Methods for automatic microarray image segmentation

IEEE Transactions on Nanobioscience
Mathias KatzerGerhard Sagerer

Abstract

This paper describes image processing methods for automatic spotted microarray image analysis. Automatic gridding is important to achieve constant data quality and is, therefore, especially interesting for large-scale experiments as well as for integration of microarray expression data from different sources. We propose a Markov random field (MRF) based approach to high-level grid segmentation, which is robust to common problems encountered with array images and does not require calibration. We also propose an active contour method for single-spot segmentation. Active contour models describe objects in images by properties of their boundaries. Both MRFs and active contour models have been used in various other computer vision applications. The traditional active contour model must be generalized for successful application to microarray spot segmentation. Our active contour model is employed for spot detection in the MRF score functions as well as for spot signal segmentation in quantitative array image analysis. An evaluation using several image series from different sources shows the robustness of our methods.

References

Dec 11, 1999·Nucleic Acids Research·X GaiV Walbot
Jan 11, 2000·Nucleic Acids Research·G SherlockJ M Cherry
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·P A PevznerC L Tang
Jul 13, 2001·Bioinformatics·M SteinfathJ O'Brien
Feb 6, 2002·Genome Research·Ajay N JainDaniel Pinkel
Mar 26, 2003·Bioinformatics·Jesús Angulo, Jean Serra
Oct 1, 1997·Journal of Biomedical Optics·Y ChenM L Bittner

❮ Previous
Next ❯

Citations

Dec 4, 2003·Journal of Biotechnology·Michael DondrupFolker Meyer
Apr 21, 2005·Bioinformatics·Omer DemirkayaMohamed M Shoukri
Jan 27, 2010·BMC Bioinformatics·Dimitris BariamisDimitris Maroulis
Mar 20, 2012·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Bogdan BeleanRomulus Terebes
Dec 25, 2015·BMC Bioinformatics·Bogdan BeleanOvidiu Balacescu
Aug 21, 2007·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Rastislav Lukac, Konstantinos N Plataniotis
Sep 29, 2005·Molecular Nutrition & Food Research·Bettina Spielbauer, Frank Stahl
Dec 2, 2014·IEEE Transactions on Nanobioscience·Stamos KatsigiannisDimitris Maroulis
Jun 17, 2008·IEEE Transactions on Nanobioscience·P SarderS L Stanley
Jun 11, 2008·IEEE Transactions on Medical Imaging·Jinn Ho, Wen-Liang Hwang
Jun 4, 2010·IEEE Transactions on Nanobioscience·Eleni Zacharia, Dimitris Maroulis
Jan 6, 2005·IEEE Transactions on Nanobioscience·Rastislav LukacAnastasios N Venetsanopoulos
Jul 11, 2006·Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP·Zhenlin JuRonald B Walter
Dec 27, 2005·Drug Discovery Today·Yu Luo, Stefano Lonardi
May 15, 2013·Computer Methods and Programs in Biomedicine·Zidong WangXiaohui Liu
Nov 22, 2005·Journal of Biomedical Informatics·Ghislain BidautMichael F Ochs
Oct 30, 2014·Medical & Biological Engineering & Computing·Bogdan BeleanAdrian Bot
May 27, 2015·IEEE Journal of Biomedical and Health Informatics·Abhik DattaKin-Choong Yow
Mar 11, 2006·Journal of Biomedical Optics·Munho RyuYong-Yook Kim
Mar 10, 2016·IEEE Journal of Biomedical and Health Informatics·Stamos KatsigiannisDimitris Maroulis
Mar 1, 2008·Journal of Signal Processing Systems·Yu-Ping WangWei-Wen Cai

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Peter Bajcsy
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Luis Rueda, Vidya Vidyadharan
IEEE Transactions on Medical Imaging
Eleni Zacharia, Dimitris Maroulis
© 2021 Meta ULC. All rights reserved