Thesis_refs.bib

@article{Biggs2010,
    title = {{3D deconvolution microscopy}},
    year = {2010},
    journal = {Current Protocols in Cytometry},
    author = {Biggs, David S.C.},
    number = {SUPPL. 52},
    pages = {1--20},
    isbn = {0471142956},
    doi = {10.1002/0471142956.cy1219s52},
    issn = {19349297},
    keywords = {Confocal, Deblurring, Deconvolution, Fluorescence, Image restoration, Point spread function, Widefield}
}

@article{Galland2015,
    title = {{3D high-and super-resolution imaging using single-objective SPIM}},
    year = {2015},
    journal = {Nature Methods},
    author = {Galland, Remi and Grenci, Gianluca and Aravind, Ajay and Viasnoff, Virgile and Studer, Vincent and Sibarita, Jean Baptiste},
    number = {7},
    pages = {641--644},
    volume = {12},
    doi = {10.1038/nmeth.3402},
    issn = {15487105}
}

@article{Gao2014,
    title = {{3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy}},
    year = {2014},
    journal = {Nature Protocols},
    author = {Gao, Liang and Shao, Lin and Chen, Bi-Chang and Betzig, Eric},
    number = {5},
    pages = {1083--1101},
    volume = {9},
    url = {http://www.nature.com/doifinder/10.1038/nprot.2014.087},
    isbn = {1754-2189},
    doi = {10.1038/nprot.2014.087},
    issn = {1754-2189},
    pmid = {24722406}
}

@article{Tang2018,
    title = {{3D mesoscopic fluorescence tomography for imaging micro-distribution of antibody-photon absorber conjugates during near infrared photoimmunotherapy in vivo}},
    year = {2018},
    journal = {Journal of Controlled Release},
    author = {Tang, Qinggong and Nagaya, Tadanobu and Liu, Yi and Horng, Hannah and Lin, Jonathan and Sato, Kazuhide and Kobayashi, Hisataka and Chen, Yu},
    number = {December 2017},
    pages = {171--180},
    volume = {279},
    publisher = {Elsevier},
    url = {https://doi.org/10.1016/j.jconrel.2018.04.027},
    doi = {10.1016/j.jconrel.2018.04.027},
    issn = {18734995},
    keywords = {Enhanced permeability and retention effect, Fluorescence laminar optical tomography (FLOT), Photoimmunotherapy (PIT), Two-photon microscopy (TPM)}
}

@article{Zhu2018,
    title = {{3D NIR-II Molecular Imaging Distinguishes Targeted Organs with High-Performance NIR-II Bioconjugates}},
    year = {2018},
    journal = {Advanced Materials},
    author = {Zhu, Shoujun and Herraiz, Sonia and Yue, Jingying and Zhang, Mingxi and Wan, Hao and Yang, Qinglai and Ma, Zhuoran and Wang, Yan and He, Jiahuan and Antaris, Alexander L. and Zhong, Yeteng and Diao, Shuo and Feng, Yi and Zhou, Ying and Yu, Kuai and Hong, Guosong and Liang, Yongye and Hsueh, Aaron J. and Dai, Hongjie},
    number = {13},
    month = {3},
    pages = {1705799},
    volume = {30},
    url = {http://doi.wiley.com/10.1002/adma.201705799},
    doi = {10.1002/adma.201705799},
    issn = {09359648},
    keywords = {3D NIR-II molecular imaging, NIR-II confocal, high-performance NIR-II bioconjugate, live ovary imaging, multicolor live molecular imaging}
}

@article{Hang2019,
    title = {{A 3D High Resolution Generative Deep-learning Network for Fluorescence Microscopy Image}},
    year = {2019},
    journal = {bioRxiv},
    author = {Hang, Zhou and Shiwei, Li and Qing, Huang and Shijie, Liu and Tingwei, Quan and Cai, Ruiyao and Ert{\"{u}}rk, Ali and Shaoqun, Zeng and Ang, Z H O U H and Hiwei, L I S and Ing, H Uang Q and Hijie, L I U S and Ingwei, Q U A N T and Uiyao, R and Ai, C and Rk, A L I E R T Ü and Haoqun, Z E N G S},
    month = {1},
    pages = {743179},
    volume = {im},
    url = {http://biorxiv.org/content/early/2019/08/22/743179.abstract},
    doi = {10.1101/743179}
}

@article{Ariel2017,
    title = {{A beginner's guide to tissue clearing}},
    year = {2017},
    journal = {International Journal of Biochemistry and Cell Biology},
    author = {Ariel, Pablo},
    pages = {35--39},
    volume = {84},
    doi = {10.1016/j.biocel.2016.12.009},
    issn = {18785875},
    keywords = {Optical clearing, Organoids, Tissue clearing, Whole organ imaging, Whole organism imaging}
}

@article{Weissleder2001,
    title = {{A clearer vision for in vivo imaging}},
    year = {2001},
    journal = {Nature Biotechnology},
    author = {Weissleder, Ralph},
    number = {4},
    month = {4},
    pages = {316--317},
    volume = {19},
    url = {http://www.nature.com/articles/nbt0401_316},
    doi = {10.1038/86684},
    issn = {1087-0156},
    pmid = {11283581}
}

@article{Power2017,
    title = {{A guide to light-sheet fluorescence microscopy for multiscale imaging}},
    year = {2017},
    journal = {Nature Methods},
    author = {Power, Rory M. and Huisken, Jan},
    number = {4},
    pages = {360--373},
    volume = {14},
    url = {http://www.nature.com/doifinder/10.1038/nmeth.4224},
    doi = {10.1038/nmeth.4224},
    issn = {15487105},
    pmid = {28362435}
}

@article{Kerstens2019,
    title = {{A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples}},
    year = {2019},
    journal = {BMC Biology},
    author = {Kerstens, Axelle and Corthout, Nikky and Pavie, Benjamin and Huang, Zengjin and Vernaillen, Frank and Vande Velde, Greetje and Munck, Sebastian},
    number = {1},
    pages = {1--17},
    volume = {17},
    publisher = {BMC Biology},
    doi = {10.1186/s12915-018-0614-4},
    issn = {17417007},
    keywords = {3D imaging, Label-free, Mesoscale, Morphology, Opaque samples, Real color, Tomography}
}

@article{Wu2013,
    title = {{A light sheet based high throughput 3D-imaging flow cytometer for phytoplankton analysis}},
    year = {2013},
    journal = {Optics Express},
    author = {Wu, Jianglai and Li, Jianping and Chan, Robert K.Y.},
    number = {12},
    pages = {14474},
    volume = {21},
    doi = {10.1364/oe.21.014474}
}

@article{Fahrbach2010a,
    title = {{A line scanned light-sheet microscope with phase shaped self-reconstructing beams}},
    year = {2010},
    journal = {Optics Express},
    author = {Fahrbach, Florian O. and Rohrbach, Alexander},
    number = {23},
    pages = {24229},
    volume = {18},
    doi = {10.1364/oe.18.024229}
}

@article{Bosschaart2014,
    title = {{A literature review and novel theoretical approach on the optical properties of whole blood}},
    year = {2014},
    journal = {Lasers in Medical Science},
    author = {Bosschaart, Nienke and Edelman, Gerda J. and Aalders, Maurice C. G. and van Leeuwen, Ton G. and Faber, Dirk J.},
    number = {2},
    month = {3},
    pages = {453--479},
    volume = {29},
    url = {http://link.springer.com/10.1007/s10103-013-1446-7 http://www.ncbi.nlm.nih.gov/pubmed/24122065 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3953607},
    isbn = {1010301314},
    doi = {10.1007/s10103-013-1446-7},
    issn = {0268-8921},
    pmid = {24122065},
    keywords = {absorption coefficient, blood, optical properties, scattering, scattering coefficient, spectroscopy}
}

@inproceedings{Prahl1989,
    title = {{A Monte Carlo model of light propagation in tissue}},
    year = {1989},
    booktitle = {Dosimetry of Laser Radiation in Medicine and Biology},
    author = {Prahl, S. A.},
    editor = {Mueller, Gerhard J. and Sliney, David H. and Potter, Roy F.},
    number = {1989},
    month = {1},
    pages = {1030509},
    volume = {10305},
    url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.2283590},
    doi = {10.1117/12.2283590},
    issn = {1996756X}
}

@article{Torres-Garcia2017,
    title = {{A new Monte Carlo code for light transport in biological tissue}},
    year = {2017},
    journal = {Medical {\&} Biological Engineering {\&} Computing},
    author = {Torres-Garc{\'{i}}a, Eugenio and Oros-Pantoja, Rigoberto and Aranda-Lara, Liliana and Vieyra-Reyes, Patricia},
    pages = {649--655},
    publisher = {Medical {\&} Biological Engineering {\&} Computing},
    url = {http://link.springer.com/10.1007/s11517-017-1713-z},
    doi = {10.1007/s11517-017-1713-z},
    issn = {0140-0118},
    keywords = {Light transport, Tissue interaction, Tissue optical, ballistic photons, diffuse photons, light transport, properties, tissue interaction, tissue optical}
}

@article{Royer2018,
    title = {{A practical guide to adaptive light-sheet microscopy}},
    year = {2018},
    journal = {Nature Protocols},
    author = {Royer, Loïc A. and Lemon, William C. and Chhetri, Raghav K. and Keller, Philipp J.},
    number = {11},
    pages = {2462--2500},
    volume = {13},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41596-018-0043-4},
    doi = {10.1038/s41596-018-0043-4},
    issn = {17502799}
}

@article{Sandell2011,
    title = {{A review of in-vivo optical properties of human tissues and its impact on PDT}},
    year = {2011},
    journal = {Journal of Biophotonics},
    author = {Sandell, Julia L. and Zhu, Timothy C.},
    number = {11-12},
    month = {11},
    pages = {773--787},
    volume = {4},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/22167862 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3321368 http://doi.wiley.com/10.1002/jbio.201100062},
    isbn = {1864-0648},
    doi = {10.1002/jbio.201100062},
    issn = {1864063X},
    pmid = {22167862},
    arxivId = {arXiv:1011.1669v3},
    keywords = {Laser-tissue interaction, Light propagation, PDT, in-vivo optical properties}
}

@article{Sandell2011a,
    title = {{A review of in-vivo optical properties of human tissues and its impact on PDT}},
    year = {2011},
    journal = {Journal of Biophotonics},
    author = {Sandell, Julia L. and Zhu, Timothy C.},
    number = {11-12},
    pages = {773--787},
    volume = {4},
    isbn = {1864-0648},
    doi = {10.1002/jbio.201100062},
    issn = {1864063X},
    pmid = {22167862},
    arxivId = {arXiv:1011.1669v3},
    keywords = {Laser-tissue interaction, Light propagation, PDT, in-vivo optical properties}
}

@misc{Cheong1990,
    title = {{A review of the optical properties of biological tissues}},
    year = {1990},
    booktitle = {IEEE journal of quantum electronics},
    author = {Cheong, Wf F and Prahl, S.a. Sa and Welch, a.J. Aj},
    number = {12},
    pages = {2166--2185},
    volume = {26},
    url = {http://www.uta.edu/rfmems/N_041101/Reference/133.pdf%5Cnhttp://ieeexplore.ieee.org/xpl/freeabs_all.jsp?tp=&arnumber=64354&isnumber=2327},
    isbn = {0018-9197},
    doi = {10.1109/3.64354},
    issn = {00189197},
    pmid = {12778170},
    keywords = {Article{\_}TI pour en savoir plus}
}

@article{Azaripour2016,
    title = {{A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue}},
    year = {2016},
    journal = {Progress in Histochemistry and Cytochemistry},
    author = {Azaripour, Adriano and Lagerweij, Tonny and Scharfbillig, Christina and Jadczak, Anna Elisabeth and Willershausen, Brita and Van Noorden, Cornelis J.F.},
    number = {2},
    pages = {9--23},
    volume = {51},
    publisher = {Elsevier B.V.},
    url = {http://dx.doi.org/10.1016/j.proghi.2016.04.001},
    doi = {10.1016/j.proghi.2016.04.001},
    issn = {18732186},
    keywords = {3D histochemistry, 3D imaging, Clearing, Connective tissue, Extracellular matrix, Gingiva, Light-sheet microscopy, Skin}
}

