Our Team

Current Members

M. Fatih Toy
Principle Investigator
Tolga Gürcan
Graduate Research Assistant/Year(2020-2022)
Zeynep Özbilgin
Undergraduate Research Assistant/Year
Damla Dikel
Undergraduate Research Assistant/Year(2023- )

Alumni

Sevdanur Akşit
Undergraduate Research Assistant/Year
Mustafa Ekrem Erakın
Graduation Project Student/Year
Ismail Erdem Bayar
Graduation Project Student/Year
Aslıgül Aksan
Graduation Project Student/Year
Toprak Ozil
MSc Student/Year
Selcen Necibe Gökduman
Graduation Project Student/Year
Baturay Özgürün
Graduate Research Assistant/Year

Collaborators

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M. Fatih Toy

Principle Investigator

Current Research Areas

Optical Computing, Biomedical Engineering, bioPhotonic, Biomedical Optics, Electrical and Electronics Engineering, Electronic, Optics and Photonics, MEMS, Optoelectronic Materials and Devices, Physics, Electromagnetism, Acoustics, Heat Transfer, Classical Mechanics and Fluid Dynamics, Optics, Engineering and Technology

Projects

  • High Resolution Total Internal Reflection Holographic Microscopy for the Investigation of Cellular Interfaces
  • Dual Mode and Multi Wavelength 3D Quantitative Phase and Fluorescence Microscopy
  • Center for Novel Microscopy Technologies
  • High Resolution Optical Spectrometer with Broad Free Spectral Range
  • Holographic Micro-Factory
  • Digital Holographic Microscopy System with Integrated Incubator
  • Projection Vein Finder
  • Epifluorescence Microscopy on a Student Microscope

Publications

Journals

  • O. Ferhanoglu, M. F. Toy, and H. Urey, "Two-wavelength grating interferometry for MEMS sensors," Photonics Technology Letters, IEEE, 19 (23), 1895-1897 (2007).
  • M. F. Toy, O. Ferhanoglu, H. Torun, and H. Urey, "Uncooled infrared thermo-mechanical detector array: Design, fabrication and testing," Sensors and Actuators A: Physical, 156 (1), 88-94 (2009).
  • Y. Cotte, M. F. Toy, E. Shaffer, N. Pavillon, and C. Depeursinge, "Sub-Rayleigh resolution by phase imaging," Optics Letters, 35 (13), 2176-2178 (2010).
  • C. Pache, J. Kühn, K. Westphal, M. F. Toy, J. Parent, O. Büchi, A. Franco-Obregón, C. Depeursinge, and M. Egli, "Digital holographic microscopy real-time monitoring of cytoarchitectural alterations during simulated microgravity," Journal of Biomedical Optics, 15, 026021 (2010).
  • Y. Cotte, M. F. Toy, N. Pavillon, and C. Depeursinge, "Microscopy image resolution improvement by deconvolution of complex fields," Optics Express, 18 (19), 19462-19478 (2010).
  • Y. Cotte, M. F. Toy, and C. Depeursinge, "Beyond the lateral resolution limit by phase imaging," Journal of Biomedical Optics, 16, 106007 (2011).
  • O. Ferhanoglu, M.F. Toy, and H. Urey, "Fourier optics analysis of grating sensors with tilt errors," Optics Letters, 36(12), 2254-2256 (2011).
  • Y. Cotte, M. F. Toy, C. Arfire, S. S. Kou, D. Boss, I. Bergoënd, and C. Depeursinge, "Realistic 3D coherent transfer function inverse filtering of complex fields," Biomedical Optics Express, 2 (8), 2216 (2011).
  • M. F. Toy, S. Richard, J. Kühn, A. Franco-Obregón, M. Egli, and C. Depeursinge, "Enhanced robustness digital holographic microscopy for demanding environment of space biology," Biomedical Optics Express, 3 (2), 313-326 (2012).
  • M. F. Toy, J. Kühn, S. Richard, J. Parent, M. Egli, and C. Depeursinge, "Accelerated autofocusing of off-axis holograms using critical sampling," Opt. Lett., 37 (24), 5094-5096 (2012).
  • Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, "Marker-free phase nanoscopy," Nature Photonics, 7 (2), 113-117 (2013).
  • A. Hong, B. Zeydan, S. Charreyron, O. Ergeneman, S. Pane, M. Toy, A. Petruska, and B. Nelson, "Real-Time Holographic Tracking and Control of Microrobots," IEEE RA-L, 2 (1), 143-148 (2017).
  • Ş. K. Çetindağ, M. F. Toy, O. Ferhanoğlu, F. Çivitci, "A Speckle-Enhanced Prism Spectrometer with High Dynamic Range," IEEE Photonics Technology Letters, 30 (24), 2139-2142 (2018).

