuts
- 2017
-
Ingår i: Discrete Applied Mathematics. - : Elsevier. - 0166-218X .- 1872-6771. ; 216:2, s. 449-460
-
Tidskriftsartikel (refereegranskat)abstract
- Seeded segmentation with minimum spanning forests, also known as segmentation by watershed cuts, is a powerful method for supervised image segmentation. Given that correct segmentation labels are provided for a small set of image elements, called seeds, the watershed cut method completes the labeling for all image elements so that the boundaries between different labels are optimally aligned with salient edges in the image. Here, a randomized version of watershed segmentation, the targeted stochastic watershed, is proposed for performing multi-label targeted image segmentation with stochastic seed input. The input to the algorithm is a set of probability density functions (PDFs), one for each segmentation label, defined over the pixels of the image. For each pixel, we calculate the probability that the pixel is assigned a given segmentation label in seeded watershed segmentation with seeds drawn from the input PDFs. We propose an efficient algorithm (quasi-linear with respect to the number of image elements) for calculating the desired probabilities exactly.
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| 34. |
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| 35. |
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| 36. |
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| 37. |
- Rübel, Oliver, et al.
(författare)
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Integrating data clustering and visualization for the analysis of 3D gene expression data
- 2010
-
Ingår i: IEEE/ACM Transactions on Computational Biology & Bioinformatics. - 1545-5963 .- 1557-9964. ; 7:1, s. 64-79
-
Tidskriftsartikel (refereegranskat)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.
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| 38. |
- Selig, Bettina, et al.
(författare)
-
Fast evaluation of the robust stochastic watershed
- 2015
-
Ingår i: Mathematical Morphology and Its Applications to Signal and Image Processing. - Cham : Springer. - 9783319187198 ; 9082, s. 705-716
-
Konferensbidrag (refereegranskat)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.
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| 39. |
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| 40. |
- Selig, Bettina, 1982-, et al.
(författare)
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Measuring Distribution of Lignin in Wood Fibre Cross-Sections
- 2009
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Ingår i: Proceedings SSBA 2009. - Halmstad : EIS, Halmstad University. - 9789163339240 ; , s. 5-8
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Lignification of wood fibres has important consequences to the paper production, but its exact effects are not well understood. To correlate exact levels of lignin in wood fibres to their mechanical properties, lignin autofluorescence is imaged in wood fibre cross-sections. Highly lignified areas can be detected and related to the area of the whole cell wall. Presently these measurements are performed manually, which is tedious and expensive. In this paper a method is proposed to estimate the degree of lignification automatically. The method is evaluated manually by an expert. Beside some difficulties segmenting cells that do not conform to our model, there was a highly significant correlation between the two methods.
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| 41. |
- Selig, Bettina, 1982-, et al.
(författare)
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Segmentation of Highly Lignified Zones in Wood Fiber Cross-Sections
- 2009
-
Ingår i: Proceedings of the 16th Scandinavian Conference on Image Analysis (SCIA). - Heidelberg : Springer Berlin. - 9783642022296 ; 5575, s. 369-378
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Konferensbidrag (refereegranskat)abstract
- Lignification of wood fibers has important consequences tothe paper production, but its exact effects are not well understood. Tocorrelate exact levels of lignin in wood fibers to their mechanical proper-ties, lignin autofluorescence is imaged in wood fiber cross-sections. Highlylignified areas can be detected and related to the area of the whole cellwall. Presently these measurements are performed manually, which is te-dious and expensive. In this paper a method is proposed to estimate thedegree of lignification automatically. A multi-stage snake-based segmen-tation is applied on each cell separately. To make a preliminary evaluationwe used an image which contained 17 complete cell cross-sections. Thisimage was segmented both automatically and manually by an expert.There was a highly significant correlation between the two methods, al-though a systematic difference indicates a disagreement in the definitionof the edges between the expert and the algorithm.
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| 42. |
- Selig, Bettina, et al.
(författare)
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Stochastic watershed – an analysis
- 2012
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Ingår i: Proceedings of Swedish Society for Image Analysis, SSBA 2012. - Stockholm : KTH Royal Institute of Technology.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 43. |
- Spörndly-Nees, Ellinor, et al.