@article{Azaripour2016a,
    title = {{A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue}},
    year = {2016},
    journal = {Progress in Histochemistry and Cytochemistry},
    author = {Azaripour, Adriano and Lagerweij, Tonny and Scharfbillig, Christina and Jadczak, Anna Elisabeth and Willershausen, Brita and Van Noorden, Cornelis J.F.},
    number = {2},
    pages = {9--23},
    volume = {51},
    publisher = {Elsevier B.V.},
    url = {http://dx.doi.org/10.1016/j.proghi.2016.04.001},
    doi = {10.1016/j.proghi.2016.04.001},
    issn = {18732186},
    keywords = {3D histochemistry, 3D imaging, Clearing, Connective tissue, Extracellular matrix, Gingiva, Light-sheet microscopy, Skin}
}

@article{Carr2018,
    title = {{Absorption by water increases fluorescence image contrast of biological tissue in the shortwave infrared}},
    year = {2018},
    journal = {Proceedings of the National Academy of Sciences},
    author = {Carr, Jessica A. and Aellen, Marianne and Franke, Daniel and So, Peter T. C. and Bruns, Oliver T. and Bawendi, Moungi G.},
    number = {37},
    month = {9},
    pages = {9080--9085},
    volume = {115},
    url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1803210115},
    doi = {10.1073/pnas.1803210115},
    issn = {0027-8424}
}

@article{Cabrera2018,
    title = {{Absorption Spectra of Ethanol and Water Using a Photothermal Lens Spectrophotometer}},
    year = {2018},
    journal = {Applied Spectroscopy},
    author = {Cabrera, Humberto and Akbar, Jehan and Korte, Dorota and Ashraf, Imrana and Ram{\'{i}}rez-Miquet, Evelio E. and Mar{\'{i}}n, Ernesto and Niemela, Joseph},
    number = {7},
    month = {7},
    pages = {1069--1073},
    volume = {72},
    url = {http://journals.sagepub.com/doi/10.1177/0003702818759073},
    doi = {10.1177/0003702818759073},
    issn = {0003-7028},
    keywords = {TLS, Thermal lens spectrometry, absorption of ethanol, absorption of water, vibration overtones}
}

@article{Tanzid2018,
    title = {{Absorption-enhanced imaging through scattering media using carbon black nano-particles: From visible to near infrared wavelengths}},
    year = {2018},
    journal = {Journal of Optics (United Kingdom)},
    author = {Tanzid, M. and Hogan, N.J. and Robatjazi, H. and Veeraraghavan, A. and Halas, N.J.},
    number = {5},
    volume = {20},
    publisher = {IOP Publishing},
    doi = {10.1088/2040-8986/aab3a2},
    issn = {20408986},
    keywords = {absorber, absorber particles, carbon black, imaging, light scattering, nanoparticles}
}

@article{Tanzid2016,
    title = {{Absorption-Induced Image Resolution Enhancement in Scattering Media}},
    year = {2016},
    journal = {ACS Photonics},
    author = {Tanzid, Mehbuba and Hogan, Nathaniel J. and Sobhani, Ali and Robatjazi, Hossein and Pediredla, Adithya K. and Samaniego, Adam and Veeraraghavan, Ashok and Halas, Naomi J.},
    number = {10},
    month = {10},
    pages = {1787--1793},
    volume = {3},
    url = {http://pubs.acs.org/doi/10.1021/acsphotonics.6b00558},
    doi = {10.1021/acsphotonics.6b00558},
    issn = {2330-4022},
    keywords = {absorption, diffusive transport, imaging, light scattering, resolution}
}

@article{Correia2015,
    title = {{Accelerated optical projection tomography applied to in vivo imaging of zebrafish}},
    year = {2015},
    journal = {PLoS ONE},
    author = {Correia, Teresa and Lockwood, Nicola and Kumar, Sunil and Yin, Jun and Ramel, Marie Christine and Andrews, Natalie and Katan, Matilda and Bugeon, Laurence and Dallman, Margaret J. and McGinty, James and Frankel, Paul and French, Paul M.W. and Arridge, Simon},
    number = {8},
    pages = {1--17},
    volume = {10},
    doi = {10.1371/journal.pone.0136213},
    issn = {19326203}
}

@article{Guo2019,
    title = {{Accelerating iterative deconvolution and multiview fusion by orders of magnitude}},
    year = {2019},
    journal = {bioRxiv},
    author = {Guo, Min and Li, Yue and Su, Yijun and Lambert, Talley and Nogare, Damian Dalle and Moyle, Mark W and Duncan, Leighton H and Ikegami, Richard and Santella, Anthony and Rey-Suarez, Ivan and Green, Daniel and Chen, Jiji and Vishwasrao, Harshad and Ganesan, Sundar and Waters, Jennifer C and Annunziata, Christina M and Hafner, Markus and Mohler, William A and Chitnis, Ajay B and Upadhyaya, Arpita and Usdin, Ted B and Bao, Zhirong and Col{\'{o}}n-Ramos, Daniel and Riviere, Patrick La and Liu, Huafeng and Wu, Yicong and Shroff, Hari and Guo, Min and Li, Yue and Su, Yijun and Lambert, Talley and Nogare, Damian Dalle and Moyle, Mark W and Duncan, Leighton H and Ikegami, Richard and Santella, Anthony and Rey-Suarez, Ivan and Green, Daniel and Chen, Jiji and Vishwasrao, Harshad and Ganesan, Sundar and Waters, Jennifer C and Annunziata, Christina M and Hafner, Markus and Mohler, William A and Chitnis, Ajay B and Upadhyaya, Arpita and Usdin, Ted B and Bao, Zhirong and Col{\'{o}}n-Ramos, Daniel and Riviere, Patrick La and Liu, Huafeng and Wu, Yicong and Shroff, Hari},
    month = {1},
    pages = {647370},
    url = {http://biorxiv.org/content/early/2019/05/23/647370.abstract},
    doi = {10.1101/647370},
    arxivId = {647370}
}

@article{Fang2012,
    title = {{Accelerating mesh-based Monte Carlo method on modern CPU architectures}},
    year = {2012},
    journal = {Biomedical Optics Express},
    author = {Fang, Qianqian and Kaeli, David R.},
    number = {12},
    pages = {3223},
    volume = {3},
    url = {https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223},
    doi = {10.1364/BOE.3.003223},
    issn = {2156-7085},
    pmid = {23243572}
}

@article{Cho2005,
    title = {{Accurate technique for complete geometric calibration of cone-beam computed tomography systems}},
    year = {2005},
    journal = {Medical Physics},
    author = {Cho, Youngbin and Moseley, Douglas J. and Siewerdsen, Jeffrey H. and Jaffray, David A.},
    number = {4},
    pages = {968--983},
    volume = {32},
    isbn = {0094-2405 (Print)},
    doi = {10.1118/1.1869652},
    issn = {00942405},
    pmid = {15895580},
    keywords = {Cone-beam computed tomography, Flat-panel detector, Geometric calibration, Image-guidance, Linear accelerator, Radiation therapy}
}

@article{Edelstein2014a,
    title = {{Advanced methods of microscope control using {$\mu$}Manager software}},
    year = {2014},
    journal = {Journal of Biological Methods},
    author = {Edelstein, Arthur D and Tsuchida, Mark A and Amodaj, Nenad and Pinkard, Henry and Vale, Ronald D and Stuurman, Nico},
    number = {2},
    month = {11},
    pages = {10},
    volume = {1},
    url = {http://www.jbmethods.org/jbm/article/view/36/28 http://www.jbmethods.org/jbm/article/view/36},
    doi = {10.14440/jbm.2014.36},
    issn = {2326-9901}
}

@article{Satat2016,
    title = {{All Photons Imaging Through Volumetric Scattering}},
    year = {2016},
    journal = {Scientific Reports},
    author = {Satat, Guy and Heshmat, Barmak and Raviv, Dan and Raskar, Ramesh},
    number = {September},
    pages = {1--8},
    volume = {6},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/srep33946},
    doi = {10.1038/srep33946},
    issn = {20452322}
}

@article{Yousuf2010,
    title = {{An Efficient Ring Artifact Reduction Method Based on Projection Data for Micro-CT Images}},
    year = {2009},
    journal = {Journal of Scientific Research},
    author = {Yousuf, M. A. and Asaduzzaman, M.},
    number = {1},
    pages = {37--45},
    volume = {2},
    url = {http://banglajol.info/index.php/JSR/article/view/2645},
    isbn = {2070-0245{\textbackslash}r2070-0237},
    doi = {10.3329/jsr.v2i1.2645},
    issn = {2070-0245},
    keywords = {10, 2010 jsr publications, 2070-0237, 2070-0245, 2645, 3329, all rights reserved, doi, filtered back-projection, flat-panel detector, issn, jsr, micro-ct, online, print, ring artifact correction, small animal imaging, v2i1}
}

@article{Kwan2006,
    title = {{An improved method for flat-field correction of flat panel x-ray detector.}},
    year = {2006},
    journal = {Medical physics},
    author = {Kwan, A L C and Seibert, J A and Boone, JM},
    pages = {391--393},
    volume = {33},
    isbn = {0094-2405 (Print){\textbackslash}n0094-2405 (Linking)},
    doi = {10.1118/1.2163388},
    issn = {00942405},
    pmid = {16532945}
}

@article{Rashid2012,
    title = {{An improved method for the removal of ring artifacts in high resolution CT imaging}},
    year = {2012},
    journal = {Eurasip Journal on Advances in Signal Processing},
    author = {Rashid, Sabrina and Lee, Soo Yeol and Hasan, Md Kamrul},
    number = {1},
    pages = {18},
    volume = {2012},
    publisher = {Springer Open Ltd},
    url = {http://asp.eurasipjournals.com/content/2012/1/93},
    isbn = {1687-6180},
    doi = {10.1186/1687-6180-2012-93},
    issn = {16876172},
    keywords = {Computed tomography, Flat panel detector, Ring artifact, Sinogram}
}

@article{Botcherby2008,
    title = {{An optical technique for remote focusing in microscopy}},
    year = {2008},
    journal = {Optics Communications},
    author = {Botcherby, E. J. and Ju{\v{s}}kaitis, R. and Booth, M. J. and Wilson, T.},
    number = {4},
    pages = {880--887},
    volume = {281},
    doi = {10.1016/j.optcom.2007.10.007},
    issn = {00304018},
    keywords = {High numerical aperture theory, Sectioning microscopy}
}

@article{Noo2000,
    title = {{Analytic method based on identification of ellipse parameters for scanner calibration in cone-beam tomography}},
    year = {2000},
    journal = {Physics in Medicine and Biology},
    author = {Noo, Fr??d??ric and Clackdoyle, Rolf and Mennessier, Catherine and White, Timothy A. and Roney, Timothy J.},
    number = {11},
    pages = {3489--3508},
    volume = {45},
    isbn = {0031-9155},
    doi = {10.1088/0031-9155/45/11/327},
    issn = {00319155},
    pmid = {11098919},
    arxivId = {0031-9155/00/113489}
}

@article{Liemert2017,
    title = {{Analytical solutions of the radiative transport equation for turbid and fluorescent layered media}},
    year = {2017},
    journal = {Scientific Reports},
    author = {Liemert, André and Reitzle, Dominik and Kienle, Alwin},
    number = {1},
    month = {12},
    pages = {3819},
    volume = {7},
    url = {http://www.nature.com/articles/s41598-017-02979-4},
    doi = {10.1038/s41598-017-02979-4},
    issn = {2045-2322}
}

@article{Albert-Smet2019,
    title = {{Applications of light-sheet microscopy in microdevices}},
    year = {2019},
    journal = {Frontiers in Neuroanatomy},
    author = {Albert-Smet, Ignacio and Marcos-Vidal, Asier and Vaquero, Juan José and Desco, Manuel and Mu{\~{n}}oz-Barrutia, Arrate and Ripoll, Jorge},
    number = {January},
    pages = {1--15},
    volume = {13},
    doi = {10.3389/fnana.2019.00001},
    issn = {16625129},
    keywords = {Cellular imaging, Light-sheet fluorescence microscopy, Microdevices, Microfluidics, SPIM}
}

@article{Albert-Smet2019a,
    title = {{Applications of light-sheet microscopy in microdevices}},
    year = {2019},
    journal = {Frontiers in Neuroanatomy},
    author = {Albert-Smet, I. and Marcos-Vidal, A. and Vaquero, J.J. and Desco, M. and Mu{\~{n}}oz-Barrutia, A. and Ripoll, J.},
    volume = {13},
    doi = {10.3389/fnana.2019.00001},
    issn = {16625129},
    keywords = {Cellular imaging, Light-sheet fluorescence microscopy, Microdevices, Microfluidics, SPIM}
}

@article{Rohrbach2009,
    title = {{Artifacts resulting from imaging in scattering media: a theoretical prediction}},
    year = {2009},
    journal = {Optics Letters},
    author = {Rohrbach, Alexander},
    number = {19},
    pages = {3041},
    volume = {34},
    doi = {10.1364/ol.34.003041},
    issn = {0146-9592}
}

