Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi

Kaan A. Kabakçi; Abdulkerim Çapar; B. Uǧur Töreyin; Mertkan Akkoç; Ozan Borazan; Ilknur Türkmen; Lütfiye Durak Ata

doi:10.1109/SIU.2016.7495873

Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi

Translated title of the contribution: A multi-level thresholding based segmentation method for microscopic fluorescence in situ hybridization (FISH) images

Kaan A. Kabakçi, Abdulkerim Çapar, B. Uǧur Töreyin, Mertkan Akkoç, Ozan Borazan, Ilknur Türkmen, Lütfiye Durak Ata

Informatics Institute

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

3 Citations (Scopus)

Abstract

Fluorescence in situ hybridization (FISH) technique widely used in cancer diagnosis is based on displaying chromosomal regions as FISH signals by staining with specific dyes. In this study, a new multi-level thresholding based FISH signal segmentation method is proposed for images produced by FISH technique. Cell nuclei are segmented on images, that are grabbed from fluorescence microcopes at high resolution, with adaptive thresholding, distance transform and watershed methods. FISH signals falling in cell boundaries are detected by applying multi-level thresholding and morphological post processes thanks to proposed segmentation method. It is observed that the detection rate of the proposed method on 49 FISH images taken from real patients, are higher than other widely used techniques in the literature.

Translated title of the contribution	A multi-level thresholding based segmentation method for microscopic fluorescence in situ hybridization (FISH) images
Original language	Turkish
Title of host publication	2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	849-852
Number of pages	4
ISBN (Electronic)	9781509016792
DOIs	https://doi.org/10.1109/SIU.2016.7495873
Publication status	Published - 20 Jun 2016
Event	24th Signal Processing and Communication Application Conference, SIU 2016 - Zonguldak, Turkey Duration: 16 May 2016 → 19 May 2016

Publication series

Name	2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings

Conference

Conference	24th Signal Processing and Communication Application Conference, SIU 2016
Country/Territory	Turkey
City	Zonguldak
Period	16/05/16 → 19/05/16

Bibliographical note

Publisher Copyright:
© 2016 IEEE.

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10.1109/SIU.2016.7495873

Cite this

Kabakçi, K. A., Çapar, A., Töreyin, B. U., Akkoç, M., Borazan, O., Türkmen, I., & Ata, L. D. (2016). Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi. In 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings (pp. 849-852). Article 7495873 (2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SIU.2016.7495873

Kabakçi, Kaan A. ; Çapar, Abdulkerim ; Töreyin, B. Uǧur et al. / Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi. 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2016. pp. 849-852 (2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings).

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title = "Mikroskobik Floresan In Situ Hibridizasyon (FISH) G{\"o}r{\"u}nt{\"u}lerde {\c C}oklu Seviye E{\c s}ikleme Tabanli B{\"o}l{\"u}tleme Y{\"o}ntemi",

abstract = "Fluorescence in situ hybridization (FISH) technique widely used in cancer diagnosis is based on displaying chromosomal regions as FISH signals by staining with specific dyes. In this study, a new multi-level thresholding based FISH signal segmentation method is proposed for images produced by FISH technique. Cell nuclei are segmented on images, that are grabbed from fluorescence microcopes at high resolution, with adaptive thresholding, distance transform and watershed methods. FISH signals falling in cell boundaries are detected by applying multi-level thresholding and morphological post processes thanks to proposed segmentation method. It is observed that the detection rate of the proposed method on 49 FISH images taken from real patients, are higher than other widely used techniques in the literature.",

keywords = "FISH signal detection, cell segmentation, fluorescence in situ hybridization (FISH), microscopic image analysis",

author = "Kabak{\c c}i, {Kaan A.} and Abdulkerim {\c C}apar and T{\"o}reyin, {B. Uǧur} and Mertkan Akko{\c c} and Ozan Borazan and Ilknur T{\"u}rkmen and Ata, {L{\"u}tfiye Durak}",

note = "Publisher Copyright: {\textcopyright} 2016 IEEE.; 24th Signal Processing and Communication Application Conference, SIU 2016 ; Conference date: 16-05-2016 Through 19-05-2016",

year = "2016",

month = jun,

day = "20",

doi = "10.1109/SIU.2016.7495873",

language = "T{\"u}rk{\c c}e",

series = "2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings",

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booktitle = "2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings",

address = "United States",

}

Kabakçi, KA, Çapar, A, Töreyin, BU, Akkoç, M, Borazan, O, Türkmen, I & Ata, LD 2016, Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi. in 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings., 7495873, 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings, Institute of Electrical and Electronics Engineers Inc., pp. 849-852, 24th Signal Processing and Communication Application Conference, SIU 2016, Zonguldak, Turkey, 16/05/16. https://doi.org/10.1109/SIU.2016.7495873

Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi. / Kabakçi, Kaan A.; Çapar, Abdulkerim; Töreyin, B. Uǧur et al.
2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2016. p. 849-852 7495873 (2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi

AU - Kabakçi, Kaan A.

AU - Çapar, Abdulkerim

AU - Töreyin, B. Uǧur

AU - Akkoç, Mertkan

AU - Borazan, Ozan

AU - Türkmen, Ilknur

AU - Ata, Lütfiye Durak

PY - 2016/6/20

Y1 - 2016/6/20

N2 - Fluorescence in situ hybridization (FISH) technique widely used in cancer diagnosis is based on displaying chromosomal regions as FISH signals by staining with specific dyes. In this study, a new multi-level thresholding based FISH signal segmentation method is proposed for images produced by FISH technique. Cell nuclei are segmented on images, that are grabbed from fluorescence microcopes at high resolution, with adaptive thresholding, distance transform and watershed methods. FISH signals falling in cell boundaries are detected by applying multi-level thresholding and morphological post processes thanks to proposed segmentation method. It is observed that the detection rate of the proposed method on 49 FISH images taken from real patients, are higher than other widely used techniques in the literature.

AB - Fluorescence in situ hybridization (FISH) technique widely used in cancer diagnosis is based on displaying chromosomal regions as FISH signals by staining with specific dyes. In this study, a new multi-level thresholding based FISH signal segmentation method is proposed for images produced by FISH technique. Cell nuclei are segmented on images, that are grabbed from fluorescence microcopes at high resolution, with adaptive thresholding, distance transform and watershed methods. FISH signals falling in cell boundaries are detected by applying multi-level thresholding and morphological post processes thanks to proposed segmentation method. It is observed that the detection rate of the proposed method on 49 FISH images taken from real patients, are higher than other widely used techniques in the literature.

KW - FISH signal detection

KW - cell segmentation

KW - fluorescence in situ hybridization (FISH)

KW - microscopic image analysis

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U2 - 10.1109/SIU.2016.7495873

DO - 10.1109/SIU.2016.7495873

M3 - Konferans katkısı

AN - SCOPUS:84982797323

T3 - 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings

SP - 849

EP - 852

BT - 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 24th Signal Processing and Communication Application Conference, SIU 2016

Y2 - 16 May 2016 through 19 May 2016

ER -

Kabakçi KA, Çapar A, Töreyin BU, Akkoç M, Borazan O, Türkmen I et al. Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi. In 2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings. Institute of Electrical and Electronics Engineers Inc. 2016. p. 849-852. 7495873. (2016 24th Signal Processing and Communication Application Conference, SIU 2016 - Proceedings). doi: 10.1109/SIU.2016.7495873

Mikroskobik Floresan In Situ Hibridizasyon (FISH) Görüntülerde Çoklu Seviye Eşikleme Tabanli Bölütleme Yöntemi

Abstract

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