Conferences

  • J. Ollila, M. F. Toy, O. Ferhanoglu, P. Karioja, and H. Urey, "Vacuum package design for a MEMS based IR detector array," Proceedings of the European Microelectronics and Packaging Conference (Oulu, 2007).
  • M. F. Toy, O. Ferhanoglu, and H. Urey, "Two-wavelength Grating Interferometry for Extended Range MEMS Metrology," IEEE/LEOS International Conference on Optical MEMS and Nanophotonics, 95 (Hualien, 2007).
  • O. Ferhanoglu, M. F. Toy, G. Unal, H. Kalyoncu, G. Kabuli, A. U. Caliskan, and H. Urey, "Thermal-mechanical Detector Array with Integrated Diffraction Grating," The 20th Annual Meeting of the IEEE Lasers and Electro-Optics Society, 836 (Orlando, October 21-25, 2007).
  • M. F. Toy, O. Ferhanoglu, H. Torun, F. L. Degertekin, and H. Urey, "MOEMS thermal imaging camera," Ph. D. Research in Microelectronics and Electronics (Istanbul, 2008).
  • O. Ferhanoglu, M. F. Toy, and H. Urey, "Parylene-based uncooled thermomechanical array," Proc. SPIE 7298, Infrared Technology and Applications XXXV, 72980H (Orlando, May 06, 2009).
  • Y. Cotte, M. F. Toy, N. Pavillon, and C. Depeursinge, "Studies on synthetic deconvolution of complex fields with digital holographic microscopy," Focus on Microscopy (Shanghai, 2010).
  • M. F. Toy, C. Pache, J. Parent, J. Kühn, M. Egli, and C. Depeursinge, "Dual-mode digital holographic and fluorescence microscopy for the study of morphological changes in cells under simulated microgravity," Proc. SPIE 7570, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XVII, 75700A (San Francisco, February 24, 2010).
  • M. Toy, J. Kühn, J. Parent, C. Pache, M. Egli, and C. Depeursinge, "Real Time 3-D Cytomorphological Imaging Using Digital Holographic Microscopy and Fluorescence Microscopy for Space Biology," in Biomedical Optics and 3-D Imaging, OSA Technical Digest (CD), DTuA5 (Miami, 2010).
  • Y. Cotte, F. Toy, D. Boss, and C. Depeursinge, "Deconvolved phase imaging for diffraction tomography," Frontiers in Optics 2011/Laser Science XXVII, OSA Technical Digest, PDPA2 (San Jose, 2011).
  • Y. Cotte, F. Toy, I. Bergoend, C. Arfire, S.S. Kou, and C. Depeursinge, "Applications of complex field deconvolution using digital holographic microscopy," Focus on Microscopy (Konstanz, 2011).
  • C. Depeursinge, Y. Cotte, M. F. Toy, and S. S. Kou, "Dealing with reconstructed complex fields in microscopy: Going to the resolution limit and beyond?," Focus on Microscopy (Singapore, 2012).
  • M. F. Toy, S. Richard, J. Kühn, A. Franco-Obregón, M. Egli, and C. Depeursinge, "Digital holographic microscopy for the cytomorphological imaging of cells under zero gravity," Proc. SPIE 8227, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIX, 82270S (San Francisco, February 9, 2012).
  • C. Depeursinge, Y. Cotte, F. Toy, P. Jourdain, D. Boss, P. Marquet, and P. Magistretti, "Super-resolution Phase Tomography," Digital Holography and Three-Dimensional Imaging, OSA Technical Digest (online), DTh1A.2 (Hawaii, 2013).
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Tolga Gürcan