@article{Glaser2016,
    title = {{Assessing the imaging performance of light sheet microscopies in highly scattering tissues}},
    year = {2016},
    journal = {Biomedical Optics Express},
    author = {Glaser, A. K. and Wang, Y. and Liu, J. T.C.},
    number = {2},
    pages = {454},
    volume = {7},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-7-2-454},
    isbn = {2156-7085},
    doi = {10.1364/BOE.7.000454},
    issn = {2156-7085},
    pmid = {26977355}
}

@article{Vollmer2017a,
    title = {{Atmospheric optics in the near infrared}},
    year = {2017},
    journal = {Appl. Opt.},
    author = {Vollmer, Michael and Shaw, Joseph A},
    number = {19},
    pages = {G145--G155},
    volume = {56},
    url = {http://ao.osa.org/abstract.cfm?URI=ao-56-19-G145},
    doi = {10.1364/AO.56.00G145},
    issn = {0003-6935},
    keywords = {Atmospheric optics, Ice crystal phenomena, Infrared imaging, Mirages and refraction}
}

@article{Mayer2018,
    title = {{Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM}},
    year = {2018},
    journal = {Light: Science and Applications},
    author = {Mayer, Jürgen and Robert-Moreno, Alexandre and Sharpe, James and Swoger, Jim},
    number = {1},
    volume = {7},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41377-018-0068-z},
    doi = {10.1038/s41377-018-0068-z},
    issn = {20477538}
}

@article{Patino2008,
    title = {{Autofluorescence of Mycobacteria as a Tool for Detection of Mycobacterium tuberculosis}},
    year = {2008},
    journal = {Journal of Clinical Microbiology},
    author = {Patino, S. and Alamo, L. and Cimino, M. and Casart, Y. and Bartoli, F. and Garcia, M. J. and Salazar, L.},
    number = {10},
    pages = {3296--3302},
    volume = {46},
    url = {http://jcm.asm.org/cgi/doi/10.1128/JCM.02183-07},
    isbn = {2125041715},
    doi = {10.1128/JCM.02183-07},
    issn = {0095-1137},
    pmid = {18836064}
}

@article{Logan2018,
    title = {{Automated high-throughput light-sheet fluorescence microscopy of larval zebrafish}},
    year = {2018},
    journal = {PLoS ONE},
    author = {Logan, Savannah L. and Dudley, Christopher and Baker, Ryan P. and Taormina, Michael J. and Hay, Edouard A. and Parthasarathy, Raghuveer},
    number = {11},
    pages = {1--14},
    volume = {13},
    isbn = {1111111111},
    doi = {10.1371/journal.pone.0198705},
    issn = {19326203}
}

@article{Zhu2012,
    title = {{Automated motion correction for in vivo optical projection tomography}},
    year = {2012},
    journal = {IEEE Transactions on Medical Imaging},
    author = {Zhu, Shouping and Dong, Di and Birk, Udo Jochen and Rieckher, Matthias and Tavernarakis, Nektarios and Qu, Xiaochao and Liang, Jimin and Tian, Jie and Ripoll, Jorge},
    number = {7},
    pages = {1358--1371},
    volume = {31},
    publisher = {IEEE},
    doi = {10.1109/TMI.2012.2188836},
    issn = {02780062},
    keywords = {Helgason-Ludwig consistency condition (HLCC), motion correction, optical projection tomography (OPT)}
}

@article{Dong2013,
    title = {{Automated recovery of the center of rotation in optical projection tomography in the presence of scattering}},
    year = {2013},
    journal = {IEEE journal of biomedical and health informatics},
    author = {Dong, Di and Zhu, Shouping and Qin, Chenghu and Kumar, Varsha and Stein, Jens V. and Oehler, Stephan and Savakis, Charalambos and Tian, Jie and Ripoll, Jorge},
    number = {1},
    month = {1},
    pages = {198--204},
    volume = {17},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/23008264},
    doi = {10.1109/TITB.2012.2219588},
    issn = {2168-2208},
    pmid = {23008264},
    keywords = {Center of rotation, Optical projection tomography (OPT), Parallel reconstruction, Scattering}
}

@article{Dong2013a,
    title = {{Automated Recovery of the Center of Rotation in Optical Projection Tomography in the Presence of Scattering}},
    year = {2013},
    journal = {IEEE Journal of Biomedical and Health Informatics},
    author = {{Di Dong} and {Shouping Zhu} and {Chenghu Qin} and Kumar, Varsha and Stein, Jens V. and Oehler, Stephan and Savakis, Charalambos and {Jie Tian} and Ripoll, Jorge},
    number = {1},
    month = {1},
    pages = {198--204},
    volume = {17},
    publisher = {IEEE},
    url = {http://ieeexplore.ieee.org/document/6307870/},
    doi = {10.1109/TITB.2012.2219588},
    issn = {2168-2194},
    keywords = {Center of rotation, Optical projection tomography (OPT), Parallel reconstruction, Scattering}
}

@article{Jia2019,
    title = {{Axial resolution enhancement of light-sheet microscopy by double scanning of Bessel beam and its complementary beam}},
    year = {2019},
    journal = {Journal of Biophotonics},
    author = {Jia, Hao and Yu, Xianghua and Yang, Yanlong and Zhou, Xing and Yan, Shaohui and Liu, Chao and Lei, Ming and Yao, Baoli},
    number = {1},
    pages = {1--10},
    volume = {12},
    doi = {10.1002/jbio.201800094},
    issn = {18640648},
    keywords = {Bessel beam, laser beam shaping, light-sheet fluorescence microscopy, three-dimensional microscopy}
}

@article{Brezner2015,
    title = {{Ballistic imaging of biological media with collimated illumination and focal plane detection}},
    year = {2015},
    journal = {Journal of Biomedical Optics},
    author = {Brezner, Barak and Cahen, Sarah and Glasser, Ziv and Sternklar, Shmuel and Granot, Er’el},
    number = {7},
    pages = {076006},
    volume = {20},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.20.7.076006},
    doi = {10.1117/1.JBO.20.7.076006},
    issn = {1083-3668},
    keywords = {14, 16, 2015, 4, accepted for publication jun, coherence imaging, diffusive medium, optical imaging, paper 150229rr received apr, published online jul, tissue imaging, tissue optics, turbid medium}
}

@article{Mie1908,
    title = {{Beitr{\"{a}}ge zur Optik tr{\"{u}}ber Medien, speziell kolloidaler Metall{\"{o}}sungen}},
    year = {1908},
    journal = {Annalen der Physik},
    author = {Mie, Gustav},
    number = {3},
    pages = {377--445},
    volume = {330},
    url = {http://doi.wiley.com/10.1002/andp.19083300302},
    doi = {10.1002/andp.19083300302},
    issn = {00033804}
}

@article{Tosheva2019,
    title = {{Between life and death : reducing phototoxicity in Super-Resolution Microscopy}},
    year = {2019},
    journal = {Preprints},
    author = {Tosheva, Kalina L and Yuan, Yue and Pereira, Pedro Matos and Culley, Siân and Henriques, Ricardo},
    number = {August},
    doi = {10.20944/preprints201908.0319.v1}
}

@article{Horl2019,
    title = {{BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples}},
    year = {2019},
    journal = {Nature Methods},
    author = {H{\"{o}}rl, David and Rojas Rusak, Fabio and Preusser, Friedrich and Tillberg, Paul and Randel, Nadine and Chhetri, Raghav K. and Cardona, Albert and Keller, Philipp J. and Harz, Hartmann and Leonhardt, Heinrich and Treier, Mathias and Preibisch, Stephan},
    number = {9},
    pages = {870--874},
    volume = {16},
    doi = {10.1038/s41592-019-0501-0},
    issn = {1548-7091}
}

@article{Weigert2018,
    title = {{Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy}},
    year = {2018},
    journal = {PLOS Computational Biology},
    author = {Weigert, Martin and Subramanian, Kaushikaram and Bundschuh, Sebastian T. and Myers, Eugene W. and Kreysing, Moritz},
    editor = {Jbabdi, Saad},
    number = {4},
    month = {4},
    pages = {e1006079},
    volume = {14},
    url = {http://dx.plos.org/10.1371/journal.pcbi.1006079},
    isbn = {1111111111},
    doi = {10.1371/journal.pcbi.1006079},
    issn = {1553-7358}
}

@article{Diao2015a,
    title = {{Biological imaging without autofluorescence in the second near-infrared region}},
    year = {2015},
    journal = {Nano Research},
    author = {Diao, Shuo and Hong, Guosong and Antaris, Alexander L. and Blackburn, Jeffrey L. and Cheng, Kai and Cheng, Zhen and Dai, Hongjie},
    number = {9},
    month = {9},
    pages = {3027--3034},
    volume = {8},
    url = {http://link.springer.com/10.1007/s12274-015-0808-9},
    doi = {10.1007/s12274-015-0808-9},
    issn = {1998-0124},
    keywords = {autofluorescence, fluorescence imaging, nanotechnology, second near-infrared}
}

@article{Ripoll2000,
    title = {{Boundary conditions for light propagation in diffusive media with nonscattering regions}},
    year = {2000},
    journal = {Journal of the Optical Society of America. A, Optics, image science, and vision},
    author = {Ripoll, Jorge and Nieto-Vesperinas, M. and Arridge, Simon R. and Dehghani, Hamid},
    number = {9},
    pages = {1671--81},
    volume = {17},
    doi = {10.1364/JOSAA.17.001671}
}

@article{Hoyer2016,
    title = {{Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT}},
    year = {2016},
    journal = {Proceedings of the National Academy of Sciences of the United States of America},
    author = {Hoyer, Patrick and De Medeiros, Gustavo and Bal{\'{a}}zs, Bálint and Norlin, Nils and Besir, Christina and Hanne, Janina and Kr{\"{a}}usslich, Hans Georg and Engelhardt, Johann and Sahl, Steffen J. and Hell, Stefan W. and Hufnagel, Lars},
    number = {13},
    pages = {3442--3446},
    volume = {113},
    doi = {10.1073/pnas.1522292113},
    issn = {10916490},
    keywords = {3d, Light-sheet microscopy, Live-cell imaging, Optical nanoscopy, Resolft}
}

@article{Schmidgunst2007,
    title = {{Calibration model of a dual gain flat panel detector for 2D and 3D x-ray imaging}},
    year = {2007},
    journal = {Medical Physics},
    author = {Schmidgunst, C. and Ritter, D. and Lang, E.},
    number = {9},
    pages = {3649--3664},
    volume = {34},
    doi = {10.1118/1.2760024},
    issn = {00942405},
    pmid = {17926969},
    keywords = {Cone beam CT, Dual dynamic range, FD calibration, FD conditioning, Flat panel detector (FD), Lag}
}

@phdthesis{ParaisoLabora2013,
    title = {{Calibration of a C-arm X-ray system for its use in tomography}},
    year = {2014},
    booktitle = {IFMBE Proceedings},
    author = {de Molina, C. and Pascau, J. and Desco, M. and Abella, M.},
    month = {2},
    pages = {245--248},
    volume = {41},
    url = {http://e-archivo.uc3m.es/handle/10016/17029},
    school = {Universidad Carlos III de Madrid},
    isbn = {9783319008455},
    doi = {10.1007/978-3-319-00846-2{\_}61},
    issn = {16800737},
    keywords = {C-arm, Calibration, Mechanical misalignments, Tomography, X-ray},
    language = {eng}
}

@article{DiDomenico2018,
    title = {{Cancellation of Bessel beam side lobes for high-contrast light sheet microscopy}},
    year = {2018},
    journal = {Scientific Reports},
    author = {Di Domenico, Giuseppe and Ruocco, Giancarlo and Colosi, Cristina and DelRe, Eugenio and Antonacci, Giuseppe},
    number = {1},
    month = {12},
    pages = {17178},
    volume = {8},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41598-018-35006-1 http://www.nature.com/articles/s41598-018-35006-1},
    doi = {10.1038/s41598-018-35006-1},
    issn = {2045-2322}
}

@article{Hong2015,
    title = {{Carbon Nanomaterials for Biological Imaging and Nanomedicinal Therapy}},
    year = {2015},
    journal = {Chemical Reviews},
    author = {Hong, Guosong and Diao, Shuo and Antaris, Alexander L. and Dai, Hongjie},
    number = {19},
    pages = {10816--10906},
    volume = {115},
    doi = {10.1021/acs.chemrev.5b00008},
    issn = {0009-2665}
}

