Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images

Mahmut Uçar; Leonardo O. Iheme; Sevgi Önal; Özden Y. Özuysal; Devrim P. Okvur; Behçet U. Töreyin; Devrim Ünay

doi:10.1109/TIPTEKNO56568.2022.9960161

Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images

Mahmut Uçar, Leonardo O. Iheme, Sevgi Önal, Özden Y. Özuysal, Devrim P. Okvur, Behçet U. Töreyin, Devrim Ünay

Informatics Institute

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

Abstract

We propose a pre-processing pipeline for the de-tection and restoration of distorted frames in phase-contrast microscopy time-series images. The analysis is based on the average intensity values of the frames within any given time- series image. The extent of the correction of intensity variation in frames is determined by the normalization of the difference between the current frame's average intensity and the median of average intensity of all frames. Our restoration algorithm preserves regional trans-passing pixels, does not cause new distortions, and increases the histogram similarity between the distorted and non-distorted frames. The algorithm was validated on 15,395 time-series image frames from 27 experiments and the results were found to be visually and quantitatively accurate.

Original language	English
Title of host publication	TIPTEKNO 2022 - Medical Technologies Congress, Proceedings
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781665454322
DOIs	https://doi.org/10.1109/TIPTEKNO56568.2022.9960161
Publication status	Published - 2022
Event	2022 Medical Technologies Congress, TIPTEKNO 2022 - Antalya, Turkey Duration: 31 Oct 2022 → 2 Nov 2022

Publication series

Name	TIPTEKNO 2022 - Medical Technologies Congress, Proceedings

Conference

Conference	2022 Medical Technologies Congress, TIPTEKNO 2022
Country/Territory	Turkey
City	Antalya
Period	31/10/22 → 2/11/22

Bibliographical note

Publisher Copyright:
© 2022 IEEE.

Funding

This work is supported by the Scientific and Technological Research Council of Turkey (TUBITAK) under grant no 119E578. The data used in this study is collected under the Marie Curie IRG grant (no: FP7 PIRG08-GA-2010-27697). 978-1-6654-5432-2/22/$31.00 ©2022 IEEE

Funders	Funder number
Türkiye Bilimsel ve Teknolojik Araştırma Kurumu	119E578, FP7 PIRG08-GA-2010-27697, 978-1-6654-5432-2/22

Keywords

blank-frame
detection
intensity variation
phase contrast mi-croscopy
pre-processing
restoration
video processing

Access to Document

10.1109/TIPTEKNO56568.2022.9960161

Cite this

Uçar, M., Iheme, L. O., Önal, S., Özuysal, Ö. Y., Okvur, D. P., Töreyin, B. U., & Ünay, D. (2022). Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images. In TIPTEKNO 2022 - Medical Technologies Congress, Proceedings (TIPTEKNO 2022 - Medical Technologies Congress, Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/TIPTEKNO56568.2022.9960161

@inproceedings{fa49dd32545540c7aeb224f56de42b55,

title = "Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images",

abstract = "We propose a pre-processing pipeline for the de-tection and restoration of distorted frames in phase-contrast microscopy time-series images. The analysis is based on the average intensity values of the frames within any given time- series image. The extent of the correction of intensity variation in frames is determined by the normalization of the difference between the current frame's average intensity and the median of average intensity of all frames. Our restoration algorithm preserves regional trans-passing pixels, does not cause new distortions, and increases the histogram similarity between the distorted and non-distorted frames. The algorithm was validated on 15,395 time-series image frames from 27 experiments and the results were found to be visually and quantitatively accurate.",

keywords = "blank-frame, detection, intensity variation, phase contrast mi-croscopy, pre-processing, restoration, video processing",

author = "Mahmut U{\c c}ar and Iheme, {Leonardo O.} and Sevgi {\"O}nal and {\"O}zuysal, {{\"O}zden Y.} and Okvur, {Devrim P.} and T{\"o}reyin, {Beh{\c c}et U.} and Devrim {\"U}nay",

note = "Publisher Copyright: {\textcopyright} 2022 IEEE.; 2022 Medical Technologies Congress, TIPTEKNO 2022 ; Conference date: 31-10-2022 Through 02-11-2022",

