@article{mem_eff,
    author = "Shuhui, Li and others",
    title = "Memory effect assisted imaging through multimode optical fibres",
    journal = "Nature Communications",
    year = "2021",
    volume = "12",
    number = "3751",
    DOI = "https://doi.org/10.1038/s41467-021-23729-1"
}

@book{fourier_optics,
    author = "Tyson, Robert K.",
    title = "Principles and Applications of Fourier Optics",
    publisher = "IOP Publishing",
    year = "2014"
}

@article{deconv,
    author = "Turcotte, Raphael and others",
    title = "Deconvolution for multimode fiber imaging modeling of spatially variant PSF",
    journal = "Biomedical Optics Express",
    year = "2020",
    volume = "11",
    number = "8",
    DOI = "https://doi.org/10.1364/BOE.399983"
}

@book{bragg_book,
    author = "Kashyap, Raman",
    title = "Fiber Bragg Gratings",
    publisher = "Academic Press",
    year = "1999"
}

@misc{mmf_sim_base,
    author = "Lee, Szu-Yu",
    title = "MMF-simulation",
    url = "https://github.com/szuyul/MMF-simulation"
}

@article{mmf_neuron,
    author = "Vasquez-Lopez, S. and others",
    title = "Subcellular spatial resolution achieved for deep-brain imaging in vivo using a minimally invasive multimode fiber",
    journal = "Light: Science and Applications",
    year = "2018",
    volume = "7",
    number = "110",
    DOI = "https://doi.org/10.1038/s41377-018-0111-0"
}

@article{scattering_approach,
    author = "Ko, D.Y.K and Sambles, J.R.",
    title = "Scattering matrix method for propagation of radiation in stratified media: attenuated total reflection studies of liquid crystals",
    journal = "journal of the Optical Society of America A",
    year = "1988",
    volume = "5",
    issue = "11",
    pages = "1863-1866"
}

% NEW references --- above are from transfer report

@book{backg_micrographia,
    author = "Hooke, R.",
    title = "Micrographia",
    publisher = "The Royal Society",
    year = "1667"
}

@article{backg_early_history_microscope,
    author = "Ball, Clara Sue",
    title = "The Early History of the Compound Microscope",
    journal = "Bios",
    year = "1966",
    volume = "37",
    issue = "2",
    pages = "51-60"
}

@article{backg_confocal_microscopy,
    author = "Elliott, A.D.",
    title = "Confocal Microscopy: Principles and Modern Practices",
    journal = "Current Protocols in Cytometry",
    year = "2020",
    volume = "92",
    issue = "1",
    pages = "e68"
}

@article{backg_fluorescence_microscopy,
    author = "Smith, I. and Parker, I. and Bootman, M.D.",
    title = "Fluorescence Microscopy",
    journal = "Cold Spring Harbor protocols",
    year = "2014",
    volume = "2014",
    issue = "10",
}

@article{backg_genetical_neuronal,
    author = "Lin, M.Z. and Schnitzer, M.J",
    title = "Genetically encoded indicators of neuronal activity",
    journal = "Nature neuroscience",
    year = "2016",
    volume = "19",
    issue = "9",
    pages = "1142-1153"
}

@article{backg_understanding_brain,
    author = "Lisman, J.",
    title = "The Challange of Understanding the Brain: Where We Stand in 2015",
    journal = "Neuron",
    year = "2015",
    volume = "86",
    issue = "4",
    pages = "864-882"
}

@article{backg_imaging_in_vivo,
    author = "Kerr, J.N.D. and Denk, W.",
    title = "Imaging in vivo: watching the brain in action",
    journal = "Nature reviews. Neuroscience",
    year = "2008",
    volume = "9",
    issue = "3",
    pages = "195-205"
}

@article{backg_in_vivo_2Ph,
    author = "Kobat, D. and Horton, N.G. and Xu, C.",
    title = "In vivo two-photon microscopy to 1.6-mm depth in mouse cortex",
    journal = "Journal of biomedical optics",
    year = "2011",
    volume = "16",
    issue = "10",
    pages = "106014"
}

@article{backg_1300_nm_3Ph,
    author = "Wang, T. and others",
    title = "Quantitative analysis of 1300-nm three-photon calcium imaging in the mouse brain",
    journal = "eLife",
    year = "2020",
    volume = "9",
}

@article{seeing_through_chaos,
    author = "Plöschner, M. and Tyc, T. and Čižmár, T.",
    title = "Seeing through chaos in multimode fibres",
    journal = "Nature photonics",
    year = "2015",
    volume = "9",
    issue = "8",
    pages = "529-535"
}

@book{backg_optical_elec,
    author = "Yariv, A.",
    title = "Optical electronics in modern communications",
    publisher = "Oxford University Press",
    year = "1997"
}

@article{backg_review_optical_fibres,
    author = "Addanki, S. and Amiri, I.S. and Yupapin, P.",
    title = "Review of optical fibres - introduction and applications in fiber lasers",
    journal = "Results in Physics",
    year = "2018",
    volume = "10",
    pages = "743-750"
}