@article{Moding2013,
    title = {{Changes in Primary Mouse Sarcomas}},
    year = {2014},
    journal = {Int J Radiat Oncol Biol Phys},
    author = {Ghaghada, Ketan and Ph, D and Johnson, G Allan and Ph, D and Kirsch, David G and Ph, D},
    number = {5},
    pages = {1353--1359},
    volume = {85},
    url = {http://www.sciencedirect.com/science/article/pii/S0360301612036358},
    doi = {10.1016/j.ijrobp.2012.09.027.Dual}
}

@phdthesis{Hirshburg2009,
    title = {{Chemical agent induced reduction of skin light scattering}},
    year = {2009},
    author = {Hirshburg, Jason M},
    number = {December},
    pages = {120},
    url = {http://search.proquest.com/docview/305118127?accountid=14725%5Cnhttp://openurl.uquebec.ca:9003/uqtr?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&genre=dissertations+%26+theses&sid=ProQ:ProQuest+Dissertations+%26+Theses+Global&atitle=&},
    school = {Texas A{\&}M University, USA},
    isbn = {9781109679076},
    pmid = {305118127},
    keywords = {0541:Biomedical engineering, Applied sciences, Biomedical engineering, Clearing agents, Collagen, Light scattering, Skin}
}

@article{Richardson2015,
    title = {{Clarifying Tissue Clearing}},
    year = {2015},
    journal = {Cell},
    author = {Richardson, Douglas S and Lichtman, Jeff W},
    number = {2},
    month = {7},
    pages = {246--257},
    volume = {162},
    publisher = {Elsevier},
    url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867415008375},
    doi = {10.1016/j.cell.2015.06.067},
    issn = {00928674}
}

@article{Anas2011,
    title = {{Classification of ring artifacts for their effective removal using type adaptive correction schemes}},
    year = {2011},
    journal = {Computers in Biology and Medicine},
    author = {Anas, Emran Mohammad Abu and Lee, Soo Yeol and Kamrul Hasan, M. D.},
    number = {6},
    pages = {390--401},
    volume = {41},
    publisher = {Elsevier},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/21513928},
    doi = {10.1016/j.compbiomed.2011.03.018},
    issn = {00104825},
    pmid = {21513928},
    keywords = {Digital X-ray detectors, Micro-CT, Ring artifacts, Ring classification, Ring detection, Type adaptive correction}
}

@article{Silvestry2016,
    title = {{Clearing of fixed tissue: a review from a microscopist’s perspective}},
    year = {2016},
    journal = {Journal of Biomedical Optics},
    author = {Silvestri, Ludovico and Costantini, Irene and Sacconi, Leonardo and Pavone, Francesco Saverio},
    number = {8},
    month = {3},
    pages = {081205},
    volume = {21},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.21.8.081205},
    doi = {10.1117/1.JBO.21.8.081205},
    issn = {1083-3668},
    keywords = {ghput microscopy, light-sheet microscopy, paper 150878ssvr received dec, published online mar, tissue clearing, tissue transformation, two-photon microscopy}
}

@article{Royer2015,
    title = {{ClearVolume: open-source live 3D visualization for light-sheet microscopy}},
    year = {2015},
    journal = {Nature Methods},
    author = {Royer, Loic A and Weigert, Martin and G{\"{u}}nther, Ulrik and Maghelli, Nicola and Jug, Florian and Sbalzarini, Ivo F and Myers, Eugene W},
    number = {6},
    month = {6},
    pages = {480--481},
    volume = {12},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.3372 http://www.nature.com/articles/nmeth.3372},
    doi = {10.1038/nmeth.3372},
    issn = {1548-7091}
}

@article{Spott2000,
    title = {{Collimated light sources in the diffusion approximation}},
    year = {2000},
    journal = {Applied Optics},
    author = {Spott, Thorsten and Svaasand, Lars O},
    number = {34},
    month = {12},
    pages = {6453},
    volume = {39},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/18354660 https://www.osapublishing.org/abstract.cfm?URI=ao-39-34-6453},
    doi = {10.1364/AO.39.006453},
    issn = {0003-6935},
    pmid = {18354660}
}

@inproceedings{Schaul2009,
    title = {{Color image dehazing using the near-infrared}},
    year = {2009},
    booktitle = {2009 16th IEEE International Conference on Image Processing (ICIP)},
    author = {Schaul, Lex and Fredembach, Clement and Susstrunk, Sabine},
    month = {11},
    pages = {1629--1632},
    publisher = {IEEE},
    url = {http://ieeexplore.ieee.org/document/5413700/},
    isbn = {978-1-4244-5653-6},
    doi = {10.1109/ICIP.2009.5413700},
    keywords = {Edge-preserving filters, Haze, Image fusion, Multi-resolution, Near-infrared, Scattering}
}

@inproceedings{Fredembach2008,
    title = {{Colouring the Near-Infrared}},
    year = {2008},
    booktitle = {Proceedings of the IS{\&}T/SID 16th Color Imaging Conference},
    author = {Fredembach, Clement and S{\"{u}}sstrunk, Sabine},
    pages = {176--182},
    url = {http://en.scientificcommons.org/38366658}
}

@inproceedings{Star1989,
    title = {{Comparing the P3-approximation with diffusion theory and with Monte Carlo calculations of light propagation in a slab geometry}},
    year = {1989},
    booktitle = {Dosimetry of Laser Radiation in Medicine and Biology},
    author = {Star, W. M.},
    editor = {Mueller, Gerhard J. and Sliney, David H. and Potter, Roy F.},
    number = {January 1989},
    month = {1},
    pages = {103050C},
    volume = {10305},
    url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.2283593},
    doi = {10.1117/12.2283593},
    issn = {1996756X}
}

@article{Trull2018,
    title = {{Comparison of image reconstruction techniques for optical projection tomography}},
    year = {2018},
    journal = {Applied Optics},
    author = {Trull, Anna K. and van der Horst, Jelle and van Vliet, Lucas J. and Kalkman, Jeroen},
    number = {8},
    pages = {1874},
    volume = {57},
    publisher = {The Optical Society},
    url = {http://dx.doi.org/10.1364/AO.57.001874},
    doi = {10.1364/ao.57.001874},
    issn = {1559-128X}
}

@article{Liu2019,
    title = {{Comparison of optical projection tomography and light-sheet fluorescence microscopy}},
    year = {2019},
    journal = {Journal of Microscopy},
    author = {Liu, A. and Xiao, W. and Li, R. and Liu, L. and Chen, L.},
    number = {1},
    pages = {3--10},
    volume = {275},
    doi = {10.1111/jmi.12796},
    issn = {13652818},
    keywords = {Light-sheet fluorescence microscopy, optical projection tomography, spatial resolution}
}

@article{Prell2009,
    title = {{Comparison of ring artifact correction methods for flat-detector CT}},
    year = {2009},
    journal = {Physics in Medicine and Biology},
    author = {Prell, Daniel and Kyriakou, Yiannis and Kalender, Willi A.},
    number = {12},
    pages = {3881--3895},
    volume = {54},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/19491452},
    isbn = {0031-9155 (Print)},
    doi = {10.1088/0031-9155/54/12/018},
    issn = {00319155},
    pmid = {19491452},
    keywords = {Algorithms, Artifacts, Computer-Assist, Radiographic Image Enhancement, Radiographic Image Enhancement: methods, Radiographic Image Interpretation, Reproducibility of Results, Sensitivity and Specificity, Tomography, X-Ray Computed, X-Ray Computed: instrumentation, X-Ray Intensifying Screens}
}

@article{Anas2011b,
    title = {{Comparison of ring artifact removal methods using flat panel detector based CT images}},
    year = {2011},
    journal = {BioMedical Engineering Online},
    author = {Abu Anas, Emran M. and Kim, Jae G. and Lee, Soo Y. and Hasan, Md K.},
    number = {1},
    pages = {72},
    volume = {10},
    publisher = {BioMed Central Ltd},
    url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3201024&tool=pmcentrez&rendertype=abstract},
    isbn = {7210118614},
    doi = {10.1186/1475-925X-10-72},
    issn = {1475925X},
    pmid = {21846411},
    keywords = {Algorithms, Artifacts, Calibration, Computer-Assisted, Computer-Assisted: instrumentati, Computer-Assisted: methods, Cone-Beam Computed Tomography, Cone-Beam Computed Tomography: instrumentation, Cone-Beam Computed Tomography: methods, Image Processing}
}

@article{Sinha2019,
    title = {{Comparison of time- and angular-domain scatter rejection in mesoscopic optical projection tomography: a simulation study}},
    year = {2019},
    journal = {Biomedical Optics Express},
    author = {Sinha, L. and Massanes, F. and Torres, V. C. and Li, C. and Tichauer, K. M. and Brankov, J. G.},
    number = {2},
    pages = {747},
    volume = {10},
    doi = {10.1364/boe.10.000747},
    issn = {2156-7085}
}

@article{Turner2005,
    title = {{Complete-angle projection diffuse optical tomography by use of early photons}},
    year = {2005},
    journal = {Optics Letters},
    author = {Turner, Gordon M. and Zacharakis, Giannis and Soubret, Antoine and Ripoll, Jorge and Ntziachristos, Vasilis},
    number = {4},
    month = {2},
    pages = {409},
    volume = {30},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-30-4-409},
    doi = {10.1364/OL.30.000409},
    issn = {0146-9592},
    keywords = {turner2005}
}

@book{Hsieh2009,
    title = {{Computed Tomography: Principles, Design, Artifacts, and Recent Advances}},
    year = {2015},
    author = {Hsieh, Jiang},
    publisher = {SPIE PRESS},
    url = {http://ebooks.spiedigitallibrary.org/book.aspx?doi=10.1117/3.2197756},
    isbn = {9781628418255},
    doi = {10.1117/3.2197756}
}

@incollection{Edelstein2010,
    title = {{Computer Control of Microscopes Using µManager}},
    year = {2010},
    booktitle = {Current Protocols in Molecular Biology},
    author = {Edelstein, Arthur and Amodaj, Nenad and Hoover, Karl and Vale, Ron and Stuurman, Nico},
    number = {SUPPL. 92},
    month = {10},
    publisher = {John Wiley {\&} Sons, Inc.},
    url = {http://doi.wiley.com/10.1002/0471142727.mb1420s92},
    address = {Hoboken, NJ, USA},
    doi = {10.1002/0471142727.mb1420s92},
    issn = {19343639},
    pmid = {20890901},
    keywords = {Automation, Cross platform, Digital imaging, Fluorescence microscopy, ImageJ, Micro-Manager, Microscopy, Multi-dimensional acquisition, Open source, {$\mu$}Manager}
}

@article{Ionita2008,
    title = {{Cone-beam micro-CT system based on LabVIEW software}},
    year = {2008},
    journal = {Journal of Digital Imaging},
    author = {Ionita, Ciprian N. and Hoffmann, Keneth R. and Bednarek, Daniel R. and Chityala, Ravishankar and Rudin, Stephen},
    number = {3},
    month = {9},
    pages = {296--305},
    volume = {21},
    url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2553273&tool=pmcentrez&rendertype=abstract},
    isbn = {08971889},
    doi = {10.1007/s10278-007-9024-9},
    issn = {08971889},
    pmid = {17333411},
    keywords = {Cone-beam micro-CT, Graphical user interface, LabVIEW, Software design}
}

@article{Silvestri2012,
    title = {{Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain}},
    year = {2012},
    journal = {Optics Express},
    author = {Silvestri, L. and Bria, A. and Sacconi, L. and Iannello, G. and Pavone, F. S.},
    number = {18},
    pages = {20582},
    volume = {20},
    doi = {10.1364/oe.20.020582}
}

@article{Medeiros2015,
    title = {{Confocal multiview light-sheet microscopy}},
    year = {2015},
    journal = {Nature Communications},
    author = {Medeiros, Gustavo De and Norlin, Nils and Gunther, Stefan and Albert, Marvin and Panavaite, Laura and Fiuza, Ulla-Maj and Peri, Francesca and Hiiragi, Takashi and Krzic, Uros and Hufnagel, Lars},
    number = {1},
    month = {12},
    pages = {8881},
    volume = {6},
    publisher = {Nature Publishing Group},
    url = {http://www.nature.com/articles/ncomms9881},
    doi = {10.1038/ncomms9881},
    issn = {2041-1723}
}