year = "2022",

doi = "10.1109/TIPTEKNO56568.2022.9960161",

language = "English",

series = "TIPTEKNO 2022 - Medical Technologies Congress, Proceedings",

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

booktitle = "TIPTEKNO 2022 - Medical Technologies Congress, Proceedings",

address = "United States",

}

Uçar, M, Iheme, LO, Önal, S, Özuysal, ÖY, Okvur, DP, Töreyin, BU & Ünay, D 2022, Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images. in TIPTEKNO 2022 - Medical Technologies Congress, Proceedings. TIPTEKNO 2022 - Medical Technologies Congress, Proceedings, Institute of Electrical and Electronics Engineers Inc., 2022 Medical Technologies Congress, TIPTEKNO 2022, Antalya, Turkey, 31/10/22. https://doi.org/10.1109/TIPTEKNO56568.2022.9960161

Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images. / Uçar, Mahmut; Iheme, Leonardo O.; Önal, Sevgi et al.
TIPTEKNO 2022 - Medical Technologies Congress, Proceedings. Institute of Electrical and Electronics Engineers Inc., 2022. (TIPTEKNO 2022 - Medical Technologies Congress, Proceedings).

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

TY - GEN

T1 - Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images

AU - Uçar, Mahmut

AU - Iheme, Leonardo O.

AU - Önal, Sevgi

AU - Özuysal, Özden Y.

AU - Okvur, Devrim P.

AU - Töreyin, Behçet U.

AU - Ünay, Devrim

PY - 2022

Y1 - 2022

N2 - We propose a pre-processing pipeline for the de-tection and restoration of distorted frames in phase-contrast microscopy time-series images. The analysis is based on the average intensity values of the frames within any given time- series image. The extent of the correction of intensity variation in frames is determined by the normalization of the difference between the current frame's average intensity and the median of average intensity of all frames. Our restoration algorithm preserves regional trans-passing pixels, does not cause new distortions, and increases the histogram similarity between the distorted and non-distorted frames. The algorithm was validated on 15,395 time-series image frames from 27 experiments and the results were found to be visually and quantitatively accurate.

AB - We propose a pre-processing pipeline for the de-tection and restoration of distorted frames in phase-contrast microscopy time-series images. The analysis is based on the average intensity values of the frames within any given time- series image. The extent of the correction of intensity variation in frames is determined by the normalization of the difference between the current frame's average intensity and the median of average intensity of all frames. Our restoration algorithm preserves regional trans-passing pixels, does not cause new distortions, and increases the histogram similarity between the distorted and non-distorted frames. The algorithm was validated on 15,395 time-series image frames from 27 experiments and the results were found to be visually and quantitatively accurate.

KW - blank-frame

KW - detection

KW - intensity variation

KW - phase contrast mi-croscopy

KW - pre-processing

KW - restoration

KW - video processing

UR - http://www.scopus.com/inward/record.url?scp=85144055607&partnerID=8YFLogxK

U2 - 10.1109/TIPTEKNO56568.2022.9960161

DO - 10.1109/TIPTEKNO56568.2022.9960161

M3 - Conference contribution

AN - SCOPUS:85144055607

T3 - TIPTEKNO 2022 - Medical Technologies Congress, Proceedings

BT - TIPTEKNO 2022 - Medical Technologies Congress, Proceedings

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2022 Medical Technologies Congress, TIPTEKNO 2022

Y2 - 31 October 2022 through 2 November 2022

ER -

Uçar M, Iheme LO, Önal S, Özuysal ÖY, Okvur DP, Töreyin BU et al. Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images. In TIPTEKNO 2022 - Medical Technologies Congress, Proceedings. Institute of Electrical and Electronics Engineers Inc. 2022. (TIPTEKNO 2022 - Medical Technologies Congress, Proceedings). doi: 10.1109/TIPTEKNO56568.2022.9960161

Detection and Restoration Pipeline for Phase Contrast Microscopy Time Series Images

Abstract

Publication series

Conference

Bibliographical note

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this