Publications

@article{oguz2026label,
  title={Label-free holotomographic imaging of brain myelin},
  author={Oguz, Tuba and Ayd{\i}n, Mehmet {\c{S}}erif and Kerman, Bilal Ersen and Toy, M Fatih},
  journal={Scientific Reports},
  year={2026},
  publisher={Nature Publishing Group UK London}
}

@article{sahloul2026all,
  title={All-optical selective target highlighting for augmented reality microscopy},
  author={Sahloul, Maha and Ak{\c{s}}it, Kaan and Toy, M Fatih},
  journal={Optics Continuum},
  volume={5},
  number={8},
  pages={2708--2723},
  year={2026},
  publisher={Optica Publishing Group}
}

@article{hussein2026dual,
  title={Dual-shot polarization digital holographic microscopy with phase bias equalization for full-field Jones matrix imaging},
  author={Hussein, Mohammad MTR and Toy, M Fatih},
  journal={Biomedical Optics Express},
  volume={17},
  number={4},
  pages={1877--1896},
  year={2026},
  publisher={Optica Publishing Group}
}

@article{altun2024visualizing,
  title={Visualizing hydrogen peroxide and nitric oxide dynamics in endothelial cells using multispectral imaging under controlled oxygen conditions},
  author={Altun, Hamza Yusuf and Secilmis, Melike and Yang, Fan and Caglar, Tuba Akgul and Vatandaslar, Emre and Toy, Muhammed Fatih and Vilain, Sven and Mann, Giovanni E and {\"O}zt{\"u}rk, G{\"u}rkan and Eroglu, Emrah},
  journal={Free Radical Biology and Medicine},
  volume={221},
  pages={89--97},
  year={2024},
  publisher={Elsevier}
}

@article{tekin2023situ,
  title={In-situ measurement of anisotropic Young’s modulus in fused deposition modeling printed cantilevers},
  author={Tekin, Engincan and {\c{C}}a{\u{g}}mel, Mehmet and Ayd{\i}n, Can Ozan and Ferhano{\u{g}}lu, Onur and Toy, Muhammed Fatih},
  journal={Journal of Micromechanics and Microengineering},
  volume={33},
  number={8},
  pages={085002},
  year={2023},
  publisher={IOP Publishing}
}

@inproceedings{ozbilgin2022integrated,
  title={An integrated top-stage incubator and lens-free holographic imaging system for culture monitoring applications},
  author={Ozbilgin, Zeynep and Aksit, Sevdenur and Toy, M Fatih},
  booktitle={Unconventional Optical Imaging III},
  volume={12136},
  pages={237--243},
  year={2022},
  organization={SPIE}
}

@inproceedings{gurcan2022maskless,
  title={Maskless lithography with holographic feedback for the fabrication of optical elements},
  author={G{\"u}rcan, Tolga and Toy, Muhammed Fatih},
  booktitle={3D Printed Optics and Additive Photonic Manufacturing III},
  volume={12135},
  pages={56--60},
  year={2022},
  organization={SPIE}
}

@inproceedings{gurcan2022total,
  title={Total internal reflection holographic microscopy for cellular imaging},
  author={G{\"u}rcan, Tolga and Toy, Muhammed Faith},
  booktitle={Unconventional Optical Imaging III},
  volume={12136},
  pages={18--22},
  year={2022},
  organization={SPIE}
}

@misc{ferhanoglu2022high,
  title={High resolution prism spectrometer comprising a diffuser film},
  author={Ferhanoglu, Onur and Toy, Muhammed Fatih and Cetindag, Sakir Kaan and Civitci, Fehmi},
  year={2022},
  month=jan # "~25",
  publisher={Google Patents},
  note={US Patent 11,231,322}
}

@inproceedings{ozbilgin2021low,
  title={Low-cost top stage incubator for live cell imaging applications},
  author={{\"O}zbilgin, Zeynep and Toy, M Fatih and Ak{\c{s}}it, Sevdenur},
  booktitle={2021 Medical Technologies Congress (TIPTEKNO)},
  pages={1--4},
  year={2021},
  organization={IEEE}
}

@article{toy2021quantitative,
  title={Quantitative phase macroscopic system for label-free imaging of tissue sections},
  author={Toy, Muhammed Fatih},
  journal={Electrica},
  year={2021},
  publisher={{\.I}stanbul University}
}

