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Methods and models for 2D and 3D image analysis in microscopy, in particular for the study of muscle cells
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)Alternative title
Metoder och modeller för två- och tredimensionell bildanalys inom mikroskopi, speciellt med inrikting mot muskelceller (Swedish)
Abstract [en]

Many research questions in biological research lead to numerous microscope images that need to be evaluated. Here digital image cytometry, i.e., quantitative, automated or semi-automated analysis of the images is an important rapidly growing discipline. This thesis presents contributions to that field. The work has been carried out in close cooperation with biomedical research partners, successfully solving real world problems.

The world is 3D and modern imaging methods such as confocal microscopy provide 3D images. Hence, a large part of the work has dealt with the development of new and improved methods for quantitative analysis of 3D images, in particular fluorescently labeled skeletal muscle cells.

A geometrical model for robust segmentation of skeletal muscle fibers was developed. Images of the multinucleated muscle cells were pre-processed using a novel spatially modulated transform, producing images with reduced complexity and facilitating easy nuclei segmentation. Fibers from several mammalian species were modeled and features were computed based on cell nuclei positions. Features such as myonuclear domain size and nearest neighbor distance, were shown to correlate with body mass, and femur length. Human muscle fibers from young and old males, and females, were related to fiber type and extracted features, where myonuclear domain size variations were shown to increase with age irrespectively of fiber type and gender.

A segmentation method for severely clustered point-like signals was developed and applied to images of fluorescent probes, quantifying the amount and location of mitochondrial DNA within cells. A synthetic cell model was developed, to provide a controllable golden standard for performance evaluation of both expert manual and fully automated segmentations. The proposed method matches the correctness achieved by manual quantification.

An interactive segmentation procedure was successfully applied to treated testicle sections of boar, showing how a common industrial plastic softener significantly affects testosterone concentrations.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2008. , 76 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 544
Keyword [en]
medical image analysis, image segmentation, fluorescence microscopy, cytometry, human skeletal muscle
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-9201ISBN: 978-91-554-7255-9 (print)OAI: oai:DiVA.org:uu-9201DiVA: diva2:172381
Public defence
2008-09-19, Polhemsalen, Ångströmlaboratoriet, Polacksbacken, Uppsala, 13:15
Opponent
Supervisors
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2013-07-03Bibliographically approved
List of papers
1. Delayed effects on plasma concentration of testosterone and testicular morphology by intramuscular low-dose di(2-ethylhexyl)phthalate or oestradiol benzoate in the prepubertal boar
Open this publication in new window or tab >>Delayed effects on plasma concentration of testosterone and testicular morphology by intramuscular low-dose di(2-ethylhexyl)phthalate or oestradiol benzoate in the prepubertal boar
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2005 (English)In: Theriogenology, ISSN 0093-691X, E-ISSN 1879-3231, Vol. 64, no 5, 1170-1184 p.Article in journal (Refereed) Published
Abstract [en]

The immediate and delayed effects of prepubertal exposure to di(2-ethylhexyl)phthalate (DEHP) or oestradiol benzoate on the plasma concentrations of testosterone, oestradiol and LH, as well as testicular morphology were examined in prepubertal boars. In a split litter design experiment, prepubertal boars were intramuscularly exposed to DEHP, oestradiol or vehicle during five weeks, starting at six weeks of age. The dose of DEHP was 50 mg/kg of bodyweight twice weekly, which is in the same range as recently used oral doses in rodents. Oestradiol-benzoate was administered at 0.25 mg/kg of bodyweight twice weekly. One set of animals was examined immediately after the exposure, and the other set was examined at an age of 7.5 months. During the exposure period concentrations of LH in plasma were lower (p = 0.02) in the oestradiol-treated animals than in the control group. In the group exposed to oestradiol, the relative to the body weight of the testicles tended to be lower (p = 0.07) than control immediately after five weeks of exposure, and the relative to the body weight of the seminal vesicles tended to be lower (p = 0.05) than control at 7.5 months of age. In the DEHP-exposed group an elevated (p = 0.005) concentration of testosterone and increased (p = 0.04) area of the Leydig cells in the testicles compared to the control group were seen at 7.5 months of age. These data suggest that DEHP early in life causes delayed effects on the reproductive system in the adult.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-97425 (URN)10.1016/j.theriogenology.2005.02.003 (DOI)
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2013-11-04Bibliographically approved
2. Segmentation and separation of point like fluorescent markers in digital images
Open this publication in new window or tab >>Segmentation and separation of point like fluorescent markers in digital images
2004 In: Proceedings of IEEE International Symposium on Biomedical Imaging, 2004, 2004- p.Chapter in book (Other academic) Published
Identifiers
urn:nbn:se:uu:diva-97426 (URN)0-7803-8388-5 (ISBN)
Available from: 2008-08-29 Created: 2008-08-29Bibliographically approved
3. Finding cells, finding molecules, finding patterns
Open this publication in new window or tab >>Finding cells, finding molecules, finding patterns
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2008 (English)In: International Journal of Signal and Imaging Systems Engineering, ISSN 1748-0698, Vol. 1, no 1, 11-17 p.Article in journal (Refereed) Published
Abstract [en]

