Informatics Institute faculty member Behçet Uğur Töreyin has coauthored the book chapter titled "Automated analysis of phase-contrast optical microscopy time-lapse images: application to wound healing and cell motility assays of breast cancer" has been published in the book titled "Diagnostic Biomedical Signal and Image Processing Applications with Deep Learning Methods: A volume in Intelligent Data-Centric Systems" by Academic Press.


DOI (chapter)
https://doi.org/10.1016/B978-0-323-96129-5.00013-5
DOI (book) : https://doi.org/10.1016/C2021-0-02190-8

Summary:
This chapter describes a workflow for analyzing phase-contrast microscopy (PCM) data from two fundamental types of biomedical assays: assays for cell motility and assays for wound healing. The workflow of the analysis is composed of the methods for acquiring, restoring, segmenting, and quantifying biomedical data. In the literature, there have been separate methods aimed at specific stages of PCM data analysis. Nonetheless, there has never been a complete workflow for all stages of analysis. This work is an innovation that proposes an end-to-end workflow for image pre-processing, deep learning segmentation, tracking, and quantification stages in cell motility and wound healing assay analyses. The findings indicate that domain knowledge can be used to make simple but significant improvements to the results of cutting-edge methods. Furthermore, even for deep learning-based methods, pre-processing is clearly a necessary step in the workflow.

İTÜ Informatics Institute

bilisim-anasayfa-hakkimizda

ITU Informatics Institute provides graduate-level education and research in applied informatics, computer sciences, computational science and engineering, communication systems under the following programs.

Faculty members and students conduct research supported by national and international organızatıons in the fields of electromagnetic fields, communication systems/regulations, computational materials design, computational chemistry/biology, cryptography, signal/data processing/visualization, big data management, climate and ocean sciences, 

  • List of Most Influential Scientists; Associate Professor. B. Uğur Töreyin (article by Dr. John PA Ioannidis, K. W. Boyack and J. Baas published in the journal PLOS Biology)
  • Beltus Nkwawir Wiysobunri, the best project award in the Science category, in the 2020 International Students Project Competition
  • Argenit company, of which Dr. Abdulkerim Çapar is among the founding partners, received the "National-International Supports" First Prize of ITU ARI Teknokent.
  • TÜBİTAK 2242 University Students Project Competition in Priority Areas: Istanbul region first place - Ahmet Burak Özyurt
  • Best Presentation Award at ICAT'18 Conference: Sena Efsun Cebeci, 2018
  • Tubitak Incentive Award; 2016 Assoc. Prof. Adem Tekin
  • “Technical Paper” and “Willis H. Carrier” Award by the American Heating, Cooling and Air Conditioning Association; 2016 Assist. Prof. Dr. H. Salih Erden
  • Science Heroes Association Young Scientist of the Year Award; 2016 Assoc. B. Uğur Töreyin Best Poster Award at PRACEdays 2016 conference; Samet Demir
  • ITU Most Successful Thesis Award; 2016 Hatice Gokcan

There is also a High Performance Computing Laboratory established with the support of the State Planning Organization within the Institute.