@article{backg_graded_index_fibres,
    author = "Flaes, D.E.B. and others",
    title = "Robustness of Light-Transport Processes to Bending Deformations in Graded-Index Multimode Waveguides",
    journal = "Physical Review Letters",
    year = "2018",
    volume = "120",
    issue = "23",
    pages = "2333901"
}

@article{backg_calibration,
    author = "Plöschner, M. and others",
    title = "GPU accelerated toolbox for real-time beam-shaping in multimode fibres",
    journal = "Optics Express",
    year = "2014",
    volume = "22",
    issue = "3",
    pages = "2933-2947"
}

@article{backg_dynamic_bending_comp,
    author = "Farahi, S. and others",
    title = "Dynamic bending compensation while focusing through a multimode fiber",
    journal = "Optics Express",
    year = "2013",
    volume = "21",
    issue = "19",
    pages = "22504-22514"
}

@article{backg_design_flexible_endoscope,
    author = "Gu, R.Y. and Mahalati, R.N. and Kahn, J.M.",
    title = "Design of flexible multi-mode fiber endoscope",
    journal = "Optics Express",
    year = "2015",
    volume = "23",
    issue = "21",
    pages = "26905-26918"
}

@article{backg_metasurface_approx_bent_TM,
    author = "Gordon, G. and others",
    title = "Characterizing Optical Fiber Transmission Matrices Using Metasurface Reflector Stacks for Lensless Imaging without Distal Access",
    journal = "Physical Review X",
    year = "2019",
    volume = "9",
    issue = "4",
    pages = "041050"
}

@article{backg_bending_deep_learning,
    author = "Liu, Y. and others",
    title = "Bending recognition based on the analysis of fiber specklegrams using deep learning",
    journal = "Optics and laser technology",
    year = "2020",
    volume = "131",
    pages = "106424"
}

@article{backg_multimode_fibres_deep_learning,
    author = "Fan, P. and Zhao, T. and Su, L.",
    title = "Deep learning the high variability and randomness inside multimode fibers",
    journal = "Optics Express",
    year = "2019",
    volume = "27",
    issue = "15",
    pages = "20241-20258"
}

@article{sao_ao_astronomy,
    author = "Davies, R. and Kasper, M.",
    title = "Adaptive Optics for Astronomy",
    journal = "Annual review of astronomy and astrophysics",
    year = "2012",
    volume = "50",
    issue = "1",
    pages = "305-351"
}

@article{sao_ao_highres_imaging,
    author = "Hampson, K.M. and others",
    title = "Adaptive optics for high-resolution imaging",
    journal = "Nature Reviews Methods Primers",
    year = "2021",
    volume = "1",
    issue = "1",
    number = "68"
}

@article{sao_shack_hartman,
    author = "Primot, J.",
    title = "Theoretical description of Shack-Hartmann wave-front sensor",
    journal = "Optics Communications",
    year = "2003",
    volume = "222",
    issue = "1-6",
    pages = "81-92"
}

@article{sao_zernike,
    author = "Lakshminarayanan, V. and Fleck, A.",
    title = "Zernike polynomials: a guide",
    journal = "Journal of modern optics",
    year = "2011",
    volume = "58",
    issue = "7",
    pages = "545-561"
}

@article{sao_lattice_geometry,
    author = "Hu, Q. and others",
    title = "The Lattice Geometry of Walsh-Function-Based Adaptive Optics",
    journal = "Photonics",
    year = "2022",
    volume = "9",
    issue = "8",
    pages = "547"
}

@article{sao_hadamard_gen,
    author = "Pehlivanoğlu, M. K. and others",
    title = "Generalisation of Hadamard matrix to generate involutory MDS matrices for lightweight cryptography",
    journal = "IET Information Security",
    year = "2018",
    volume = "12",
    issue = "4",
    pages = "348-355"
}

@misc{sao_hadamard_wiki,
author = "Wikipedia",
url = "https://en.wikipedia.org/wiki/Hadamard_transform",
note = "Accessed on 20.08.2024"
}

@article{mem_effect_general_use,
    author = "Osnabrugge, G. and others",
    title = "Generalized optical memory effect",
    journal = "Optica",
    year = "2017",
    volume = "4",
    issue = "8",
    pages = "886-892"
}

@phdthesis{Bragg_master_thesis,
    author = "Zhang, J.",
    title = "Multimode optical fiber Bragg gratings: modeling, simulation and experiments",
    school = "McMaster University",
    year = "2004"
}

@misc{LP_generation_code,
    author = "Lee, Szu-Yu",
    url = "https://github.com/szuyul/MMF-simulation.git",
    note = "GitHub repository containing Matlab functions for generating the LP modes of an optical fibre. Last accessed on 12-10-2024"
}

@book{phase_shifting_interferometry,
    author = "Schwiegerling, Jim",
    title = "Optical Specification, Fabrication, and Testing",
    publisher = "SPIE Press",
    year = "2009"
}