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author={Liu, Tairan
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and Ozcan, Aydogan},
title={Deep learning-based super-resolution in coherent imaging systems},
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year={2019},
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volume={9},
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issn={2045-2322},
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}
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author = {Zhenxiang Luo and Abdulkadir Yurt and Richard Stahl and Andy Lambrechts and Veerle Reumers and Dries Braeken and Liesbet Lagae},
journal = {Opt. Express},
keywords = {High numerical aperture optics; Holographic microscopy; Image processing; Image registration; Spatial resolution; Synthetic aperture imaging},
number = {10},
pages = {13581--13595},
publisher = {OSA},
title = {Pixel super-resolution for lens-free holographic microscopy using deep learning neural networks},
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month = {May},
year = {2019},
url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-10-13581},
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author={Z. {Ren} and H. K. -. {So} and E. Y. {Lam}},
journal={IEEE Transactions on Industrial Informatics}, 
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year={2019},
volume={15},
number={11},
pages={6179-6186}}
@article{dl_stain_holography1,
author = {Liu, Tairan and Wei, Zhensong and Rivenson, Yair and de Haan, Kevin and Zhang, Yibo and Wu, Yichen and Ozcan, Aydogan},
title = {Deep learning-based color holographic microscopy},
journal = {Journal of Biophotonics},
volume = {12},
number = {11},
pages = {e201900107},
keywords = {color holography, computational microscopy, deep learning, digital holography, neural networks},
doi = {10.1002/jbio.201900107},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.201900107},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jbio.201900107},
year = {2019}
}
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	author = {Nygate, Yoav N. and Levi, Mattan and Mirsky, Simcha K. and Turko, Nir A. and Rubin, Moran and Barnea, Itay and Dardikman-Yoffe, Gili and Haifler, Miki and Shalev, Alon and Shaked, Natan T.},
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	volume = {117},
	number = {17},
	pages = {9223--9231},
	year = {2020},
	doi = {10.1073/pnas.1919569117},
	publisher = {National Academy of Sciences},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/117/17/9223},
	eprint = {https://www.pnas.org/content/117/17/9223.full.pdf},
	journal = {Proceedings of the National Academy of Sciences}
}
@article{dl_holographic_reconstruction,
author = {Zhenbo Ren and Zhimin Xu and Edmund Y. M. Lam},
title = {{End-to-end deep learning framework for digital holographic reconstruction}},
volume = {1},
journal = {Advanced Photonics},
number = {1},
publisher = {SPIE},
pages = {1 -- 12},
keywords = {digital holography, computational imaging, image reconstruction techniques, machine learning, deep learning, Holograms, 3D image reconstruction, Reconstruction algorithms, Holography, Digital holography, Photonics, Convolution, Phase imaging, Principal component analysis, Wavefronts},
year = {2019},
doi = {10.1117/1.AP.1.1.016004},
URL = {https://doi.org/10.1117/1.AP.1.1.016004}
}
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title = "Deep learning-based digital in-line holographic microscopy for high resolution with extended field of view",
journal = "Optics \& Laser Technology",
volume = "113",
pages = "77 - 86",
year = "2019",
issn = "0030-3992",
doi = "https://doi.org/10.1016/j.optlastec.2018.12.014",
url = "http://www.sciencedirect.com/science/article/pii/S0030399218313902",
author = "Hyeokjun Byeon and Taesik Go and Sang Joon Lee",
keywords = "Digital in-line holographic microscopy, 3D measurement, Artificial intelligence"
}
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@article{dl_autofocus_ren,
author = {Zhenbo Ren and Zhimin Xu and Edmund Y. Lam},
journal = {Optica},
keywords = {Computational imaging ; Digital holography ; Image reconstruction techniques; Digital holographic imaging; Holographic microscopy; Image processing; Neural networks; Off axis digital holography; Three dimensional imaging},
number = {4},
pages = {337--344},
publisher = {OSA},
title = {Learning-based nonparametric autofocusing for digital holography},
volume = {5},
month = {Apr},
year = {2018},
url = {http://www.osapublishing.org/optica/abstract.cfm?URI=optica-5-4-337},
doi = {10.1364/OPTICA.5.000337}
}
@article{dl_autofocus_wu,
author = {Yichen Wu and Yair Rivenson and Yibo Zhang and Zhensong Wei and Harun G\"{u}naydin and Xing Lin and Aydogan Ozcan},
journal = {Optica},
keywords = {Phase retrieval; Self-focusing; Digital holography ; Pattern recognition, neural networks ; Extended depth of field; Holographic microscopy; Image processing; Image reconstruction; Imaging systems; Phase recovery},
number = {6},
pages = {704--710},
publisher = {OSA},
title = {Extended depth-of-field in holographic imaging using deep-learning-based autofocusing and phase recovery},
volume = {5},
month = {Jun},
year = {2018},
url = {http://www.osapublishing.org/optica/abstract.cfm?URI=optica-5-6-704},
doi = {10.1364/OPTICA.5.000704}
}
@article{dl_autofocus_pitkaaho,
author = {Tomi Pitk\"{a}aho and Aki Manninen and Thomas J. Naughton},
journal = {Appl. Opt.},
keywords = {Digital holographic imaging; Feature extraction; Holographic applications; Holographic microscopy; Image analysis; Neural networks},
number = {5},
pages = {A202--A208},
publisher = {OSA},
title = {Focus prediction in digital holographic microscopy using deep convolutional neural networks},
volume = {58},
month = {Feb},
year = {2019},
url = {http://ao.osa.org/abstract.cfm?URI=ao-58-5-A202},
doi = {10.1364/AO.58.00A202}
}
@article{dl_autofocus_jaferzadeh,
author = {Keyvan Jaferzadeh and Seung-Hyeon Hwang and Inkyu Moon and Bahram Javidi},
journal = {Biomed. Opt. Express},
keywords = {Digital holographic imaging; Digital imaging; Holographic applications; Holographic microscopy; Image analysis; Image quality},
number = {8},
pages = {4276--4289},
publisher = {OSA},
title = {No-search focus prediction at the single cell level in digital holographic imaging with deep convolutional neural network},
volume = {10},
month = {Aug},
year = {2019},
url = {http://www.osapublishing.org/boe/abstract.cfm?URI=boe-10-8-4276},
doi = {10.1364/BOE.10.004276}
}
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	title = {Holographic deep learning for rapid optical screening of anthrax spores},
	volume = {3},
	number = {8},
	elocation-id = {e1700606},
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	doi = {10.1126/sciadv.1700606},
	publisher = {American Association for the Advancement of Science},
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	eprint = {https://advances.sciencemag.org/content/3/8/e1700606.full.pdf},
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}
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@misc{trackpy,
  author       = {Dan Allan and
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  title        = {soft-matter/trackpy: Trackpy v0.4.2},
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}
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