Effective quantification of gene expression levels in microarray images using a spot-adaptive compound clustering - enhancement - segmentation scheme

 
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2007 (EN)
Effective quantification of gene expression levels in microarray images using a spot-adaptive compound clustering - enhancement - segmentation scheme (EN)

Δασκαλάκης, Αντώνης (EL)
Μπουγιούκος, Παναγιώτης (EL)
Κάβουρας, Διονύσης Α. (EL)
Κωστόπουλος, Σπυρίδων (EL)
Γεωργιάδης, Παντελής (EL)

Νικηφορίδης, Γεώργιος Σ. (EL)
Τ.Ε.Ι. Αθήνας. Σχολή Τεχνολογικών Εφαρμογών. Τμήμα Μηχανικών Βιοϊατρικής Τεχνολογίας Τ.Ε. (EL)
Καλατζής, Ιωάννης (EL)
Καγκάδης, Γεώργιος Χ. (EL)

A spot-adaptive compound clustering-enhancement-segmentation (CES) scheme was developed for the quantification of gene expression levels in microarray images. The CES-scheme employed 1/griding, for locating spot-regions, 2/Fuzzy C-means clustering, for segmenting spots from background, 3/ background noise estimation and spot’s center localization, 4/emphasizing of spot’s outline by the CLAHE image enhancement technique, 5/segmentation by the SRG algorithm, using information from step 3, and 6/microarray spot intensity extraction. Extracted intensities by the CES-Scheme were compared against those obtained by the MAGIC TOOL’s SRG. Kullback-Liebler metric’s values for the CES-Scheme were on average double than MAGIC TOOL’s, with differences ranging from 1.45bits to 2.77bits in 7 cDNA images. Coefficient-of-Variation results showed significantly higher reproducibility (p<0.001) for the CES-Scheme in quantifying gene expression levels. Processing times for 1024x1024 16-bit microarray images containing 6400 spots were 300 and 487 seconds for the CES-Scheme and MAGIC TOOL respectively. (EN)

full paper
conferenceItem

Microarray griding (EN)
Microarray image analysis (EN)
Ανάλυση εικόνων μικροσυστοιχιών (EN)
Τριβή μικροσυστοιχιών (EN)

ΤΕΙ Αθήνας (EL)
Technological Educational Institute of Athens (EN)

International Conference of Computational Science and Its Applications (EN)

English

2007

DOI 10.1007/978-3-540-74484-9_48

Springer Berlin Heidelberg (EN)



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