@article{Dwyer2006,
    title = {{Confocal reflectance theta line scanning microscope for imaging human skin in vivo}},
    year = {2006},
    journal = {Optics Letters},
    author = {Dwyer, Peter J. and DiMarzio, Charles A. and Zavislan, James M. and Fox, William J. and Rajadhyaksha, Milind},
    number = {7},
    month = {4},
    pages = {942},
    volume = {31},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-31-7-942},
    isbn = {1557528071},
    doi = {10.1364/OL.31.000942},
    issn = {0146-9592}
}

@article{Soloviev2006,
    title = {{Consideration of a spread-out source in problems of near-infrared optical tomography}},
    year = {2006},
    journal = {Applied Optics},
    author = {Soloviev, Vadim Y and Krasnosselskaia, Lada V},
    number = {19},
    pages = {4765},
    volume = {45},
    doi = {10.1364/AO.45.004765},
    issn = {0003-6935},
    pmid = {16799692}
}

@article{Davis2019,
    title = {{Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish}},
    year = {2019},
    journal = {Journal of Biophotonics},
    author = {Davis, Samuel P. X. and Kumar, Sunil and Alexandrov, Yuriy and Bhargava, Ajay and da Silva Xavier, Gabriela and Rutter, Guy A. and Frankel, Paul and Sahai, Erik and Flaxman, Seth and French, Paul M. W. and McGinty, James},
    month = {8},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.201900128},
    doi = {10.1002/jbio.201900128},
    issn = {1864-063X}
}

@article{tarvainen2005,
    title = {{Coupled radiative transfer equation and diffusion approximation model for photon migration in turbid medium with low-scattering and non-scattering regions}},
    year = {2005},
    journal = {Physics in Medicine and Biology},
    author = {Tarvainen, Tanja and Vauhkonen, Marko and Kolehmainen, Ville and Arridge, Simon R and Kaipio, Jari P},
    number = {20},
    month = {10},
    pages = {4913--4930},
    volume = {50},
    url = {http://stacks.iop.org/0031-9155/50/i=20/a=011?key=crossref.74f5502574215fc9febfcdcf99b6df40},
    doi = {10.1088/0031-9155/50/20/011},
    issn = {0031-9155}
}

@article{Tsuboi2018,
    title = {{Critical Review—Water-Soluble Near-Infrared Fluorophores Emitting over 1000 nm and Their Application to In Vivo Imaging in the Second Optical Window (1000–1400 nm)}},
    year = {2018},
    journal = {ECS Journal of Solid State Science and Technology},
    author = {Tsuboi, Setsuko and Yamada, Sayumi and Nakane, Yuko and Sakata, Takao and Yasuda, Hidehiro and Jin, Takashi},
    number = {1},
    pages = {R3093-R3101},
    volume = {7},
    url = {http://jss.ecsdl.org/lookup/doi/10.1149/2.0141801jss},
    doi = {10.1149/2.0141801jss},
    issn = {2162-8769}
}

@article{Sarder2006,
    title = {{Deconvolution methods for 3-D fluorescence microscopy images}},
    year = {2006},
    journal = {IEEE Signal Processing Magazine},
    author = {Sarder, Pinaki and Nehorai, Arye},
    number = {3},
    pages = {32--45},
    volume = {23},
    publisher = {IEEE},
    doi = {10.1109/MSP.2006.1628876},
    issn = {10535888}
}

@article{Dean2015,
    title = {{Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy}},
    year = {2015},
    journal = {Biophysical Journal},
    author = {Dean, Kevin M. and Roudot, Philippe and Welf, Erik S. and Danuser, Gaudenz and Fiolka, Reto},
    number = {12},
    pages = {2807--2815},
    volume = {108},
    publisher = {The Authors},
    url = {http://dx.doi.org/10.1016/j.bpj.2015.05.013},
    doi = {10.1016/j.bpj.2015.05.013},
    issn = {15420086}
}

@article{Truong2011,
    title = {{Deep and fast live imaging with two-photon scanned light-sheet microscopy}},
    year = {2011},
    journal = {Nature Methods},
    author = {Truong, Thai V. and Supatto, Willy and Koos, David S. and Choi, John M. and Fraser, Scott E.},
    number = {9},
    month = {9},
    pages = {757--760},
    volume = {8},
    url = {http://www.nature.com/articles/nmeth.1652},
    doi = {10.1038/nmeth.1652},
    issn = {1548-7091}
}

@article{Pediredla2016,
    title = {{Deep Imaging in Scattering Media with Single Photon Selective Plane Illumination Microscopy (SPIM)}},
    year = {2016},
    author = {Pediredla, Adithya Kumar and Zhang, Shizheng and Avants, Ben and Ye, Fan and Nagayama, Shin and Chen, Ziying and Kemere, Caleb and Robinson, Jacob and Veeraraghavan, Ashok},
    number = {April},
    url = {http://arxiv.org/abs/1604.06965%0Ahttp://dx.doi.org/10.1117/1.JBO.21.12.126009},
    isbn = {1083-3668},
    doi = {10.1117/1.JBO.21.12.126009},
    issn = {1083-3668},
    pmid = {27997019},
    arxivId = {1604.06965}
}

@article{Welsher2011,
    title = {{Deep-tissue anatomical imaging of mice using carbon nanotube fluorophores in the second near-infrared window.}},
    year = {2011},
    journal = {Proceedings of the National Academy of Sciences of the United States of America},
    author = {Welsher, Kevin and Sherlock, Sarah P. and Dai, Hongjie},
    number = {22},
    month = {5},
    pages = {8943--8},
    volume = {108},
    url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1014501108 http://www.ncbi.nlm.nih.gov/pubmed/21576494 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3107273},
    doi = {10.1073/pnas.1014501108},
    issn = {1091-6490},
    pmid = {21576494},
    arxivId = {1105.3536}
}

@article{Elaloufi2003,
    title = {{Definition of the diffusion coefficient in scattering and absorbing media}},
    year = {2003},
    journal = {Journal of the Optical Society of America A},
    author = {Elaloufi, Rachid and Carminati, Rémi and Greffet, Jean-Jacques},
    number = {4},
    month = {4},
    pages = {678},
    volume = {20},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-20-4-678},
    isbn = {0465015409},
    doi = {10.1364/JOSAA.20.000678},
    issn = {1084-7529},
    pmid = {12683494}
}

@article{Rieckher2018,
    title = {{Demonstrating Improved Multiple Transport-Mean-Free-Path Imaging Capabilities of Light Sheet Microscopy in the Quantification of Fluorescence Dynamics}},
    year = {2018},
    journal = {Biotechnology Journal},
    author = {Rieckher, Matthias and Psycharakis Daniele Ancora, Stylianos E. and Liapis, Evangelos and Zacharopoulos, Athanasios and Ripoll, Jorge and Tavernarakis, Nektarios and Zacharakis, Giannis},
    number = {1},
    pages = {1--7},
    volume = {13},
    doi = {10.1002/biot.201700419},
    issn = {18607314},
    keywords = {caenorhabditis elegans, cancer cell spheroids, light sheet fluorescence microscopy, optical projection tomography, phase retrieved tomography}
}

@article{Wong2013,
    title = {{Design and Implementation of a Custom Built Optical Projection Tomography System}},
    year = {2013},
    journal = {PLoS ONE},
    author = {Wong, Michael D. and Dazai, Jun and Walls, Johnathon R. and Gale, Nicholas W. and Henkelman, R. Mark},
    number = {9},
    volume = {8},
    doi = {10.1371/journal.pone.0073491},
    issn = {19326203}
}

@article{Choi2005,
    title = {{Determination of chemical agent optical clearing potential using in vitro human skin}},
    year = {2005},
    journal = {Lasers in Surgery and Medicine},
    author = {Choi, Bernard and Tsu, Laura and Chen, Eric and Ishak, Teresa S. and Iskandar, Sarah M. and Chess, Samuel and Nelson, J. Stuart},
    number = {2},
    month = {2},
    pages = {72--75},
    volume = {36},
    url = {http://doi.wiley.com/10.1002/lsm.20116},
    doi = {10.1002/lsm.20116},
    issn = {0196-8092},
    keywords = {Dermatology, Glycerol, Hyperosmotic agents, Port wine stains, Scattering}
}

@article{Zhou2008,
    title = {{Development of phase-contrast X-ray imaging techniques and potential medical applications}},
    year = {2008},
    journal = {Physica Medica},
    author = {Zhou, Shu Ang and Brahme, Anders},
    number = {3},
    pages = {129--148},
    volume = {24},
    isbn = {1120-1797 (Print){\textbackslash}r1120-1797 (Linking)},
    doi = {10.1016/j.ejmp.2008.05.006},
    issn = {11201797},
    pmid = {18602852},
    keywords = {Phase-contrast, Phase-contrast stereography, Soft tissue contrast, X-ray imaging}
}

@article{Laroche2019,
    title = {{Development of sample-adaptable holders for lightsheet microscopy}},
    year = {2019},
    journal = {Frontiers in Neuroanatomy},
    author = {Laroche, Thierry and Burri, Olivier and Dubey, Lalit Kumar and Seitz, Arne},
    number = {March},
    pages = {1--8},
    volume = {13},
    doi = {10.3389/fnana.2019.00026},
    issn = {16625129},
    keywords = {Clearing, Custom, Fluorescence, Imaging, Lightsheet microscopy, Lymph node, Microscopy, Sample preparation}
}

@article{Hoffmann2019,
    title = {{Diffractive oblique plane microscopy}},
    year = {2019},
    journal = {Optica},
    author = {Hoffmann, Maximilian and Judkewitz, Benjamin},
    number = {9},
    pages = {1166},
    volume = {6},
    doi = {10.1364/optica.6.001166}
}

@article{Taylor2018,
    title = {{Diffuse light-sheet microscopy for stripe-free calcium imaging of neural populations}},
    year = {2018},
    journal = {Journal of Biophotonics},
    author = {Taylor, Michael A. and Vanwalleghem, Gilles C. and Favre-Bulle, Itia A. and Scott, Ethan K.},
    number = {12},
    pages = {1--9},
    volume = {11},
    doi = {10.1002/jbio.201800088},
    issn = {18640648},
    keywords = {calcium imaging, fluorescence, light-sheet microscope, zebrafish}
}

@article{Pattelli2016,
    title = {{Diffusive light transport in semitransparent media}},
    year = {2016},
    journal = {Physical Review A},
    author = {Pattelli, Lorenzo and Mazzamuto, Giacomo and Wiersma, Diederik S. and Toninelli, Costanza},
    number = {4},
    pages = {1--6},
    volume = {94},
    doi = {10.1103/PhysRevA.94.043846},
    issn = {24699934},
    arxivId = {1509.04030}
}

@article{Elaloufi2004,
    title = {{Diffusive-to-ballistic transition in dynamic light transmission through thin scattering slabs: a radiative transfer approach.}},
    year = {2004},
    journal = {Journal of the Optical Society of America. A, Optics, image science, and vision},
    author = {Elaloufi, Rachid and Carminati, Rémi and Greffet, Jean-Jacques},
    number = {8},
    pages = {1430--1437},
    volume = {21},
    doi = {10.1364/JOSAA.21.001430},
    issn = {1084-7529},
    pmid = {15330470}
}

@article{Chan2017,
    title = {{Direct inversion algorithm for focal plane scanning optical projection tomography}},
    year = {2017},
    journal = {Biomedical Optics Express},
    author = {Chan, Kevin G. and Liebling, Michael},
    number = {11},
    pages = {5349},
    volume = {8},
    doi = {10.1364/boe.8.005349},
    issn = {2156-7085}
}

@article{Chan2017b,
    title = {{Direct inversion algorithm for focal plane scanning optical projection tomography}},
    year = {2017},
    journal = {Biomedical Optics Express},
    author = {Chan, Kevin G. and Liebling, Michael},
    number = {11},
    month = {11},
    pages = {5349},
    volume = {8},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-8-11-5349},
    doi = {10.1364/BOE.8.005349},
    issn = {2156-7085}
}

@article{Durduran1997,
    title = {{Does the photon-diffusion coefficient depend on absorption ?}},
    year = {1997},
    journal = {Journal of the Optical Society of America. A, Optics, image science, and vision},
    author = {Durduran, T and Yodh, A G and Chance, B},
    number = {12},
    pages = {3358--3365},
    volume = {14},
    doi = {10.1364/JOSAA.14.003358},
    keywords = {light propagation in tissues, multiple scattering, photon diffusion, photon migration, tomographic imaging, transport and diffusion equation}
}

