- Our book chapter “Automated Analysis of Phase-Contrast Optical Microscopy Time-Lapse Images: Application to Wound Healing and Cell Motility Assays of Breast Cancer” is published in Diagnostic Biomedical Signal and Image Processing Applications.
- Prof. Unay gave an invited talk at the 16th Multinational Congress on Microscopy (September 5th, 2022 at the session IM1: Multi-dimensional Image Processing).
- We organized a special session on Microscopy Image Analysis at the TıpTekno'22 conference.
- 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.

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), Kenan Morani (PhD 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.)


Exemplary deformations observed in PCM videos

Monotonic intensity variation
High intensity variation
Geometric shift
Blank frame
Lens distortion
Background variation