(författare)
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Effect of Pre-Fixation Delay and Freezing on Mink Testicular Endpoints for Environmental Research
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- There is growing interest in using wild animals to monitor the real-life cocktail effect of environmental chemicals on male reproduction. However, practical difficulties, such as long distances to the laboratory, generally prolong the time between euthanisation and specimen handling. For instance, tissue fixation is often performed on frozen material or on material where deterioration has started, which may affect tissue morphology. This study examined the effect of pre-fixation delay and freezing on mink testicular endpoints in order to determine robust endpoints in suboptimally handled specimens. Sexually mature farmed mink (n=30) selected at culling were divided into six groups and subjected to different time intervals between euthanisation and fixation or freezing: 0 hours (fixed immediately post mortem), 6 hours, 18 hours, 30 hours, 42 hours, or frozen 6 hours post mortem and thawed overnight. Unaffected endpoints when pre-fixation storage was extended to 30 hours included: area and diameter of the seminiferous tubules, length and weight of the testes, and acrosomes marked with Gata-4. Epithelial height, Sertoli cells marked with Gata-4 and cell morphology were affected endpoints after 6 hours of storage. Freezing the tissue prior to fixation severely altered cell morphology and reduced testicular weight, tubular diameter and area. Morphological changes seen after 6 hours included shredded germ cells and excess cytoplasm in seminiferous tubular lumen, chromatin rearrangements and increased germ cell death. Extended delay before fixation and freezing affected many endpoints in the mink testicular tissue. Some of these endpoints may mimic chemically induced effects, which is important to consider when evaluating specimens from wild animals for environmental toxicity.
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| 44. |
- Weber, Gunther H., et al.
(författare)
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Visual exploration of three-dimensional gene expression using physical views and linked abstract views
- 2009
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Ingår i: IEEE/ACM Transactions on Computational Biology & Bioinformatics. - 1545-5963 .- 1557-9964. ; 6:2, s. 296-309
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Tidskriftsartikel (refereegranskat)abstract
- During animal development, complex patterns of gene expression provide positional information within the embryo. To better understand the underlying gene regulatory networks, the Berkeley Drosophila Transcription Network Project (BDTNP) has developed methods that support quantitative computational analysis of three-dimensional (3D) gene expression in early Drosophila embryos at cellular resolution. We introduce PointCloudXplore (PCX), an interactive visualization tool that supports visual exploration of relationships between different genes' expression using a combination of established visualization techniques. Two aspects of gene expression are of particular interest: 1) gene expression patterns defined by the spatial locations of cells expressing a gene and 2) relationships between the expression levels of multiple genes. PCX provides users with two corresponding classes of data views: 1) Physical Views based on the spatial relationships of cells in the embryo and 2) Abstract Views that discard spatial information and plot expression levels of multiple genes with respect to each other. Cell Selectors highlight data associated with subsets of embryo cells within a View. Using linking, these selected cells can be viewed in multiple representations. We describe PCX as a 3D gene expression visualization tool and provide examples of how it has been used by BDTNP biologists to generate new hypotheses.
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| 45. |
- Wernersson, Erik, 1984-, et al.
(författare)
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Generating synthetic μCT images of wood fibre materials
- 2009
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Ingår i: Proc. 6th International Symposium on Image and Signal Processing and Analysis. - Piscataway, NJ : IEEE. - 9789531841351 ; , s. 365-370
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Konferensbidrag (refereegranskat)abstract
- X-ray Computerized Tomography at micrometer resolution (μCT) is an important tool for understanding the properties of wood fibre materials such as paper, carton and wood fibre composites. While many image analysis methods have been developed for μCT images in wood science, the evaluation of these methods if often not thorough enough because of the lack of a dataset with ground truth. This paper describes the generation of synthetic μCT volumes of wood fibre materials. Fibres with a high degree of morphological variations are modeled and densely packed into a volume of the material. Using a simulation of the μCT image acquisition process, realistic synthetic images are obtained. This simulation uses noise characterized from a set of μCT images. The synthetic images have a known ground truth, and can therefore be used when evaluating image analysis methods.
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| 46. |
- Wernersson, Erik, 1984-, et al.
(författare)
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Segmentation of Wood Fibres in 3D CT Images Using Graph Cuts
- 2009
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Ingår i: Image Analysis and Processing – ICIAP 2009. - Berlin : Springer-Verlag. - 9783642041457 ; 5716, s. 92-102
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Konferensbidrag (refereegranskat)abstract
- To completely segment all individual wood fibres in volume images of fibrous materials presents a challenging problem but is important in understanding the micro mechanical properties of composite materials. This paper presents a filter that identifies and closes pores in wood fibre walls, simplifying the shape of the fibres. After this filter, a novel segmentation method based on graph cuts identifies individual fibres. The methods are validated on a realistic synthetic fibre data set and then applied on μCT images of wood fibre composites.
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