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| 2. |
- Allalou, Amin, 1981-
(författare)
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Methods for 2D and 3D Quantitative Microscopy of Biological Samples
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- New microscopy techniques are continuously developed, resulting in more rapid acquisition of large amounts of data. Manual analysis of such data is extremely time-consuming and many features are difficult to quantify without the aid of a computer. But with automated image analysis biologists can extract quantitative measurements and increases throughput significantly, which becomes particularly important in high-throughput screening (HTS). This thesis addresses automation of traditional analysis of cell data as well as automation of both image capture and analysis in zebrafish high-throughput screening. It is common in microscopy images to stain the nuclei in the cells, and to label the DNA and proteins in different ways. Padlock-probing and proximity ligation are highly specific detection methods that produce point-like signals within the cells. Accurate signal detection and segmentation is often a key step in analysis of these types of images. Cells in a sample will always show some degree of variation in DNA and protein expression and to quantify these variations each cell has to be analyzed individually. This thesis presents development and evaluation of single cell analysis on a range of different types of image data. In addition, we present a novel method for signal detection in three dimensions. HTS systems often use a combination of microscopy and image analysis to analyze cell-based samples. However, many diseases and biological pathways can be better studied in whole animals, particularly those that involve organ systems and multi-cellular interactions. The zebrafish is a widely-used vertebrate model of human organ function and development. Our collaborators have developed a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae. This thesis presents improvements to the system, including accurate positioning of the fish which incorporates methods for detecting regions of interest, making the system fully automatic. Furthermore, the thesis describes a novel high-throughput tomography system for screening live zebrafish in both fluorescence and bright field microscopy. This 3D imaging approach combined with automatic quantification of morphological changes enables previously intractable high-throughput screening of vertebrate model organisms.
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| 3. |
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Annual Report 2008
- 2009. - 250
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Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Astruc, Marine, et al.
(författare)
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Cluster detection and field-of-view quality rating : Applied to automated Pap-smear analysis
- 2013
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Ingår i: Proc. 2nd International Conference on Pattern Recognition Applications and Methods. - : SciTePress. - 9789898565419 ; , s. 355-364
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Konferensbidrag (refereegranskat)abstract
- Automated cervical cancer screening systems require high resolution analysis of a large number of epithelial cells, involving complex algorithms, mainly analysing the shape and texture of cell nuclei. This can be a very time consuming process. An initial selection of relevant fields-of-view in low resolution images could limit the number of fields to be further analysed at a high resolution. In particular, the detection of cell clusters is of interest for nuclei segmentation improvement, and for diagnostic purpose, malignant and endometrial cells being more prone to stick together in clusters than other cells. In this paper, we propose methods aiming at evaluating the quality of fields-of-view in bright-field microscope images of cervical cells. The approach consists in the construction of neighbourhood graphs using the nuclei as the set of vertices. Transformations are then applied on such graphs in order to highlight the main structures in the image. The methods result in the delineation of regions with varying cell density and the identification of cell clusters. Clustering methods are evaluated using a dataset of manually delineated clusters and compared to a related work.
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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
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| 9. |
- Barrera, Tony, et al.
(författare)
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A chronological and mathematical overview of digital circle generation algorithms : Introducing efficient 4- and 8-connected circles
- 2016
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Ingår i: International Journal of Computer Mathematics. - : Informa UK Limited. - 0020-7160 .- 1029-0265. ; 93:8, s. 1241-1253
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Tidskriftsartikel (refereegranskat)abstract
- Circles are one of the basic drawing primitives for computers and while the naive way of setting up an equation for drawing circles is simple, implementing it in an efficient way using integer arithmetic has resulted in quite a few different algorithms. We present a short chronological overview of the most important publications of such digital circle generation algorithms. Bresenham is often assumed to have invented the first all integer circle algorithm. However, there were other algorithms published before his first official publication, which did not use floating point operations. Furthermore, we present both a 4- and an 8-connected all integer algorithm. Both of them proceed without any multiplication, using just one addition per iteration to compute the decision variable, which makes them more efficient than previously published algorithms.
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| 10. |
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| 11. |
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| 12. |
- Barrera, Tony, et al.
(författare)
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Connected Minimal Acceleration Trigonometric Curves
- 2005
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Ingår i: SIGRAD 2005 The Annual SIGRAD Conference Special Theme – Mobile Graphics November 23-24, 2005 Lund, Sweden.
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Konferensbidrag (refereegranskat)abstract
- We present a technique that can be used to obtain a series of connected minimal bending trigonometric splines that will intersect any number of predefined points in space. The minimal bending property is obtained by a least square minimization of the acceleration. Each curve segment between two consecutive points will be a trigonometric Hermite spline obtained from a Fourier series and its four first terms. The proposed method can be used for a number of points and predefined tangents. The tangent length will then be optimized to yield a minimal bending curve. We also show how both the tangent direction and length can be optimized to give as smooth curves as possible. It is also possible to obtain a closed loop of minimal bending curves. These types of curves can be useful tools for 3D modelling, etc.
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| 13. |
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| 14. |
- Barrera, Tony, et al.
(författare)
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Minimal Acceleration Hermite Curves
- 2005
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Ingår i: Game programming gems 5. - Hingham, Massachusetts : Charles River Media, inc.. - 1584503521 ; , s. 225-231
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Bokkapitel (populärvet., debatt m.m.)