@article{Badea2012a,
    title = {{Dual-energy micro-CT of the rodent lung}},
    year = {2012},
    journal = {AJP: Lung Cellular and Molecular Physiology},
    author = {Badea, C. T. and Guo, X. and Clark, D. and Johnston, S. M. and Marshall, C. D. and Piantadosi, C. A.},
    number = {10},
    month = {5},
    pages = {L1088-L1097},
    volume = {302},
    url = {http://ajplung.physiology.org/cgi/doi/10.1152/ajplung.00359.2011},
    isbn = {1522-1504 (Electronic){\textbackslash}r1040-0605 (Linking)},
    doi = {10.1152/ajplung.00359.2011},
    issn = {1040-0605},
    pmid = {22427526},
    keywords = {Animals, Computer Simulation, Computer-Assisted, Contrast Media, Contrast Media: chemistry, Image Processing, Imaging, In Vitro Techniques, Lung, Lung: physiology, Lung: radiography, Mice, Positive-Pressure Respiration, Rats, Reproducibility of Results, Respiration, Respiratory-Gated Imaging Techniques, Respiratory-Gated Imaging Techniques: instrumentat, Respiratory-Gated Imaging Techniques: methods, Sensitivity and Specificity, Sprague-Dawley, Three-Dimensional, Tidal Volume, Tidal Volume: physiology, Tomography, X-Ray Computed, X-Ray Computed: instrumentation, X-Ray Computed: methods}
}

@article{Cho2010,
    title = {{Dual-Energy Technique at Low Tube Voltages for Small Animal Imaging}},
    year = {2010},
    journal = {Tsinghua Science and Technology},
    author = {Cho, Seungryong and Sidky, Emil Y. and Bian, Junguo and Pan, Xiaochuan},
    number = {1},
    pages = {79--86},
    volume = {15},
    url = {http://www.sciencedirect.com/science/article/pii/S1007021410700134},
    isbn = {1007-0214 (Print){\textbackslash}r1007-0214 (Linking)},
    doi = {10.1016/S1007-0214(10)70013-4},
    issn = {10070214},
    pmid = {20589233},
    keywords = {dual-energy, specimen radiography, spectrum estimation}
}

@article{Kumar2014,
    title = {{Dual-view plane illumination microscopy for rapid and spatially isotropic imaging}},
    year = {2014},
    journal = {Nature Protocols},
    author = {Kumar, Abhishek and Wu, Yicong and Christensen, Ryan and Chandris, Panagiotis and Gandler, William and McCreedy, Evan and Bokinsky, Alexandra and Col{\'{o}}n-Ramos, Daniel A and Bao, Zhirong and McAuliffe, Matthew and Rondeau, Gary and Shroff, Hari},
    number = {11},
    month = {11},
    pages = {2555--2573},
    volume = {9},
    url = {http://www.nature.com/articles/nprot.2014.172},
    doi = {10.1038/nprot.2014.172},
    issn = {1754-2189},
    keywords = {microbial communities, microbial ecology, microbiota, multivariate, ordination, statistics}
}

@article{Berndt2018,
    title = {{Dynamic and non-contact 3D sample rotation for microscopy}},
    year = {2018},
    journal = {Nature Communications},
    author = {Berndt, Frederic and Shah, Gopi and Power, Rory M. and Brugu{\'{e}}s, Jan and Huisken, Jan},
    number = {1},
    pages = {1--7},
    volume = {9},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41467-018-07504-3},
    doi = {10.1038/s41467-018-07504-3},
    issn = {20411723}
}

@article{Freund1988,
    title = {{Dynamic multiple scattering: Ballistic photons and the breakdown of the photon-diffusion approximation}},
    year = {1988},
    journal = {Physical Review Letters},
    author = {Freund, Isaac and Kaveh, Moshe and Rosenbluh, Michael},
    number = {12},
    pages = {1130--1133},
    volume = {60},
    doi = {10.1103/PhysRevLett.60.1130},
    issn = {00319007},
    pmid = {10037949}
}

@article{Hohn2015,
    title = {{Dynamics of a Volvox embryo turning itself inside out}},
    year = {2015},
    journal = {Physical Review Letters},
    author = {H{\"{o}}hn, Stephanie and Honerkamp-Smith, Aurelia R. and Haas, Pierre A. and Trong, Philipp Khuc and Goldstein, Raymond E.},
    number = {17},
    pages = {1--5},
    volume = {114},
    doi = {10.1103/PhysRevLett.114.178101},
    issn = {10797114}
}

@article{Jahr2016,
    title = {{eduSPIM: Light Sheet Microscopy in the Museum}},
    year = {2016},
    journal = {PLOS ONE},
    author = {Jahr, Wiebke and Schmid, Benjamin and Weber, Michael and Huisken, Jan},
    editor = {Gilestro, Giorgio F},
    number = {8},
    month = {8},
    pages = {e0161402},
    volume = {11},
    publisher = {Public Library of Science},
    url = {http://dx.plos.org/10.1371/journal.pone.0161402},
    doi = {10.1371/journal.pone.0161402},
    issn = {1932-6203}
}

@article{Glasser2013,
    title = {{Effect of measurement on the ballistic–diffusive transition in turbid media}},
    year = {2013},
    journal = {Journal of Biomedical Optics},
    author = {Glasser, Ziv and Yaroshevsky, Andre and Barak, Bavat and Granot, Er’el and Sternklar, Shmuel},
    number = {10},
    pages = {106006},
    volume = {18},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.18.10.106006},
    doi = {10.1117/1.JBO.18.10.106006},
    issn = {1083-3668},
    keywords = {2013, 3, 5, 8, 9, accepted for publication sep, biomedical optics, collimators, diffusion, illumination, online oct, paper 130330rr received may, published, revised manuscript received sep, scattering, tissues}
}

@article{Preibisch2014,
    title = {{Efficient bayesian-based multiview deconvolution}},
    year = {2014},
    journal = {Nature Methods},
    author = {Preibisch, Stephan and Amat, Fernando and Stamataki, Evangelia and Sarov, Mihail and Singer, Robert H. and Myers, Eugene and Tomancak, Pavel},
    number = {6},
    pages = {645--648},
    volume = {11},
    doi = {10.1038/nmeth.2929},
    issn = {15487105}
}

@article{Xu2004,
    title = {{Electric field Monte Carlo simulation of polarized light propagation in turbid media}},
    year = {2004},
    journal = {Optics Express},
    author = {Xu, Min},
    number = {26},
    month = {12},
    pages = {6530},
    volume = {12},
    url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-12-26-6530},
    doi = {10.1364/OPEX.12.006530},
    issn = {1094-4087}
}

@article{Nolte2018,
    title = {{Enabling second harmonic generation as a contrast mechanism for optical projection tomography (OPT) and scanning laser optical tomography (SLOT)}},
    year = {2018},
    journal = {Biomedical Optics Express},
    author = {Nolte, Lena and Antonopoulos, Georgios C. and R{\"{a}}misch, Lisa and Heisterkamp, Alexander and Ripken, Tammo and Meyer, Heiko},
    number = {6},
    month = {6},
    pages = {2627},
    volume = {9},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-9-6-2627},
    doi = {10.1364/BOE.9.002627},
    issn = {2156-7085}
}

@article{Yang2019a,
    title = {{Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution}},
    year = {2019},
    journal = {Nature Methods},
    author = {Yang, Bin and Chen, Xingye and Wang, Yina and Feng, Siyu and Pessino, Veronica and Stuurman, Nico and Cho, Nathan H. and Cheng, Karen W. and Lord, Samuel J. and Xu, Linfeng and Xie, Dan and Mullins, R. Dyche and Leonetti, Manuel D. and Huang, Bo},
    number = {6},
    month = {6},
    pages = {501--504},
    volume = {16},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41592-019-0401-3 http://www.nature.com/articles/s41592-019-0401-3},
    doi = {10.1038/s41592-019-0401-3},
    issn = {1548-7091}
}

@article{Pampaloni2015a,
    title = {{Erratum to: Light sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues [Cell Tissue Res, DOI 10.1007/s00441-015-2144-5]}},
    year = {2015},
    journal = {Cell and Tissue Research},
    author = {Pampaloni, Francesco and Chang, Bo Jui and Stelzer, Ernst H.K.},
    number = {1},
    pages = {265},
    volume = {362},
    doi = {10.1007/s00441-015-2247-z},
    issn = {14320878}
}

@article{Ford2011,
    title = {{Estimation of CT cone-beam geometry using a novel method insensitive to phantom fabrication inaccuracy: Implications for isocenter localization accuracy}},
    year = {2011},
    journal = {Medical Physics},
    author = {Chetley Ford, J. and Zheng, Dandan and Williamson, Jeffrey F.},
    number = {6},
    pages = {2829--2840},
    volume = {38},
    isbn = {0094-2405 (Print){\textbackslash}r0094-2405 (Linking)},
    doi = {10.1118/1.3589130},
    issn = {00942405},
    pmid = {21815358},
    keywords = {cone-beam computed tomography, fiducial phantom, geometric calibration, image-guidance, isocenter, radiation therapy}
}

@article{Wan2018,
    title = {{Evaluation of seven optical clearing methods in mouse brain}},
    year = {2018},
    journal = {Neurophotonics},
    author = {Wan, Peng and Zhu, Jingtan and Xu, Jianyi and Li, Yusha and Yu, Tingting and Zhu, Dan},
    number = {03},
    pages = {1},
    volume = {5},
    doi = {10.1117/1.nph.5.3.035007},
    keywords = {2, 2018, 21, 25, accepted for publication jun, clearing capability, fluorescence retention, imaging depth, mouse brain, paper 18018ssr received apr, published online aug, size change, tissue optical clearing}
}

@article{Huisken2007,
    title = {{Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM)}},
    year = {2007},
    journal = {Optics Letters},
    author = {Huisken, Jan and Stainier, Didier Y. R.},
    number = {17},
    pages = {2608},
    volume = {32},
    doi = {10.1364/ol.32.002608},
    issn = {0146-9592}
}

@article{Ripoll2005,
    title = {{Experimental determination of photon propagation in highly absorbing and scattering media}},
    year = {2005},
    journal = {Journal of the Optical Society of America. A, Optics, image science, and vision},
    author = {Ripoll, Jorge and Yessayan, Doreen and Zacharakis, Giannis and Ntziachristos, Vasilis},
    number = {3},
    month = {3},
    pages = {546--51},
    volume = {22},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/15770993 https://www.osapublishing.org/abstract.cfm?URI=josaa-22-3-546},
    doi = {10.1364/JOSAA.22.000546},
    issn = {1084-7529},
    pmid = {15770993},
    keywords = {Animals, Anisotropy, Computer-Assisted, Computer-Assisted: methods, Connective Tissue, Connective Tissue: anatomy {\&} histology, Connective Tissue: physiology, Humans, Image Interpretation, Light, Optical, Optical: methods, Photometry, Photometry: methods, Photons, Radiation, Scattering, Tomography}
}

@article{Hemmer2016,
    title = {{Exploiting the biological windows: current perspectives on fluorescent bioprobes emitting above 1000 nm}},
    year = {2016},
    journal = {Nanoscale Horizons},
    author = {Hemmer, Eva and Benayas, Antonio and L{\'{e}}gar{\'{e}}, François and Vetrone, Fiorenzo},
    number = {3},
    pages = {168--184},
    volume = {1},
    url = {http://xlink.rsc.org/?DOI=C5NH00073D},
    doi = {10.1039/C5NH00073D},
    issn = {2055-6756}
}

@article{VanAarle2016,
    title = {{Fast and flexible X-ray tomography using the ASTRA toolbox}},
    year = {2016},
    journal = {Optics express},
    author = {van Aarle, Wim and Palenstijn, Willem Jan and Cant, Jeroen and Janssens, Eline and Bleichrodt, Folkert and Dabravolski, Andrei and De Beenhouwer, Jan and Joost Batenburg, K. and Sijbers, Jan},
    number = {22},
    month = {10},
    pages = {25129--25147},
    volume = {24},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-24-22-25129 http://www.ncbi.nlm.nih.gov/pubmed/27828452},
    doi = {10.1364/OE.24.025129},
    issn = {1094-4087},
    pmid = {27828452}
}

@article{Duocastella2017,
    title = {{Fast Inertia-Free Volumetric Light-Sheet Microscope}},
    year = {2017},
    journal = {ACS Photonics},
    author = {Duocastella, Martí and Sancataldo, Giuseppe and Saggau, Peter and Ramoino, Paola and Bianchini, Paolo and Diaspro, Alberto},
    number = {7},
    month = {7},
    pages = {1797--1804},
    volume = {4},
    publisher = {UTC},
    url = {https://pubs.acs.org/sharingguidelines https://pubs.acs.org/doi/10.1021/acsphotonics.7b00382},
    doi = {10.1021/acsphotonics.7b00382},
    issn = {2330-4022},
    keywords = {acouto-optic devices, flow cytometry, light-sheet microscopy, three-dimensional microscopy}
}