Graduate Research Assistant/Year(2020-2022)

Current Research Areas

Ph.D. , Electrical and Computer Engineering (Princeton University, Princeton/NJ/USA)

Projects

  • Biophotonics and Optical Imaging Laboratory (September 2020 – June 2022): Working on off-axis digital holography for phase imaging, total internal reflection microscopy, UV grayscale lithography under the direction of Assist. Prof. Muhammed Fatih Toy.
  • Medical & Biological Physics Research Group (May 2017 – June 2022): Working on ultrafast laser development, photoacoustic imaging, holographic image projection with spatial light modulator, total internal reflection digital holographic microscopy under the direction of Prof. Burçin Ünlü.
  • Lumos Laser (July 2018 - September 2018): Worked on electronic control of an ultrashort pulsed laser such as creating trigger signal for AOM by using an input signal from oscillator’s photodiode and controlling different stage’s power by controlling corresponding diode drivers from FPGA.
  • EMT Control (June 2019 - July 2019): Worked on FPGA based DC motor control systems

Publications

Poster Presentation

  • T. Gürcan, M. Fatih Toy, Total Internal Reflection Holographic Microscopy for Interfacial Imaging, Poster presented at 22nd National Optics, Electro-Optics and Photonics Workshop, September 10, 2021.

Oral Presentation

  • T. Gürcan, M. Fatih Toy, Total internal reflection holographic microscopy for cellular imaging, Presented at SPIE 2022 Photonics Europe, April 2022
  • T. Gürcan, M. Fatih Toy, Maskless lithography with holographic feedback for the fabrication of optical elements, Presented at SPIE 2022 Photonics Europe, April 2022.

Awards and Scholarships

  • TUBITAK 2210- Yurtiçi Yüksek Lisans Programi (The Scientific and Technological Research Council of Turkey - Graduate Scholarship Program, 2020)
  • TUBITAK 2205- Yurtiçi Lisans Programi (The Scientific and Technological Research Council of Turkey - Undergraduate Scholarship Program, 2015)
  • International Physics Olympiad – 2015 Silver Medal (Total 5 students are selected each year to represent Turkey at IPhO through a 4-stage examination. Nearly 450 students and 120 countries all around the world participate in IPhO)
  • International Physics Olympiad – 2014 Bronze Medal
  • TUBITAK National Science Olympiad Physics – 2014 Gold Medal
  • TUBITAK National Science Olympiad Physics – 2013 Gold Medal
  • First Lego League Open European Championship (2012) – Third place in presentation
  • First Lego League Turkey Championship (2012) – Second Place
  • Turkish Patent Institute (TPE) Invention Owner (Patent for a device which spontaneously calculates the expiry date according to the temperature of the medium for things like chicken, meat, laboratory equipment. Applied for a patent in 2013 and got approval in 2016.)
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Zeynep Özbilgin

Undergraduate Research Assistant/Year

Current Research Areas

I am doing my master's degree in "Communication with Visible Light". At the same time, I work in the Communication Theory and Technologies Research Group (CT&T) as a TUBITAK Fellow.

