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| 2. |
- Azar, Jimmy, et al.
(författare)
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Automated Classification of Glandular Tissue by Statistical Proximity Sampling
- 2015
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Ingår i: International Journal of Biomedical Imaging. - : Hindawi Limited. - 1687-4188 .- 1687-4196.
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Tidskriftsartikel (refereegranskat)abstract
- Due to the complexity of biological tissue and variations in staining procedures, features that are based on the explicit extraction of properties from subglandular structures in tissue images may have difficulty generalizing well over an unrestricted set of images and staining variations. We circumvent this problem by an implicit representation that is both robust and highly descriptive, especially when combined with a multiple instance learning approach to image classification. The new feature method is able to describe tissue architecture based on glandular structure. It is based on statistically representing the relative distribution of tissue components around lumen regions, while preserving spatial and quantitative information, as a basis for diagnosing and analyzing different areas within an image. We demonstrate the efficacy of the method in extracting discriminative features for obtaining high classification rates for tubular formation in both healthy and cancerous tissue, which is an important component in Gleason and tubule-based Elston grading. The proposed method may be used for glandular classification, also in other tissue types, in addition to general applicability as a region-based feature descriptor in image analysis where the image represents a bag with a certain label (or grade) and the region-based feature vectors represent instances.
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| 3. |
- Azar, Jimmy, 1984-
(författare)
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Automated Tissue Image Analysis Using Pattern Recognition
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Automated tissue image analysis aims to develop algorithms for a variety of histological applications. This has important implications in the diagnostic grading of cancer such as in breast and prostate tissue, as well as in the quantification of prognostic and predictive biomarkers that may help assess the risk of recurrence and the responsiveness of tumors to endocrine therapy.In this thesis, we use pattern recognition and image analysis techniques to solve several problems relating to histopathology and immunohistochemistry applications. In particular, we present a new method for the detection and localization of tissue microarray cores in an automated manner and compare it against conventional approaches.We also present an unsupervised method for color decomposition based on modeling the image formation process while taking into account acquisition noise. The method is unsupervised and is able to overcome the limitation of specifying absorption spectra for the stains that require separation. This is done by estimating reference colors through fitting a Gaussian mixture model trained using expectation-maximization.Another important factor in histopathology is the choice of stain, though it often goes unnoticed. Stain color combinations determine the extent of overlap between chromaticity clusters in color space, and this intrinsic overlap sets a main limitation on the performance of classification methods, regardless of their nature or complexity. In this thesis, we present a framework for optimizing the selection of histological stains in a manner that is aligned with the final objective of automation, rather than visual analysis.Immunohistochemistry can facilitate the quantification of biomarkers such as estrogen, progesterone, and the human epidermal growth factor 2 receptors, in addition to Ki-67 proteins that are associated with cell growth and proliferation. As an application, we propose a method for the identification of paired antibodies based on correlating probability maps of immunostaining patterns across adjacent tissue sections.Finally, we present a new feature descriptor for characterizing glandular structure and tissue architecture, which form an important component of Gleason and tubule-based Elston grading. The method is based on defining shape-preserving, neighborhood annuli around lumen regions and gathering quantitative and spatial data concerning the various tissue-types.
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| 4. |
- Azar, Jimmy C., et al.
(författare)
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Image segmentation and identification of paired antibodies in breast tissue
- 2014
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Ingår i: Computational & Mathematical Methods in Medicine. - : Hindawi Limited. - 1748-670X .- 1748-6718. ; , s. 647273:1-11
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Tidskriftsartikel (refereegranskat)abstract
- Comparing staining patterns of paired antibodies designed towards a specific protein but toward different epitopes of the protein provides quality control over the binding and the antibodies' ability to identify the target protein correctly and exclusively. We present a method for automated quantification of immunostaining patterns for antibodies in breast tissue using the Human Protein Atlas database. In such tissue, dark brown dye 3,3'-diaminobenzidine is used as an antibody-specific stain whereas the blue dye hematoxylin is used as a counterstain. The proposed method is based on clustering and relative scaling of features following principal component analysis. Our method is able (1) to accurately segment and identify staining patterns and quantify the amount of staining and (2) to detect paired antibodies by correlating the segmentation results among different cases. Moreover, the method is simple, operating in a low-dimensional feature space, and computationally efficient which makes it suitable for high-throughput processing of tissue microarrays.
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| 5. |
- Boyd, Stephen, et al.
(författare)
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MIMO PID Tuning via Iterated LMI Restriction
- 2015
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Ingår i: International Journal of Robust and Nonlinear Control. - : Wiley. - 1099-1239 .- 1049-8923. ; 26:8, s. 1718-1731
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Tidskriftsartikel (refereegranskat)abstract
- We formulate multi-input multi-output (MIMO) proportional-integral-derivative (PID) controller design as an optimization problem that involves nonconvex quadratic matrix inequalities. We propose a simple method that replaces the nonconvex matrix inequalities with a linear matrix inequality (LMI) restriction, and iterates to convergence. This method can be interpreted as a matrix extension of the convex-concave procedure, or as a particular majorization-minimization (MM) method. Convergence to a local minimum can be guaranteed. While we do not know that the resulting controller is globally optimal, the method works well in practice, and provides a simple automated method for tuning MIMO PID controllers. The method is readily extended in many ways, for example to the design of more complex, structured controllers.
