Please use this identifier to cite or link to this item: http://hdl.handle.net/11400/10371
Title: Genes expression level quantification using a spot-based algorithmic pipeline
Authors: Δασκαλάκης, Αντώνης
Κάβουρας, Διονύσης Α.
Μπουγιούκος, Παναγιώτης
Κωστόπουλος, Σπυρίδων
Γεωργιάδης, Παντελής
Contributors: Καλατζής, Ιωάννης
Καγκάδης, Γεώργιος Χ.
Νικηφορίδης, Γεώργιος Σ.
Item type: Conference publication
Conference Item Type: Full Paper
Keywords: Gene;Microarray images;Γονίδιο;Εικόνες μικροσυστοιχιών
Subjects: Medicine
Biomedical engineering
Ιατρική
Βιοϊατρική τεχνολογία
Issue Date: 14-May-2015
2007
Publisher: IEEE
Abstract: An efficient spot-based (SB) algorithmic pipeline of clustering, enhancement, and segmentation techniques was developed to quantify gene expression levels in microarray images. The SB-pipeline employed i/a griding procedure to locate spot-regions, ii/a clustering algorithm (enhanced fuzzy c- means or EnFCM) to roughly segment spots from background and estimate background noise and spot's center, iii/an adaptive histogram modification technique to accentuate spot's boundaries, and iv/a segmentation algorithm (Seeded Region Growing or SRG), to extract microarray spots' intensities. Extracted intensities were comparatively evaluated in term of Mean Absolute Error (MAE) against the MAGIC TOOL's SRG employing a dataset of 7 replicated microarray images (6400 spots each). MAE box-plots mean values were 0.254 and 0.630 for the SB-pipeline and the MAGIC TOOL respectively. Total processing times for the dataset evaluated (7 images) were 2100 seconds and 3410 seconds for the SB-pipeline and MAGIC TOOL respectively.
Description: Proceedings
Language: English
Citation: Daskalakis, A., Cavouras, D., Bougioukos, P., Kostopoulos, S., Georgiadis, P., et al. (2007). Genes expression level quantification using a spot-based algorithmic pipeline. Proceedings of the 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. pp. 1148–1151. France, Lyon, 23th-26th August, 2007. IEEE: 2007.
Conference: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Access scheme: Embargo
License: Αναφορά Δημιουργού-Μη Εμπορική Χρήση-Όχι Παράγωγα Έργα 3.0 Ηνωμένες Πολιτείες
URI: http://hdl.handle.net/11400/10371
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