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Histological Stain Evaluation for Machine Learning Applications
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
2012 (English)In: Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention, 2012Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
2012.
National Category
Medical Image Processing
Identifiers
URN: urn:nbn:se:uu:diva-183619OAI: oai:DiVA.org:uu-183619DiVA: diva2:563622
Conference
MICCAI 2012, the 15th International Conference on Medical Image Computing and Computer Assisted Intervention, October 1-5, 2012, Nice, France
Available from: 2012-10-30 Created: 2012-10-30 Last updated: 2015-01-23
In thesis
1. Automated Tissue Image Analysis Using Pattern Recognition
Open this publication in new window or tab >>Automated Tissue Image Analysis Using Pattern Recognition
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 106 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1175
Keyword
tissue image analysis, pattern recognition, digital histopathology, immunohistochemistry, paired antibodies, histological stain evaluation
National Category
Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-231039 (URN)978-91-554-9028-7 (ISBN)
Public defence
2014-10-20, Häggsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2014-09-29 Created: 2014-09-02 Last updated: 2016-04-18Bibliographically approved

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Azar, JimmyBusch, ChristerCarlbom, Ingrid

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