@article{ccetindaug2020scattering,
  title={Scattering metal waveguide based speckle-enhanced prism spectrometry},
  author={{\c{C}}etinda{\u{g}}, Sakir Kaan and Toy, Muhammed Fatih and Ferhano{\u{g}}lu, Onur and Civitci, Fehmi},
  journal={Journal of Lightwave Technology},
  volume={38},
  number={7},
  pages={2022--2027},
  year={2020},
  publisher={IEEE}
}

@article{toy2019wedge,
  title={Wedge prism assisted quantitative phase imaging on standard microscopes},
  author={Toy, Muhammed Fatih},
  journal={Optics Communications},
  volume={451},
  pages={361--366},
  year={2019},
  publisher={Elsevier}
}

@inproceedings{ccetindaug2019speckle,
  title={Speckle-enhanced prism spectrometer},
  author={{\c{C}}etinda{\u{g}}, {\c{S}} Kaan and Ferhano{\u{g}}lu, Onur and Toy, M Fatih and Civitci, Fehmi},
  booktitle={2019 International Conference on Optical MEMS and Nanophotonics (OMN)},
  pages={84--85},
  year={2019},
  organization={IEEE}
}

@article{ccetindaug2018speckle,
  title={A speckle-enhanced prism spectrometer with high dynamic range},
  author={{\c{C}}etinda{\u{g}}, {\c{S}} Kaan and Toy, M Fatih and Ferhano{\u{g}}lu, Onur and Civitci, Fehmi},
  journal={IEEE Photonics Technology Letters},
  volume={30},
  number={24},
  pages={2139--2142},
  year={2018},
  publisher={IEEE}
}

@inproceedings{toy2018quantitative,
  title={Quantitative phase imaging upgrade on a standard microscope},
  author={Toy, M. Fatih },
  booktitle={14th Nanoscience and Nanotechnology Conference},
  pages={257},
  year={2018},
  organization={NANOTR-14}
}

@inproceedings{toy2019refractive,
  title={Refractive index tomography of myelinating glial cells},
  author={Toy, Muhammed Fatih and Vatandaslar, Burcu Kurt and Kerman, Bilal Ersen},
  booktitle={Quantitative Phase Imaging V},
  volume={10887},
  pages={97--101},
  year={2019},
  organization={SPIE}
}

@article{hong2016real,
  title={Real-time holographic tracking and control of microrobots},
  author={Hong, Ayoung and Zeydan, Burak and Charreyron, Samuel and Ergeneman, Olga{\c{c}} and Pane, Salvador and Toy, M Fatih and Petruska, Andrew J and Nelson, Bradley J},
  journal={IEEE Robotics and Automation Letters},
  volume={2},
  number={1},
  pages={143--148},
  year={2016},
  publisher={IEEE}
}

@inproceedings{depeursinge2013super,
  title={Super-resolution Phase Tomography},
  author={Depeursinge, Christian and Cotte, Yann and Toy, Fatih and Jourdain, Pascal and Boss, Daniel and Marquet, Pierre and Magistretti, Pierre},
  booktitle={Digital Holography and Three-Dimensional Imaging},
  pages={DTh1A--2},
  year={2013},
  organization={Optica Publishing Group}
}

@article{cotte2013marker,
  title={Marker-free phase nanoscopy},
  author={Cotte, Yann and Toy, Fatih and Jourdain, Pascal and Pavillon, Nicolas and Boss, Daniel and Magistretti, Pierre and Marquet, Pierre and Depeursinge, Christian},
  journal={Nature Photonics},
  volume={7},
  number={2},
  pages={113--117},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{toy2012accelerated,
  title={Accelerated autofocusing of off-axis holograms using critical sampling},
  author={Toy, M Fatih and K{\"u}hn, Jonas and Richard, St{\'e}phane and Parent, J{\'e}r{\^o}me and Egli, Marcel and Depeursinge, Christian},
  journal={Optics letters},
  volume={37},
  number={24},
  pages={5094--5096},
  year={2012},
  publisher={Optica Publishing Group}
}

@article{depeursinge2012dealing,
  title={Dealing with reconstructed complex fields in microscopy: Going to the resolution limit and beyond?},
  author={Depeursinge, Christian and Cotte, Yann and Toy, M. Fatih and Kou, Shan Shan},
  journal={Proceedings of Focus on Microscopy 2012},
  pages={WE-MO2-PAR-A},
  year={2012}
}

