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Image Filtering Methods for Biomedical Applications
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Filtering is a key step in digital image processing and analysis. It is mainly used for amplification or attenuation of some frequencies depending on the nature of the application. Filtering can either be performed in the spatial domain or in a transformed domain. The selection of the filtering method, filtering domain, and the filter parameters are often driven by the properties of the underlying image. This thesis presents three different kinds of biomedical image filtering applications, where the filter parameters are automatically determined from the underlying images.

Filtering can be used for image enhancement. We present a robust image dependent filtering method for intensity inhomogeneity correction of biomedical images. In the presented filtering method, the filter parameters are automatically determined from the grey-weighted distance transform of the magnitude spectrum. An evaluation shows that the filter provides an accurate estimate of intensity inhomogeneity.

Filtering can also be used for analysis. The thesis presents a filtering method for heart localization and robust signal detection from video recordings of rat embryos. It presents a strategy to decouple motion artifacts produced by the non-rigid embryonic boundary from the heart. The method also filters out noise and the trend term with the help of empirical mode decomposition. Again, all the filter parameters are determined automatically based on the underlying signal.

Transforming the geometry of one image to fit that of another one, so called image registration, can be seen as a filtering operation of the image geometry. To assess the progression of eye disorder, registration between temporal images is often required to determine the movement and development of the blood vessels in the eye. We present a robust method for retinal image registration. The method is based on particle swarm optimization, where the swarm searches for optimal registration parameters based on the direction of its cognitive and social components. An evaluation of the proposed method shows that the method is less susceptible to becoming trapped in local minima than previous methods.

With these thesis contributions, we have augmented the filter toolbox for image analysis with methods that adjust to the data at hand.

 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2011. , 61 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 852
Keyword [en]
Digital image analysis, Image filtering, Intensity inhomogeneity correction, Empirical mode decomposition, Particle Swarm optimization, Image registration
National Category
Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
URN: urn:nbn:se:uu:diva-158679ISBN: 978-91-554-8155-1 (print)OAI: oai:DiVA.org:uu-158679DiVA: diva2:440756
Public defence
2011-10-25, Room 10134, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2011-10-03 Created: 2011-09-13 Last updated: 2014-07-21
List of papers
1. An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
Open this publication in new window or tab >>An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
(English)Manuscript (preprint) (Other academic)
National Category
Signal Processing Medical Image Processing
Research subject
Computerized Image Processing; Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-158673 (URN)
Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2011-10-04
2. Bias field correction using grey-weighted distance transform applied on MR volumes
Open this publication in new window or tab >>Bias field correction using grey-weighted distance transform applied on MR volumes
2011 (English)In: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, 357-360 p.Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Piscataway, NJ: IEEE conference proceedings, 2011
National Category
Medical Image Processing
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-144827 (URN)10.1109/ISBI.2011.5872423 (DOI)000298849400082 ()978-1-4244-4127-3 (ISBN)
Conference
8th IEEE International Symposium on Biomedical Imaging (ISBI)
Available from: 2011-06-09 Created: 2011-02-02 Last updated: 2012-06-09Bibliographically approved
3. Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
Open this publication in new window or tab >>Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
Show others...
2011 (English)In: Computer analysis of images and patterns: 14th International Conference, CAIP 2011, pt 2, Springer-Verlag , 2011, 523-530 p.Conference paper, Published paper (Refereed)
Abstract [en]

To develop an accurate and suitable method for measuring the embryonic heart rate in vitro, a system combining Laplacian eigenmaps and empirical mode decomposition has been proposed. The proposed method assess the heart activity in two steps; signal generation and heart signal analysis. Signal generation is achieved by Laplacian eigenmaps (LEM) in conjunction with correlation co-efficient, while the signal analysis of the heart motion has been performed by the modified empirical mode decomposition (EMD). LEM helps to find the template for the atrium and the ventricle respectively, whereas EMD helps to find the non-linear trend term without defining any regression model. The proposed method also removes the motion artifacts produced due to the the non-rigid deformation in the shape of the embryo, the noise induced during the data acquisition, and the higher order harmonics. To check the authenticity of the proposed method, 151 videos have been investigated. Experimental results demonstrate the superiority of the proposed method in comparison to three recent methods.