@article{Krstajic2007,
    title = {{Fast laser scanning optical-CT apparatus for 3D radiation dosimetry}},
    year = {2007},
    journal = {Physics in Medicine and Biology},
    author = {Krstaji{\'{c}}, Nikola and Doran, Simon J.},
    number = {11},
    month = {6},
    pages = {N257-N263},
    volume = {52},
    url = {http://stacks.iop.org/0031-9155/52/i=11/a=N01?key=crossref.67ee74478e38f6e198143caf2859c513},
    doi = {10.1088/0031-9155/52/11/N01},
    issn = {0031-9155}
}

@article{Holekamp2008,
    title = {{Fast Three-Dimensional Fluorescence Imaging of Activity in Neural Populations by Objective-Coupled Planar Illumination Microscopy}},
    year = {2008},
    journal = {Neuron},
    author = {Holekamp, Terrence F. and Turaga, Diwakar and Holy, Timothy E.},
    number = {5},
    month = {3},
    pages = {661--672},
    volume = {57},
    url = {https://linkinghub.elsevier.com/retrieve/pii/S0896627308000445},
    doi = {10.1016/j.neuron.2008.01.011},
    issn = {08966273},
    keywords = {SYSBIO, SYSNEURO}
}

@article{Keller2010,
    title = {{Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy}},
    year = {2010},
    journal = {Nature Methods},
    author = {Keller, Philipp J. and Schmidt, Annette D. and Santella, Anthony and Khairy, Khaled and Bao, Zhirong and Wittbrodt, Joachim and Stelzer, Ernst H.K.},
    number = {8},
    pages = {637--642},
    volume = {7},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.1476},
    doi = {10.1038/nmeth.1476},
    issn = {15487091}
}

@article{Sakhalkar2008,
    title = {{Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation}},
    year = {2007},
    journal = {Medical Physics},
    author = {Sakhalkar, H. S. and Oldham, M.},
    number = {1},
    month = {12},
    pages = {101--111},
    volume = {35},
    url = {http://doi.wiley.com/10.1118/1.2804616},
    doi = {10.1118/1.2804616},
    issn = {00942405},
    keywords = {3D dosimetry, Optical-CT, PRESAGE™, Quality assurance, Radiation, Telecentric}
}

@article{Schindelin2012,
    title = {{Fiji: an open-source platform for biological-image analysis}},
    year = {2012},
    journal = {Nature Methods},
    author = {Schindelin, Johannes and Arganda-Carreras, Ignacio and Frise, Erwin and Kaynig, Verena and Longair, Mark and Pietzsch, Tobias and Preibisch, Stephan and Rueden, Curtis and Saalfeld, Stephan and Schmid, Benjamin and Tinevez, Jean-Yves and White, Daniel James and Hartenstein, Volker and Eliceiri, Kevin and Tomancak, Pavel and Cardona, Albert},
    number = {7},
    month = {7},
    pages = {676--682},
    volume = {9},
    url = {http://www.nature.com/articles/nmeth.2019},
    doi = {10.1038/nmeth.2019},
    issn = {1548-7091},
    pmid = {22743772}
}

@article{Seibert1998,
    title = {{Flat-field correction technique for digital detectors}},
    year = {1998},
    journal = {Proc. SPIE},
    author = {Seibert, J A and Boone, J M and Lindfors, K K},
    number = {February},
    pages = {348--354},
    volume = {3336},
    url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=942278},
    isbn = {2036392598},
    doi = {10.1117/12.317034},
    issn = {0277786X},
    pmid = {18366567},
    arxivId = {arXiv:1503.07998v1},
    keywords = {1, conventional flat-field implementation, detective quantum efficiency, digital detectors, digital detectors are prone, digital mammography biopsy system, fixed-point, flat field correction, image optimization, image quality, in ccd or flat-, noise power spectrum, noise sources, stationary, such as pixel dropouts, to several sources of}
}

@article{Sancataldo2019,
    title = {{Flexible multi-beam light-sheet fluorescence microscope for live imaging without striping artifacts}},
    year = {2019},
    journal = {Frontiers in Neuroanatomy},
    author = {Sancataldo, Giuseppe and Gavryusev, Vladislav and de Vito, Giuseppe and Turrini, Lapo and Locatelli, Massimiliano and Fornetto, Chiara and Tiso, Natascia and Vanzi, Francesco and Silvestri, Ludovico and Pavone, Francesco Saverio},
    number = {February},
    pages = {1--8},
    volume = {13},
    doi = {10.3389/fnana.2019.00007},
    issn = {16625129},
    keywords = {Acousto optic deflector, Brain imaging, Fast volumetric imaging, Light-sheet fluorescence microscopy, Striping artifacts, Zebrafish}
}

@article{Diao2015,
    title = {{Fluorescence Imaging In Vivo at Wavelengths beyond 1500 nm}},
    year = {2015},
    journal = {Angewandte Chemie International Edition},
    author = {Diao, Shuo and Blackburn, Jeffrey L. and Hong, Guosong and Antaris, Alexander L. and Chang, Junlei and Wu, Justin Z. and Zhang, Bo and Cheng, Kai and Kuo, Calvin J. and Dai, Hongjie},
    number = {49},
    month = {12},
    pages = {14758--14762},
    volume = {54},
    url = {http://doi.wiley.com/10.1002/anie.201507473},
    doi = {10.1002/anie.201507473},
    issn = {14337851},
    pmid = {26460151},
    arxivId = {1502.02775},
    keywords = {cancer, fluorescence, imaging agents, nanotechnology, near infrared}
}

@article{Ntziachristos2003,
    title = {{Fluorescence imaging with near-infrared light: new technological advances that enable in vivo molecular imaging.}},
    year = {2003},
    journal = {European radiology},
    author = {Ntziachristos, Vasilis and Bremer, Christoph and Weissleder, Ralph},
    number = {1},
    pages = {195--208},
    volume = {13},
    isbn = {0938-7994},
    doi = {10.1007/s00330-002-1524-x},
    issn = {0938-7994},
    pmid = {12541130},
    keywords = {fluorescence, in vivo, molecular imaging, near infrared}
}

@article{Schotland2007,
    title = {{Fourier-Laplace structure of the inverse scattering problem for the radiative transport equation}},
    year = {2007},
    journal = {Inverse Problems and Imaging},
    author = {Schotland, John C and Markel, Vadim A},
    number = {1},
    month = {1},
    pages = {181--188},
    volume = {1},
    url = {http://www.aimsciences.org/journals/displayArticles.jsp?paperID=2091},
    doi = {10.3934/ipi.2007.1.181},
    issn = {1930-8337},
    keywords = {and phrases, by the nsf grants, dms-0554100 and eec-0615857, inverse scattering, radiative transport, this research was supported}
}

@article{Bucci1994,
    title = {{From Wave Theory to Ray Optics}},
    year = {1994},
    journal = {IEEE Antennas and Propagation Magazine},
    author = {Bucci, Ovidio M. and Pelosi, Giuseppe},
    number = {4},
    pages = {35--42},
    volume = {36},
    doi = {10.1109/74.317769},
    issn = {10459243}
}

@article{Koskela2019,
    title = {{Gaussian Light Model in Brightfield Optical Projection Tomography}},
    year = {2019},
    journal = {Scientific Reports},
    author = {Koskela, Olli and Montonen, Toni and Belay, Birhanu and Figueiras, Edite and Pursiainen, Sampsa and Hyttinen, Jari},
    number = {1},
    month = {12},
    pages = {13934},
    volume = {9},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41598-019-50469-6 http://www.nature.com/articles/s41598-019-50469-6},
    doi = {10.1038/s41598-019-50469-6},
    issn = {2045-2322}
}

@article{Yao2015,
    title = {{Generalized mesh-based Monte Carlo for wide-field illumination and detection via mesh retessellation}},
    year = {2016},
    journal = {Biomedical Optics Express},
    author = {Yao, Ruoyang and Intes, Xavier and Fang, Qianqian},
    number = {1},
    pages = {171},
    volume = {7},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-7-1-171},
    doi = {10.1364/BOE.7.000171},
    issn = {2156-7085},
    keywords = {Light propagation in tissues, Photon migration, Spatial light modulators, Time-resolved imaging, Turbid media}
}

@article{Ogura2019,
    title = {{Generation of a subdiffraction-limit light sheet with micrometer-order thickness using a computer-generated hologram}},
    year = {2019},
    journal = {Optical Review},
    author = {Ogura, Yusuke and Kanai, Ryoko and Tanida, Jun},
    number = {0123456789},
    publisher = {Springer Japan},
    url = {https://doi.org/10.1007/s10043-019-00523-5},
    isbn = {0123456789},
    doi = {10.1007/s10043-019-00523-5},
    issn = {1340-6000},
    keywords = {Light sheet,Computer-generated hologram,Subdiffrac, computer-generated hologram, cylindrical lens, light sheet, spatial light modulator, subdiffraction limit}
}

@article{Daly2008,
    title = {{Geometric calibration of a mobile C-arm for intraoperative cone-beam CT}},
    year = {2008},
    journal = {Medical Physics},
    author = {Daly, M. J. and Siewerdsen, J. H. and Cho, Y. B. and Jaffray, D. A. and Irish, J. C.},
    number = {5},
    pages = {2124--2136},
    volume = {35},
    isbn = {0094-2405 (Print){\textbackslash}n0094-2405 (Linking)},
    doi = {10.1118/1.2907563},
    issn = {00942405},
    pmid = {18561688},
    keywords = {C-arm, Cone-beam CT, Flat-panel detector, Geometric calibration, Image-guided interventions, Imaging performance, Intraoperative imaging}
}

@article{Ntziachristos2010,
    title = {{Going deeper than microscopy: The optical imaging frontier in biology}},
    year = {2010},
    journal = {Nature Methods},
    author = {Ntziachristos, Vasilis},
    number = {8},
    month = {8},
    pages = {603--614},
    volume = {7},
    publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
    url = {http://dx.doi.org/10.1038/nmeth.1483},
    doi = {10.1038/nmeth.1483},
    issn = {15491676},
    pmid = {20676081},
    arxivId = {arXiv:1011.1669v3}
}

@article{Jia2011,
    title = {{GPU-based fast Monte Carlo simulation for radiotherapy dose calculation}},
    year = {2011},
    journal = {Physics in Medicine and Biology},
    author = {Jia, Xun and Gu, Xuejun and Graves, Yan Jiang and Folkerts, Michael and Jiang, Steve B},
    number = {22},
    month = {11},
    pages = {7017--7031},
    volume = {56},
    url = {http://stacks.iop.org/0031-9155/56/i=22/a=002?key=crossref.72a55fefdfb66cc52777ad13b2cc63c1},
    doi = {10.1088/0031-9155/56/22/002},
    issn = {0031-9155}
}

@article{Pfeiffer2013,
    title = {{Grating-based X-ray phase contrast for biomedical imaging applications}},
    year = {2013},
    journal = {Zeitschrift fur Medizinische Physik},
    author = {Pfeiffer, Franz and Herzen, Julia and Willner, Marian and Chabior, Michael and Auweter, Sigrid and Reiser, Maximilian and Bamberg, Fabian},
    number = {3},
    month = {9},
    pages = {176--185},
    volume = {23},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/23453793},
    isbn = {1876-4436},
    doi = {10.1016/j.zemedi.2013.02.002},
    issn = {09393889},
    pmid = {23453793},
    keywords = {Grating interferometry, Phase-contrast tomography, X-ray imaging, X-ray phase contrast}
}

@article{Reynaud2014,
    title = {{Guide to light-sheet microscopy for adventurous biologists}},
    year = {2014},
    journal = {Nature Methods},
    author = {Reynaud, Emmanuel G. and Peychl, Jan and Huisken, Jan and Tomancak, Pavel},
    number = {1},
    pages = {30--34},
    volume = {12},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.3222},
    doi = {10.1038/nmeth.3222},
    issn = {15487105}
}

@book{Pawley2006Confocal,
    title = {{Handbook Of Biological Confocal Microscopy}},
    year = {2006},
    author = {Pawley, James B.},
    publisher = {Springer US},
    url = {http://link.springer.com/10.1007/978-0-387-45524-2},
    address = {Boston, MA},
    isbn = {978-0-387-25921-5},
    doi = {10.1007/978-0-387-45524-2}
}

