LATEST NEWS - Prof. Unay gave an invited talk at the 16th Multinational Congress on Microscopy (September 5th, 2022 at the session IM1: Multi-dimensional Image Processing). - Mahmut Uçar presented our work "Detection and restoration pipeline for phase contrast microscopy time series images" at the Microscopy Image Analysis special session at TıpTekno'22 conference. - We organized a special session on Microscopy Image Analysis at the TıpTekno'22 conference. - Mahmut Uçar presented our work "Detection and Restoration of Intensity Variation in Microscopy Time Series Images" at the nternational Graduate Research Symposium IGRS'22 (Day 2).
Title: Development of Image Processing and Machine Learning based Tools for Analysis of Phase-Contrast Optical Microscopy Time Series Images
Funding: TÜBİTAK ARDEB 1001.
Duration: 1.7.2020-1.7.2023
Partners: İzmir Democracy University (IDU), İstanbul Technical University (ITU), İzmir Institute of Technology (IYTE)
Description: In this project image processing and machine learning-based approaches will be developed for morphological and movement analyses of breast cancer cell lines from phase-contrast optical microscopy time-series images. Towards this aim, our focus will be on the biological problems of cell motility (the case where a low number of isolated cells independently translocate) and wound healing (the case where cells move as tightly or loosely associated cohesive groups).
The team:
- Researchers: Devrim Ünay – PI (IDU), Behçet Uğur Töreyin (ITU), Devrim Pesen Okvur (IYTE), Özden Yalçın Özuysal (IYTE)
- Scholarship holders: Yusuf Sait Erdem (MS student, IDU), Mahmut Uçar (MS student, IDU), Berkay Mayalı (Undergrad student, IDU)
- External researchers: Sevgi Önal (University of Canterbury), Leonardo O. Iheme (Mayo Clinic)
- Alumni: Aydın Ayanzadeh (Ph.D. student, Univ. Maryland Baltimore), Özge Nur Belli (Tübitak Star grantee, IYTE), Muhammed Balıkçi (Undergrad student, IYTE), Mehmet Kaan Erol (Tübitak Star grantee, Marmara U.)
Publications:
- Erdem, Y.S., Ayanzadeh, A., Mayalı, B., Balıkçi, M., Belli, Ö.N., Uçar, M., Yalçın Özyusal, Ö.,Pesen Okvur, D., Önal, S., Morani, K., Obinna Iheme, L., Töreyin, B.U., Ünay, D., “Automated Analysis of Phase-Contrast Optical Microscopy Time-Lapse Images: Application to Wound Healing and Cell Motility Assays of Breast Cancer”, in Diagnostic Biomedical Signal and Image Processing Applications, ed. Kemal Polat and Şaban Öztürk, Academic Press, Chp.7, 137-154, 2023.
- Ucar, M., Iheme, L. O., Onal, S., Ozuysal, O. Y., Okvur, D. P., Toreyin, B. U., & Unay, D. “Detection and restoration pipeline for phase contrast microscopy time series images“, Proc. of IEEE National Congress on Medical Technologies (TipTekno), Antalya – Turkey, 2022.
- Ayanzadeh, A., Ozuysal, O. Y., Okvur, D. P., Önal, S., Töreyin, B. U., Unay, D. “Improved Cell Segmentation Using Deep Learning in Label-Free Optical Microscopy Images”, Turk J Elec Eng & Comp Sci, 29.SI-1: 2855-2868 (2021).
- Erdem, Y. S., Ozuysal, O. Y., Okvur, D. P., Töreyin, B. U., Unay, D.“An Image Segmentation Method for Wound Healing Assay Images”, Izmir Democracy University Natural and Applied Sciences Journal, 4.1: 30-37 (2021).
- Mayalı, B., Şaylığ, O., Ozuysal, O. Y., Okvur, D. P., Töreyin, B. U., Unay, D. “Faz-Kontrast Optik Mikroskopi Videolarından Otomatik Yara İyileşmesi Analizi”, İzmir Demokrasi Üniversitesi Uluslararası Mühendislik Sempozyumu (IES), Çevrimiçi, Özet Metin Bildiri Kitabı, 221-223, 2020.
- Kayan, E., Kavuşan, T., Önal, S., Okvur, D. P., Ozuysal, O. Y., Töreyin, B. U., Unay, D. “Faz-Kontrast Mikroskobu Görüntü Serilerinden Hücre Hareketliliği Analizi Ön-Çalışması”, İzmir Demokrasi Üniversitesi Uluslararası Mühendislik Sempozyumu (IES), Çevrimiçi, Özet Metin Bildiri Kitabı, 250-253, 2020.
- Erdem, Y. S., Ozuysal, O. Y., Okvur, D. P., Töreyin, B. U., Unay, “An Image Segmentation Method for Wound Healing Assay Images”, İzmir Demokrasi Üniversitesi Uluslararası Mühendislik Sempozyumu (IES), Çevrimiçi, Özet Metin Bildiri Kitabı, 254-256, 2020.
- Ayanzadeh, A., Ozuysal, O. Y., Okvur, D. P., Önal, S., Töreyin, B. U., Unay, D. “Deep Learning based Segmentation Pipeline for Label-Free Phase-Contrast Microscopy Images“, Proc. of IEEE 28th Signal Processing and Communications Applications Conference (SIU), Virtual, 2020.
- Mayalı, B., Şaylığ, O., Ozuysal, O. Y., Okvur, D. P., Töreyin, B. U., Unay, D. “Automated Analysis of Wound Healing Microscopy Image Series – A Preliminary Study“, Proc. of IEEE National Congress on Medical Technologies (TipTekno), Virtual, 2020.
- Kayan, E., Kavuşan, T., Önal, S., Okvur, D. P., Ozuysal, O. Y., Töreyin, B. U., Unay, D. “A Preliminary Study on Cell Motility Analysis from Phase-Contrast Microscopy Image Series“, Proc. of IEEE National Congress on Medical Technologies (TipTekno), Virtual, 2020.
- Ayanzadeh, A., Yagar, H. O., Ozuysal, O. Y., Okvur, D. P., Töreyin, B. U., Unay, D., Önal, S. “Cell Segmentation of 2D Phase-Contrast Microscopy Images with Deep Learning Method”, Proc. of IEEE National Congress on Medical Technologies (TipTekno), Izmir – Turkey, 2019.
- Binici, R. C., Sahin, U., Ayanzadeh, A., Töreyin, B. U., Önal, S., Okvur, D. P., Ozuysal, O. Y., Unay, D. “Automated Segmentation of Cells in Phase Contrast Optical Microscopy Time Series Images”, Proc. of IEEE National Congress on Medical Technologies (TipTekno), Izmir – Turkey, 2019.