Place, publisher, year, edition, pages
Springer-Verlag, 2011
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 6855
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:uu:diva-155123 (URN)000300567300062 ()978-3-642-23677-8 (ISBN)
Conference
14th International Conference on Computer Analysis of Images and Patterns (CAIP) AUG 29-31, 2011 Seville, SPAIN
Available from: 2011-06-16 Created: 2011-06-16 Last updated: 2012-04-04Bibliographically approved
4. Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
Open this publication in new window or tab >>Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
2009 (English)In: Transactions on Mass-Data Analysis of Images and Signals, ISSN 1868-6451, Vol. 1, no 2, 132-146 p.Article in journal (Refereed) Published
Abstract [en]

Embryo cultures of rodents is an established technique for monitoring adverse effects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of rat embryos. First it detects the heart location by using decimation free directional filter bank along with first absolute moment, and then it counts the number of heart beats for a predetermined period of time. Using this automated method many more embryos can be evaluated at reasonable cost.

Place, publisher, year, edition, pages
Leipzig, Germany: IBAI Publishing, 2009
Keyword
heart detection, absolute central moments, embryo culture, directional analysis, edge delineation
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Signal Processing
Identifiers
urn:nbn:se:uu:diva-111495 (URN)
Available from: 2009-12-15 Created: 2009-12-15 Last updated: 2012-09-21Bibliographically approved
5. Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
Open this publication in new window or tab >>Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
Show others...
2010 (English)In: Reproductive Toxicology, ISSN 0890-6238, E-ISSN 1873-1708, Vol. 29, no 2, 156-163 p.Article in journal (Refereed) Published
Abstract [en]

Drugs blocking the potassium current IKr of the heart (via hERG channel-inhibition) have the potential to cause hypoxia-related teratogenic effects. However, this activity may be missed in conventional teratology studies because repeat dosing may cause resorptions. The aim of the present study was to investigate an alternative protocol to reveal the teratogenic potential of IKr-blocking drugs. The IKr blocker astemizole, given as a single dose (80mg/kg) on gestation day (GD) 13 to pregnant rats caused digital defects. In whole rat embryo culture (2h) on GD 13, astemizole caused a decrease in embryonic heart rate at 20nM, and arrhythmias at 200-400nM. Cetirizine, without IKr-blocking properties, did not affect the rat embryonic heart in vitro. The present study shows that single dose testing on sensitive days of development, together with whole embryo culture, can be a useful methodology to better characterize the teratogenic potential of IKr-blocking drugs.

Place, publisher, year, edition, pages
Elsevier, 2010
Keyword
Astemizole, hERG channel, IKr, Teratogenicity, Hypoxia, Embryonic cardiac adverse effects, Embryotoxicity, Toxicology
National Category
Pharmaceutical Sciences Computer Vision and Robotics (Autonomous Systems)
Research subject
Toxicology; Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-118335 (URN)10.1016/j.reprotox.2010.01.014 (DOI)000276326900004 ()20144703 (PubMedID)
Available from: 2010-02-23 Created: 2010-02-23 Last updated: 2017-12-12Bibliographically approved
6. A Modified Particle Swarm Optimization Applied in Image Registration
Open this publication in new window or tab >>A Modified Particle Swarm Optimization Applied in Image Registration
2010 (English)In: Proceedings of 20th International Conference on Pattern Recognition, IEEE computer society , 2010, 2302-2305 p.Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
IEEE computer society, 2010
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-141213 (URN)
Conference
20th International Conference on Pattern Recognition (ICPR 2010)
Available from: 2011-01-11 Created: 2011-01-11 Last updated: 2011-10-04Bibliographically approved

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