Automated segmentation of cells in phase contrast optical microscopy time series images

Rifki Can Binici; Umut Sahin; Aydin Ayanzadeh; Behcet Ugur Toreyin; Sevgi Onal; Devrim Pesen Okvur; Ozden Yalcin Ozuysal; Devrim Unay

doi:10.1109/TIPTEKNO.2019.8895080

Automated segmentation of cells in phase contrast optical microscopy time series images

Rifki Can Binici, Umut Sahin, Aydin Ayanzadeh, Behcet Ugur Toreyin, Sevgi Onal, Devrim Pesen Okvur, Ozden Yalcin Ozuysal, Devrim Unay

Informatics Institute

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

6 Citations (Scopus)

Abstract

Phase contrast optical microscopy is a preferred imaging technique for live-cell, temporal analysis. Segmentation of cells from time series data acquired with this technique is a labor-intensive and time-consuming task that cell biology researchers need solution for. In this study traditional image processing and deep learning based approaches for automated cell segmentation from phase contrast optical microscopy time series are presented, and their performances are evaluated against manually annotated datasets.

Translated title of the contribution	Faz kontrast optik mikroskopi zaman serisi görüntülerinde hücrelerin otomatik bölütlenmesi
Original language	English
Title of host publication	TIPTEKNO 2019 - Tip Teknolojileri Kongresi
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781728124209
DOIs	https://doi.org/10.1109/TIPTEKNO.2019.8895080
Publication status	Published - Oct 2019
Event	2019 Medical Technologies Congress, TIPTEKNO 2019 - Izmir, Turkey Duration: 3 Oct 2019 → 5 Oct 2019

Publication series

Name	TIPTEKNO 2019 - Tip Teknolojileri Kongresi

Conference

Conference	2019 Medical Technologies Congress, TIPTEKNO 2019
Country/Territory	Turkey
City	Izmir
Period	3/10/19 → 5/10/19

Bibliographical note

Publisher Copyright:
© 2019 IEEE.

Keywords

Cell segmentation
Deep learning
Phase contrast optical microscopy
SegNet
Time series

Access to Document

10.1109/TIPTEKNO.2019.8895080

Cite this

Binici, R. C., Sahin, U., Ayanzadeh, A., Toreyin, B. U., Onal, S., Okvur, D. P., Ozuysal, O. Y., & Unay, D. (2019). Automated segmentation of cells in phase contrast optical microscopy time series images. In TIPTEKNO 2019 - Tip Teknolojileri Kongresi Article 8895080 (TIPTEKNO 2019 - Tip Teknolojileri Kongresi). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/TIPTEKNO.2019.8895080

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title = "Automated segmentation of cells in phase contrast optical microscopy time series images",

abstract = "Phase contrast optical microscopy is a preferred imaging technique for live-cell, temporal analysis. Segmentation of cells from time series data acquired with this technique is a labor-intensive and time-consuming task that cell biology researchers need solution for. In this study traditional image processing and deep learning based approaches for automated cell segmentation from phase contrast optical microscopy time series are presented, and their performances are evaluated against manually annotated datasets.",

keywords = "Cell segmentation, Deep learning, Phase contrast optical microscopy, SegNet, Time series",

author = "Binici, {Rifki Can} and Umut Sahin and Aydin Ayanzadeh and Toreyin, {Behcet Ugur} and Sevgi Onal and Okvur, {Devrim Pesen} and Ozuysal, {Ozden Yalcin} and Devrim Unay",

note = "Publisher Copyright: {\textcopyright} 2019 IEEE.; 2019 Medical Technologies Congress, TIPTEKNO 2019 ; Conference date: 03-10-2019 Through 05-10-2019",

year = "2019",

month = oct,

doi = "10.1109/TIPTEKNO.2019.8895080",

language = "English",

series = "TIPTEKNO 2019 - Tip Teknolojileri Kongresi",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

booktitle = "TIPTEKNO 2019 - Tip Teknolojileri Kongresi",

address = "United States",

}

Binici, RC, Sahin, U, Ayanzadeh, A, Toreyin, BU, Onal, S, Okvur, DP, Ozuysal, OY & Unay, D 2019, Automated segmentation of cells in phase contrast optical microscopy time series images. in TIPTEKNO 2019 - Tip Teknolojileri Kongresi., 8895080, TIPTEKNO 2019 - Tip Teknolojileri Kongresi, Institute of Electrical and Electronics Engineers Inc., 2019 Medical Technologies Congress, TIPTEKNO 2019, Izmir, Turkey, 3/10/19. https://doi.org/10.1109/TIPTEKNO.2019.8895080

Automated segmentation of cells in phase contrast optical microscopy time series images. / Binici, Rifki Can; Sahin, Umut; Ayanzadeh, Aydin et al.
TIPTEKNO 2019 - Tip Teknolojileri Kongresi. Institute of Electrical and Electronics Engineers Inc., 2019. 8895080 (TIPTEKNO 2019 - Tip Teknolojileri Kongresi).

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

TY - GEN

T1 - Automated segmentation of cells in phase contrast optical microscopy time series images

AU - Binici, Rifki Can

AU - Sahin, Umut

AU - Ayanzadeh, Aydin

AU - Toreyin, Behcet Ugur

AU - Onal, Sevgi

AU - Okvur, Devrim Pesen

AU - Ozuysal, Ozden Yalcin

AU - Unay, Devrim

PY - 2019/10

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N2 - Phase contrast optical microscopy is a preferred imaging technique for live-cell, temporal analysis. Segmentation of cells from time series data acquired with this technique is a labor-intensive and time-consuming task that cell biology researchers need solution for. In this study traditional image processing and deep learning based approaches for automated cell segmentation from phase contrast optical microscopy time series are presented, and their performances are evaluated against manually annotated datasets.

AB - Phase contrast optical microscopy is a preferred imaging technique for live-cell, temporal analysis. Segmentation of cells from time series data acquired with this technique is a labor-intensive and time-consuming task that cell biology researchers need solution for. In this study traditional image processing and deep learning based approaches for automated cell segmentation from phase contrast optical microscopy time series are presented, and their performances are evaluated against manually annotated datasets.

KW - Cell segmentation

KW - Deep learning

KW - Phase contrast optical microscopy

KW - SegNet

KW - Time series

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M3 - Conference contribution

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T3 - TIPTEKNO 2019 - Tip Teknolojileri Kongresi

BT - TIPTEKNO 2019 - Tip Teknolojileri Kongresi

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2019 Medical Technologies Congress, TIPTEKNO 2019

Y2 - 3 October 2019 through 5 October 2019

ER -

Automated segmentation of cells in phase contrast optical microscopy time series images

Abstract

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Bibliographical note

Keywords

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