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| 15. |
- Barrera, Tony, et al.
(författare)
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Minimal Acceleration Hermite Curves
- 2005
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Ingår i: Game Programming Gems 5. - : Charles River Media, Hingham, Massachusetts. - 1584503521 ; , s. 225-231
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Bokkapitel (refereegranskat)abstract
- This gem shows how a curve with minimal acceleration can be obtained using Hermite splines [Hearn04]. Acceleration is higher in the bends and therefore this type of curve is a minimal bending curve. This type of curve can be useful for subdivision surfaces when it is required that the surface has this property, which assures that the surface is as smooth as possible. A similar approach for Bézier curves and subdivision can be found in [Overveld97]. It could also be very useful for camera movements [Vlachos01] since it allows that both the position and the direction of the camera can be set for the curve. Moreover, we show how several such curves can be connected in order to achieve continuity between the curve segments.
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| 16. |
- Barrera, Tony, et al.
(författare)
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Trigonometric splines
- 2008. - 1
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Ingår i: Game programming Gems 7. - Boston : Charles River Media. - 9781584505273 - 1584505273 ; , s. 191-198
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Bokkapitel (populärvet., debatt m.m.)
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| 17. |
- Barrera, Tony, et al.
(författare)
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Vectorized table driven algorithms for double precision elementary functions using Taylor expansions
- 2009
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Ingår i: APLIMAT 8th international conference. ; 2, s. 171-178
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Konferensbidrag (refereegranskat)abstract
- This paper presents fast implementations of the inverse square root and arcsine, both in double precision. In single precision it is often possible to use a small table and one ordinary Newton-Raphson iteration to compute elementary functions such as the square root. In double precision a substantially larger table is necessary to obtain the desired precision, or, if a smaller table is used, the additional Newton-Raphson iterations required to obtain the precision often requires the evaluation of other expensive elementary functions. Furthermore, large tables use a lot of the cash memory that should have been used for the application code.Obtaining the desired precision using a small table can instead be realised by using a higher order method than the second order Newton-Raphson method. A generalization of Newton's method to higher order is Householder's method, which unfortunately often results in very complicated expressions requiring many multiplications, additions, and even divisions.We show how a high-order method can be used, which only requires a few extra additions and multiplications for each degree of higher order. The method starts from the Taylor expansion of the difference of the value of the elementary function and a starting guess value for each iteration. If the Taylor series is truncated after the second term, ordinary Newton iterations are obtained. In several cases it is possible to algebraically simplify the difference between the true value and the starting guess value. In those cases we show that it is advantageous to use the Taylor series to higher order to obtain the fast convergent method. Moreover, we will show how the coefficients of a Chebyshev polynomial can be fitted to give as little error as possible for the functions close to zero and in the same time reduce the terms in the Taylor expansion.In the paper we benchmark two example implementations of the method on the x86_64 architecture. The first is the inverse square root, where the actual table (to 12 bit precision) is provided by the processor hardware. The inverse square root is important in many application programs, including computer graphics, and explicit particle simulation codes, for instance the Monte Carlo and Molecular Dynamics methods of statistical mechanics. The other example is the arcsine function, which has a slow converging Taylor expansion and where no tables are provided by the hardware. The vectorized versions of the implementations of the inverse square root are 3.5 times faster than compiled code on the Athlon64 and about 5 times faster on the Core 2. The scalar version of the arcsine function is, depending on order and table size, between 2 and 3 times faster than the compiled code, and the vectorized version is between 3 and 4 times faster on the Athlon64, while it is between 4 and 5 times faster than the compiled version on the Core 2.
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| 19. |
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| 20. |
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| 21. |
- Bengtsson, Ewert
(författare)
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Analysis of 3D images of molecules, cells, tissues and organs
- 2007
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Ingår i: Medicinteknikdagarna 2007. ; , s. 1-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Our world is three dimensional. With our eyes we mainly see the surfaces of 3D objects and in conventional imaging we see projections of parts of the 3D world down to 2D. But over the last decades new imaging techniques such as tomography and confocal microscopy have evolved that make true 3D volume images available,. These images can reveal information about the inner properties and conditions of objects, e.g. our bodies, that can be of immense value to science and medicine. But to really explore the information in these images we need computer support.At the Centre for Image Analysis in Uppsala we are developing methods for the analysis and visualisation of volume images. A nice aspect of image processing methods is that they in most cases are independent of the scale in the images. In this presentation we will give examples of how images of widely different scales can be analysed and visualised.- At the highest resolution we have images of protein molecules created by cryo-electron tomography with voxels of a few nanometers.- Using confocal microscopy we can also image single molecules, but then only seeing them as bright spots that need to be localized at micrometer scales in the cells.- The cells build up tissue and using conventional pathology stains or micro CT we can image the tissue in 2D and 3D. We are using such images to develop methods for studying tissue integration of implants.- Finally conventional X-ray tomography and magnetic resonance tomography provide images on the organ level with voxels in the millimetre range. We are developing methods for liver segmentation in CT data and visualising the contrast uptake over time in MR angiography images of breasts.
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| 22. |
- Bengtsson, Ewert, et al.
(författare)
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Annual Report 2007
- 2008
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Rapport (populärvet., debatt m.m.)
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