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| 6. |
- Ericsson, Martin, et al.
(författare)
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Design and Implementation of a Stereoscopic Display in a Lecture-room
- 2008
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Ingår i: SIGRAD 2008. - : Linköping University Electronic Press. ; , s. 79-80
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Konferensbidrag (refereegranskat)abstract
- This paper describes the master thesis project 3DIS4U: Design and implementation of a distributed visualization system with a stereoscopic display carried out at Uppsala University. The main contributions of the thesis are the installation and evaluation of a wallsized stereoscopic display in a class room-like environment and improvement of the quality, interactivity and usability of visualizations at Uppsala University by connecting the system to one of UPPMAX high-performance computing (HPC) clusters. The project involved modifications to open source softwares, mainly the Visualization ToolKit (VTK) and ParaView. Furthermore, software was developed to aid users in creating interactive stereoscopic simulations. Software was installed and modified for better usability. The option of using HPC resources for larger interactive visualizations also exists. As a final step, evaluations of the display and of the software were carried out together with background research on distributed rendering techniques to be able to produce a proposal for further development of the project. The result of this work is a class room environment which in a few minutes can be turned into a visualization studio with a stereoscopic Linköpings universitetdisplay with the ability to create interactive visualizations. The lecture room retains its function as a class room and can support up to 30 simultaneous viewers.
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| 7. |
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| 8. |
- Hast, Anders, et al.
(författare)
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Multiscale Texture Synthesis and Colourization of Greyscale Textures
- 2010
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Ingår i: 18th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, WSCG 2010 - In Co-operation with EUROGRAPHICS. - Plzen : Union Agency Science Press. - 9788086943879 - 9788086943886 ; , s. 55-61
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Konferensbidrag (refereegranskat)abstract
- The main idea presented herein is to use a multiscale texture synthesis approach in order to both colourize and upscale greyscale textures. Such textures can be vintage photos to be used in archaeological or urban 3D visualizations and obviously the colour needs to be reconstructed some way. Due to limited quality, walls etc in such 3D visualizations will appear either pixelized or blurry when the viewer approaches them on a close distance. The latter if some kind of interpolation technique is being used to reduce the pixelization. The low resolution greyscale texture and a high resolution coloured texture is used for the colourization and upscaling, which will produce a colour version of the greyscale texture with 4 times higher resolution in each upscale step. The novel idea is to use multiscale texture synthesis in HSV space for the first upscale in order to create a RGB colour image for subsequent upscaling, using either ordinary RGB multiscale texture synthesis or continue using HSV multiscale texture synthesis. These two main approaches will be compared and discussed.
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| 9. |
- Hast, Martin
(författare)
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Design of Low-Order Controllers using Optimization Techniques
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In many applications, especially in the process industry, low-level controllers are the workhorses of the automated production lines. The aim of this study has been to provide simple tuning procedures, either optimization-based methods or tuning rules, for design of low-order controllers. The first part of this thesis deals with PID tuning. Design methods or both SISO and MIMO PID controllers based on convex optimization are presented. The methods consist of solving a nonconvex optimization problem by deriving convex approximations of the original problem and solving these iteratively until convergence. The algorithms are fast because of the convex approximations. The controllers obtained minimize low-frequency sensitivity subject to constraints that ensure robustness to process variations and limitations of control signal effort. The second part of this thesis deals with tuning of feedforward controllers. Tuning rules that minimize the integrated-squared-error arising from measurable step disturbances are derived for a controller that can be interpreted as a filtered and possibly time-delayed PD controller. Using a controller structure that decouples the effects of the feedforward and feedback controllers, the controller is optimal both in open and closed loop settings. To improve the high-frequency noise behavior of the feedforward controller, it is proposed that the optimal controller is augmented with a second-order filter. Several aspects on the tuning of this filter are discussed. For systems with PID controllers, the response to step changes in the reference can be improved by introducing set-point weighting. This can be interpreted as feedforward from the reference signal to the control signal. It is shown how these weights can be found by solving a convex optimization problem. Proportional set-point weight that minimizes the integrated-absolute-error was obtained for a batch of over 130 different processes. From these weights, simple tuning rules were derived and the performance was evaluated on all processes in the batch using five different feedback controller tuning methods. The proposed tuning rules could improve the performance by up to 45% with a modest increase in actuation.
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| 10. |
- Hast, Martin, et al.
(författare)
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Design of Optimal Low-Order Feedforward Controllers
- 2012
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Ingår i: 2nd IFAC Conference on Advances in PID Control 2012. - 9781627483247 ; , s. 483-488
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Konferensbidrag (refereegranskat)abstract
- Design rules for optimal feedforward controllers with lead-lag structure in the presence of measurable disturbances are presented. The design rules are based on stable first-order models with time delays, FOTD, and are optimal in the sense of minimizing the integrated-squared error. The rules are derived for an open-loop setting, considering a step disturbance. This paper also discusses a general feedforward structure, which enables decoupling in the design of feedback and feedforward controllers, and justifies the open-loop setting.
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