@inproceedings{toy2012digital,
  title={Digital holographic microscopy for the cytomorphological imaging of cells under zero gravity},
  author={Toy, M Fatih and Richard, Stephane and K{\"u}hn, Jonas and Franco-Obreg{\'o}n, Alfredo and Egli, Marcel and Depeursinge, Christian},
  booktitle={Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIX},
  volume={8227},
  pages={133--138},
  year={2012},
  organization={SPIE}
}

@article{toy2012enhanced,
  title={Enhanced robustness digital holographic microscopy for demanding environment of space biology},
  author={Toy, M Fatih and Richard, St{\'e}phane and K{\"u}hn, Jonas and Franco-Obreg{\'o}n, Alfredo and Egli, Marcel and Depeursinge, Christian},
  journal={Biomedical optics express},
  volume={3},
  number={2},
  pages={313--326},
  year={2012},
  publisher={Optica Publishing Group}
}

@inproceedings{Cotte:11,
author = {Yann Cotte and Fatih M. Toy and Daniel Boss and Christian Depeursinge},
booktitle = {Frontiers in Optics 2011/Laser Science XXVII},
journal = {Frontiers in Optics 2011/Laser Science XXVII},
keywords = {Microscopy; Digital holography ; Diffraction optics; Digital holography; Holographic microscopy; Imaging techniques; Phase imaging; Point spread function},
pages = {PDPA2},
publisher = {Optica Publishing Group},
title = {Deconvolved phase imaging for diffraction tomography},
year = {2011},
url = {https://opg.optica.org/abstract.cfm?URI=FiO-2011-PDPA2},
doi = {10.1364/FIO.2011.PDPA2},
abstract = {We present a new technique for coherent imaging based on digital holographic microscopy. For high-resolution tomography, the diffraction effect of the microscope objective is corrected by the system's complex point spread function.},
}

@article{cotte2011beyond,
  title={Beyond the lateral resolution limit by phase imaging},
  author={Cotte, Yann and Toy, M Fatih and Depeursinge, Christian},
  journal={Journal of biomedical optics},
  volume={16},
  number={10},
  pages={106007--106007},
  year={2011},
  publisher={Society of Photo-Optical Instrumentation Engineers}
}

@article{cotte2011realistic,
  title={Realistic 3D coherent transfer function inverse filtering of complex fields},
  author={Cotte, Yann and Toy, Fatih M and Arfire, Cristian and Kou, Shan Shan and Boss, Daniel and Bergo{\"e}nd, Isabelle and Depeursinge, Christian},
  journal={Biomedical Optics Express},
  volume={2},
  number={8},
  pages={2216--2230},
  year={2011},
  publisher={Optica Publishing Group}
}

@article{ferhanoglu2011fourier,
  title={Fourier optics analysis of grating sensors with tilt errors},
  author={Ferhanoglu, Onur and Toy, M Fatih and Urey, Hakan},
  journal={Optics letters},
  volume={36},
  number={12},
  pages={2254--2256},
  year={2011},
  publisher={Optica Publishing Group}
}

@article{cotte2011applications,
  title={Applications of complex field deconvolution using digital holographic microscopy},
  author={Cotte, Yann and Toy, M. Fatih and Borgoend, Isabelle and Arfire, Cristian and Kou, Shan Shan and Depeursinge, Christian},
  journal={Proceedings of Focus on Microscopy 2011},
  pages={142--142},
  year={2011}
}

@article{cotte2010microscopy,
  title={Microscopy image resolution improvement by deconvolution of complex fields},
  author={Cotte, Yann and Toy, M Fatih and Pavillon, Nicolas and Depeursinge, Christian},
  journal={Optics Express},
  volume={18},
  number={19},
  pages={19462--19478},
  year={2010},
  publisher={Optica Publishing Group}
}

@article{cotte2010sub,
  title={Sub-Rayleigh resolution by phase imaging},
  author={Cotte, Yann and Toy, M Fatih and Shaffer, Etienne and Pavillon, Nicolas and Depeursinge, Christian},
  journal={Optics letters},
  volume={35},
  number={13},
  pages={2176--2178},
  year={2010},
  publisher={Optica Publishing Group}
}