Projects

  • 2021 – 2022 TUBITAK 2209-A University Students Research Projects Support Program Project Manager The undergraduate research project “The Low-Cost Top Stage Incubator and Integrated In-Line Holography Microscope” is supported by TUBITAK 2209-A Program.
  • TUBITAK 2209-A "Efficient Implementation of Multicast via Cell Broadcast for 5G Systems"

Publications

Conferences

  • Low-Cost Top Stage Incubator for Live Cell Imaging Applications – 2021 Z. Ozbilgin, M. F. Toy, and S. Aksit, “Low-Cost Top Stage Incubator for Live Cell Imaging Applications,” TIPTEKNO 2021 - Tip Teknol. Kongresi - 2021 Med. Technol. Congr., 2021, doi: 10.1109/TIPTEKNO53239.2021.9632885.
  • An integrated top-stage incubator and lens-free holographic imaging system for culture monitoring applications – 2022 Z. Ozbilgin, S. Aksit, and M. F. Toy, “An integrated top-stage incubator and lens-free holographic imaging system for culture monitoring applications,” no. May, p. 74, 2022, doi: 10.1117/12.2622639.
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Damla Dikel

Undergraduate Research Assistant/Year(2023-)

Current Research Areas

Projects

  • (11-14/06/2021) TUBITAK 2237-A Preparation and execution of applied project proposals for Undergraduate Students in the Field of Health, Nature and Science /3
  • (12/11/2021 – 07/02/2022) Autonomous Car
  • (05/04/2023 – Current) TUBITAK BIDEB: High Resolution All Internal Reflection Holographic Microscope Development And Use In Studying Cellular Interfaces
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Sevdanur Akşit

Undergraduate Research Assistant/Year

Current Research Areas

Projects

  • 06/2020 American Astronautical Society CanSat Competition (8th of the World) CanSat competition is an annual student design-build-launch competition for space-related topics organized by the American Astronautical Society (AAS) and it's completed with the 8/40 ranking in the world.
  • 02/2020 – 08/2020 TUBITAK STAR (Trainee Researcher Scholarship Program) Program The STAR program is a funding program for undergraduates due to work on determined research projects. The working area of the specific project is highresolution holographic microscope development.
  • 2021 – 2022 TUBITAK 2209-A University Students Research Projects Support Program Project Manager The undergraduate research project “The Low-Cost Top Stage Incubator and Integrated In-Line Holography Microscope” is supported by TUBITAK 2209-A Program.

Publications

Conferences

  • Low-Cost Top Stage Incubator for Live Cell Imaging Applications – 2021 Z. Ozbilgin, M. F. Toy, and S. Aksit, “Low-Cost Top Stage Incubator for Live Cell Imaging Applications,” TIPTEKNO 2021 - Tip Teknol. Kongresi - 2021 Med. Technol. Congr., 2021, doi: 10.1109/TIPTEKNO53239.2021.9632885.
  • An integrated top-stage incubator and lens-free holographic imaging system for culture monitoring applications – 2022 Z. Ozbilgin, S. Aksit, and M. F. Toy, “An integrated top-stage incubator and lens-free holographic imaging system for culture monitoring applications,” no. May, p. 74, 2022, doi: 10.1117/12.2622639.
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member6

Mustafa Ekrem Erakın

Graduation Project Studen/Year

Current Research Areas

Projects

Publications

Conferences

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Ismail Erdem Bayar

Graduation Project Studen/Year

Current Research Areas

Projects

Publications

Conferences

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member8

Aslıgül Aksan

Graduation Project Studen/Year

Current Research Areas

Projects

Publications

Conferences

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Toprak Özil

MSc Student/Year

Current Research Areas

Projects

Publications

Conferences

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Selcen Necibe Gökduman

Graduation Project Student/Year

Current Research Areas

Recently I am working on "Touch Vision" and an "ABAPKO" Project. The Touch Vision is about developing a sensory substitution system for visually impaired persons. On the other hand, in the ABAPKO Project, the role of microorganisms in the formation of plagues caused by atherosclerosis is investigated by the research team. The obtained results are being edited for publication.

Projects

  • TUBITAK 2209/A Project – Epifluorescence Imaging on a Student Microscope (2020)
  • ABAPKO Scholar in Medical Biotechnology Lab (2022- )
  • TUSEB Group A Emergency R&D Project – Touch Vision (2023-)

Publications

Conferences

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Baturay Özgürün

Graduate Research Assistant/Year

Current Research Areas

Projects

Publications

Conferences