Many modern molecular labelling techniques result in bright point signals. Signals from molecules that are detected directly inside a cell can be captured by fluorescence microscopy. Signals representing different types of molecules may be randomly distributed in the cells or show systematic patterns, indicating that the corresponding molecules have specific, non-random localisations and functions in the cell. Assessing this information requires high speed robust image segmentation followed by signal detection, and finally, pattern analysis. We present and discuss these types of methods and show an example of how the distribution of different variants of mitochondrial DNA can be analysed.

Keyword
mass data analysis, image analysis, cytometry, single molecule detection, padlock probes, pattern analysis
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-97427 (URN)10.1504/IJSISE.2008.017768 (DOI)
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2017-02-08Bibliographically approved
4. Non-uniform 3D distance transform for anisotropic signal correction in confocal image volumes of skeletal muscle cell nuclei
Open this publication in new window or tab >>Non-uniform 3D distance transform for anisotropic signal correction in confocal image volumes of skeletal muscle cell nuclei
2008 (English)In: Proc. 5th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE , 2008, 1363-1366 p.Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Piscataway, NJ: IEEE, 2008
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-97428 (URN)10.1109/ISBI.2008.4541258 (DOI)978-1-4244-2002-5 (ISBN)
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2010-03-22Bibliographically approved
5. Effects of ageing and gender on the spatial organization of nuclei in single human skeletal muscle cells
Open this publication in new window or tab >>Effects of ageing and gender on the spatial organization of nuclei in single human skeletal muscle cells
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2009 (English)In: Neuromuscular Disorders, ISSN 0960-8966, Vol. 19, 605-606 p.Article in journal (Refereed) Published
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-97429 (URN)10.1016/j.nmd.2009.06.196 (DOI)
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2017-02-08Bibliographically approved
6. Myonuclear domain size and myosin isoform expression in muscle fibres from mammals representing a 100 000-fold difference in body size
Open this publication in new window or tab >>Myonuclear domain size and myosin isoform expression in muscle fibres from mammals representing a 100 000-fold difference in body size
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2009 (English)In: Experimental Physiology, ISSN 0958-0670, E-ISSN 1469-445X, Vol. 94, no 1, 117-129 p.Article in journal (Refereed) Published
Abstract [en]

This comparative study of myonuclear domain (MND) size in mammalian species representing a 100 000-fold difference in body mass, ranging from 25 g to 2500 kg, was undertaken to improve our understanding of myonuclear organization in skeletal muscle fibres. Myonuclear domain size was calculated from three-dimensional reconstructions in a total of 235 single muscle fibre segments at a fixed sarcomere length. Irrespective of species, the largest MND size was observed in muscle fibres expressing fast myosin heavy chain (MyHC) isoforms, but in the two smallest mammalian species studied (mouse and rat), MND size was not larger in the fast-twitch fibres expressing the IIA MyHC isofom than in the slow-twitch type I fibres. In the larger mammals, the type I fibres always had the smallest average MND size, but contrary to mouse and rat muscles, type IIA fibres had lower mitochondrial enzyme activities than type I fibres. Myonuclear domain size was highly dependent on body mass in the two muscle fibre types expressed in all species, i.e. types I and IIA. Myonuclear domain size increased in muscle fibres expressing both the β/slow (type I; r= 0.84, P < 0.001) and the fast IIA MyHC isoform (r= 0.90; P < 0.001). Thus, MND size scales with body size and is highly dependent on muscle fibre type, independent of species. However, myosin isoform expression is not the sole protein determining MND size, and other protein systems, such as mitochondrial proteins, may be equally or more important determinants of MND size.

National Category
Physiology
Identifiers
urn:nbn:se:uu:diva-87940 (URN)10.1113/expphysiol.2008.043877 (DOI)000261961800014 ()18820003 (PubMedID)
Available from: 2009-01-15 Created: 2009-01-15 Last updated: 2013-07-03Bibliographically approved
7. Introduction to the Mean-Shift Procedure: Filtering and Segmentation
Open this publication in new window or tab >>Introduction to the Mean-Shift Procedure: Filtering and Segmentation
2008 (English)Report (Other academic)
Place, publisher, year, edition, pages
Centre for Image Analysis, Uppsala University, 2008
Series
Internal Report, 47
Identifiers
urn:nbn:se:uu:diva-97431 (URN)
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2010-03-29Bibliographically approved

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