@inproceedings{toy2010real,
  title={Real Time 3D Cytomorphological Imaging using Digital Holographic Microscopy and Fluorescence Microscopy for Space Biology},
  author={Toy, M Fatih and K{\"u}hn, Jonas and Parent, J{\'e}r{\^o}me and Pache, Christophe and Egli, Marcel and Depeursinge, Christian},
  booktitle={Digital Holography and Three-Dimensional Imaging},
  pages={DTuA5},
  year={2010},
  organization={Optica Publishing Group}
}

@article{cotte2010studies,
  title={Studies on synthetic deconvolution of complex fields with digital holographic microscopy},
  author={Cotte, Yann and Toy, Muhammed Fatih and Pavillon, Nicolas and Depeursinge, Christian},
  journal={Proceedings of Focus on Microscopy 2010},
  pages={MO--MO},
  year={2010}
}

@article{pache2010digital,
  title={Digital holographic microscopy real-time monitoring of cytoarchitectural alterations during simulated microgravity},
  author={Pache, Christophe and K{\"u}hn, Jonas and Westphal, Kriss and Toy, M Fatih and Parent, J{\'e}r{\^o}me and B{\"u}chi, Oralea and Franco-Obregon, Alfredo and Depeursinge, Christian and Egli, Marcel},
  journal={Journal of biomedical optics},
  volume={15},
  number={2},
  pages={026021--026021},
  year={2010},
  publisher={Society of Photo-Optical Instrumentation Engineers}
}

@inproceedings{toy2010dual,
  title={Dual-mode digital holographic and fluorescence microscopy for the study of morphological changes in cells under simulated microgravity},
  author={Toy, M Fatih and Pache, Christophe and Parent, J{\'e}r{\^o}me and K{\"u}hn, Jonas and Egli, Marcel and Depeursinge, Christian},
  booktitle={Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XVII},
  volume={7570},
  pages={65--68},
  year={2010},
  organization={SPIE}
}

@article{toy2009uncooled,
  title={Uncooled infrared thermo-mechanical detector array: Design, fabrication and testing},
  author={Toy, M Fatih and Ferhanoglu, Onur and Torun, Hamdi and Urey, Hakan},
  journal={Sensors and Actuators A: Physical},
  volume={156},
  number={1},
  pages={88--94},
  year={2009},
  publisher={Elsevier}
}

@inproceedings{ferhanoglu2009parylene,
  title={Parylene-based uncooled thermomechanical array},
  author={Ferhanoglu, Onur and Toy, M Fatih and Urey, Hakan},
  booktitle={Infrared Technology and Applications XXXV},
  volume={7298},
  pages={194--201},
  year={2009},
  organization={SPIE}
}

@inproceedings{toy2008moems,
  title={MOEMS thermal imaging camera},
  author={Toy, M Fatih and Ferhanoglu, Onur and Torun, Hamdi and Degertekin, F Levent and Urey, Hakan},
  booktitle={2008 Ph. D. Research in Microelectronics and Electronics},
  pages={101--104},
  year={2008},
  organization={IEEE}
}

@article{ferhanoglu2007two,
  title={Two-wavelength grating interferometry for MEMS sensors},
  author={Ferhanoglu, Onur and Toy, M Fatih and Urey, Hakan},
  journal={IEEE Photonics Technology Letters},
  volume={19},
  number={23},
  pages={1895--1897},
  year={2007},
  publisher={IEEE}
}

@inproceedings{ferhanoglu2007thermal,
  title={Thermal-mechanical Detector Array with Integrated Diffraction Grating},
  author={Ferhanoglu, O and Toy, MF and Unal, G and Kalyoncu, H and Kabuli, G and Caliskan, AU and Urey, H},
  booktitle={LEOS 2007-IEEE Lasers and Electro-Optics Society Annual Meeting Conference Proceedings},
  pages={836--837},
  year={2007},
  organization={IEEE}
}

@inproceedings{toy2007two,
  title={Two-wavelength Grating Interferometry for Extended Range MEMS Metrology},
  author={Toy, MF and Ferhanoglu, O and Urey, H},
  booktitle={2007 IEEE/LEOS International Conference on Optical MEMS and Nanophotonics},
  pages={95--96},
  year={2007},
  organization={IEEE}
}