@article{Arranz2013,
    title = {{Helical optical projection tomography}},
    year = {2013},
    journal = {Optics Express},
    author = {Arranz, Alicia and Dong, Di and Zhu, Shouping and Rudin, Markus and Tsatsanis, Christos and Tian, Jie and Ripoll, Jorge},
    number = {22},
    pages = {25912},
    volume = {21},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-21-22-25912},
    doi = {10.1364/OE.21.025912},
    issn = {1094-4087},
    pmid = {24216818},
    keywords = {Algorithms, Animals, Computer-Assisted, Computer-Assisted: instrumen, Equipment Design, Equipment Failure Analysis, Fluorescence microscopy, Image Interpretation, Image reconstruction techniques, Imaging, Light propagation in tissues, Mice, Microscopy, Microscopy: instrumentation, Reproducibility of Results, Sensitivity and Specificity, Three, Three-Dimensional, Three-Dimensional: instrumentation, Whole Body Imaging, Whole Body Imaging: instrumentation, dimensional microscopy}
}

@article{Arranz2013a,
    title = {{Helical optical projection tomography}},
    year = {2013},
    journal = {Optics Express},
    author = {Arranz, Alicia and Dong, Di and Zhu, Shouping and Rudin, Markus and Tsatsanis, Christos and Tian, Jie and Ripoll, Jorge},
    number = {22},
    month = {11},
    pages = {25912},
    volume = {21},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-21-22-25912},
    doi = {10.1364/OE.21.025912},
    issn = {1094-4087}
}

@article{Martelli2018,
    title = {{Heuristic model for ballistic photon detection in collimated transmittance measurements}},
    year = {2018},
    journal = {Optics Express},
    author = {Martelli, Fabrizio and Binzoni, Tiziano},
    number = {2},
    month = {1},
    pages = {744},
    volume = {26},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-26-2-744},
    doi = {10.1364/OE.26.000744},
    issn = {1094-4087}
}

@article{Fei2012,
    title = {{High dynamic range optical projection tomography (HDR-OPT)}},
    year = {2012},
    journal = {Optics Express},
    author = {Fei, Peng and Yu, Zhilong and Wang, Xu and Lu, Peter J and Fu, Yusi and He, Zi and Xiong, Jingwei and Huang, Yanyi},
    number = {8},
    month = {4},
    pages = {8824},
    volume = {20},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/22513593 https://www.osapublishing.org/oe/abstract.cfm?uri=oe-20-8-8824},
    doi = {10.1364/OE.20.008824},
    issn = {1094-4087},
    pmid = {22513593}
}

@article{Sarapata2014,
    title = {{High energy x-ray phase contrast CT using glancing-angle grating interferometers}},
    year = {2014},
    journal = {Medical Physics},
    author = {Sarapata, A. and Stayman, J. W. and Finkenthal, M. and Siewerdsen, J. H. and Pfeiffer, F. and Stutman, D.},
    number = {2},
    month = {2},
    pages = {021904},
    volume = {41},
    url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3981561&tool=pmcentrez&rendertype=abstract http://scitation.aip.org/content/aapm/journal/medphys/41/2/10.1118/1.4860275},
    isbn = {doi:10.1118/1.4860275},
    doi = {10.1118/1.4860275},
    issn = {00942405},
    pmid = {24506625},
    keywords = {glancing angle grating interferometer, high fringe visibility, x-ray phase contrast ct}
}

@article{Sikkel2016,
    title = {{High speed sCMOS-based oblique plane microscopy applied to the study of calcium dynamics in cardiac myocytes}},
    year = {2016},
    journal = {Journal of Biophotonics},
    author = {Sikkel, Markus B. and Kumar, Sunil and Maioli, Vincent and Rowlands, Christina and Gordon, Fabiana and Harding, Sian E. and Lyon, Alexander R. and MacLeod, Kenneth T. and Dunsby, Chris},
    number = {3},
    month = {3},
    pages = {311--323},
    volume = {9},
    url = {http://doi.wiley.com/10.1002/jbio.201500193},
    doi = {10.1002/jbio.201500193},
    issn = {1864063X},
    keywords = {3D imaging, Calcium dynamics, High-speed imaging, Light-sheet microscopy, Oblique Plane Microscopy}
}

@article{Sisniega2015,
    title = {{High-fidelity artifact correction for cone-beam CT imaging of the brain}},
    year = {2015},
    journal = {Physics in Medicine and Biology},
    author = {Sisniega, A. and Zbijewski, W. and Xu, J. and Dang, H. and Stayman, J. W. and Yorkston, J. and Aygun, N. and Koliatsos, V. and Siewerdsen, J. H.},
    number = {4},
    month = {2},
    pages = {1415--1439},
    volume = {60},
    url = {http://stacks.iop.org/0031-9155/60/i=4/a=1415?key=crossref.ff5c134a2a7a4263e696e19c9cdf4241},
    doi = {10.1088/0031-9155/60/4/1415},
    issn = {0031-9155},
    keywords = {Monte Carlo, artifact correction, cone beam CT, scatter correction, soft-tissue brain imaging, traumatic brain injury, variance reduction}
}

@article{Mcgorty2017,
    title = {{High-NA open-top selective-plane illumination microscopy for biological imaging}},
    year = {2017},
    journal = {Optics Express},
    author = {Mcgorty, Ryan and Xie, Dan and Huang, Bo},
    number = {15},
    month = {7},
    pages = {17798},
    volume = {25},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-25-15-17798},
    doi = {10.1364/OE.25.017798},
    issn = {1094-4087}
}

@article{Anas2011a,
    title = {{High-quality 3D correction of ring and radiant artifacts in flat panel detector-based cone beam volume CT imaging}},
    year = {2011},
    journal = {Physics in Medicine and Biology},
    author = {Anas, Emran Mohammad Abu and Kim, Jae Gon and Lee, Soo Yeol and Hasan, Md Kamrul},
    number = {19},
    pages = {6495--6519},
    volume = {56},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/21934193},
    isbn = {0031-9155},
    doi = {10.1088/0031-9155/56/19/020},
    issn = {00319155},
    pmid = {21934193},
    keywords = {Algorithms, Animals, Artifacts, Calibration, Computer-Assisted, Computer-Assisted: instrumentati, Computer-Assisted: methods, Cone-Beam Computed Tomography, Cone-Beam Computed Tomography: instrumentation, Cone-Beam Computed Tomography: methods, Image Processing, Imaging, Models, Phantoms, Semiconductors, Theoretical, Three-Dimensional, Three-Dimensional: instrumentation, Three-Dimensional: methods, X-Ray Intensifying Screens}
}

@article{Mickoleit2014,
    title = {{High-resolution reconstruction of the beating zebrafish heart}},
    year = {2014},
    journal = {Nature Methods},
    author = {Mickoleit, Michaela and Schmid, Benjamin and Weber, Michael and Fahrbach, Florian O. and Hombach, Sonja and Reischauer, Sven and Huisken, Jan},
    number = {9},
    pages = {919--922},
    volume = {11},
    publisher = {Nature Publishing Group},
    url = {http://www.nature.com/doifinder/10.1038/nmeth.3037},
    isbn = {1548-7105 (Electronic){\textbackslash}n1548-7091 (Linking)},
    doi = {10.1038/nmeth.3037},
    issn = {15487105},
    pmid = {25042787}
}

@article{Verveer2007,
    title = {{High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy}},
    year = {2007},
    journal = {Nature Methods},
    author = {Verveer, Peter J. and Swoger, Jim and Pampaloni, Francesco and Greger, Klaus and Marcello, Marco and Stelzer, Ernst H K},
    number = {4},
    pages = {311--313},
    volume = {4},
    doi = {10.1038/nmeth1017},
    issn = {15487091}
}

@article{Remacha2019,
    title = {{How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach}},
    year = {2019},
    journal = {bioRxiv},
    author = {Remacha, Elena and Friedrich, Lars and Vermot, Julien and Fahrbach, Florian O.},
    month = {9},
    pages = {783589},
    publisher = {Cold Spring Harbor Laboratory},
    doi = {10.1101/783589}
}

@article{Ripoll2010,
    title = {{Hybrid Fourier-real space method for diffuse optical tomography.}},
    year = {2010},
    journal = {Optics letters},
    author = {Ripoll, Jorge},
    number = {5},
    pages = {688--90},
    volume = {35},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/20195320},
    doi = {10.1364/OL.35.000688},
    issn = {1539-4794},
    pmid = {20195320},
    keywords = {Algorithms, Fourier Analysis, Image Enhancement, Image Enhancement: methods, Image Interpretation, Computer-Assisted, Image Interpretation, Computer-Assisted: methods, Imaging, Three-Dimensional, Imaging, Three-Dimensional: methods, Phantoms, Imaging, Reproducibility of Results, Sensitivity and Specificity, Tomography, Optical, Tomography, Optical: instrumentation, Tomography, Optical: methods}
}

@article{Lee2018,
    title = {{Hybrid Monte Carlo simulation with ray tracing for fluorescence measurements in turbid media}},
    year = {2018},
    journal = {Optics Letters},
    author = {Lee, Seung Yup and Mycek, Mary-Ann},
    number = {16},
    pages = {3846},
    volume = {43},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-43-16-3846},
    doi = {10.1364/OL.43.003846},
    issn = {0146-9592}
}

@article{Hayashi2003,
    title = {{Hybrid Monte Carlo-diffusion method for light propagation in tissue with a low-scattering region}},
    year = {2003},
    journal = {Applied Optics},
    author = {Hayashi, Toshiyuki and Kashio, Yoshihiko and Okada, Eiji},
    number = {16},
    month = {6},
    pages = {2888},
    volume = {42},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-42-16-2888},
    doi = {10.1364/AO.42.002888},
    issn = {0003-6935}
}

@article{Jahr2015,
    title = {{Hyperspectral light sheet microscopy}},
    year = {2015},
    journal = {Nature Communications},
    author = {Jahr, Wiebke and Schmid, Benjamin and Schmied, Christopher and Fahrbach, Florian O. and Huisken, Jan},
    pages = {1--7},
    volume = {6},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/ncomms8990},
    doi = {10.1038/ncomms8990},
    issn = {20411723}
}

@article{Olarte2012,
    title = {{Image formation by linear and nonlinear digital scanned light-sheet fluorescence microscopy with Gaussian and Bessel beam profiles}},
    year = {2012},
    journal = {Biomedical Optics Express},
    author = {Olarte, Omar E. and Licea-Rodriguez, Jacob and Palero, Jonathan a. and Gualda, Emilio J. and Artigas, David and Mayer, Jürgen and Swoger, Jim and Sharpe, James and Rocha-Mendoza, Israel and Rangel-Rojo, Raul and Loza-Alvarez, Pablo},
    number = {7},
    month = {7},
    pages = {1492},
    volume = {3},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-3-7-1492},
    doi = {10.1364/BOE.3.001492},
    issn = {2156-7085}
}

@article{Walker1997,
    title = {{Image reconstruction by backprojection from frequency-domain optical measurements in highly scattering media}},
    year = {1997},
    journal = {Applied Optics},
    author = {Walker, Scott a and Fantini, Sergio and Gratton, Enrico},
    number = {1},
    month = {1},
    pages = {170},
    volume = {36},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-36-1-170},
    isbn = {0003-6935 (Print) 0003-6935 (Linking)},
    doi = {10.1364/AO.36.000170},
    issn = {0003-6935},
    pmid = {18250659},
    keywords = {backprojection, frequency domain, image reconstruction, photon migration, tomography}
}

@article{VanderHorst2016,
    title = {{Image resolution and deconvolution in optical tomography}},
    year = {2016},
    journal = {Optics Express},
    author = {van der Horst, Jelle and Kalkman, Jeroen},
    number = {21},
    month = {10},
    pages = {24460},
    volume = {24},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-24-21-24460},
    doi = {10.1364/OE.24.024460},
    issn = {1094-4087}
}

@article{Wang2010,
    title = {{Imaging complex structures with diffuse light}},
    year = {2008},
    journal = {Optics Express},
    author = {Konecky, Soren D. and Panasyuk, George Y. and Lee, Kijoon and Markel, Vadim and Yodh, Arjun G. and Schotland, John C.},
    number = {7},
    month = {3},
    pages = {5048},
    volume = {16},
    url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-16-7-5048},
    isbn = {8756564080225},
    doi = {10.1364/OE.16.005048},
    issn = {1094-4087},
    pmid = {1000000221},
    arxivId = {NIHMS150003},
    keywords = {a large population of, as it is one, bacteria, bacterial conjugation has important, by which antiobiotic resistance, can be transferred to, conjugation, consequences for human health, cryo-em, helical polymers, of the means, polymorphisms, real space reconstruction, scanning transmission em}
}

@article{Zhu2010,
    title = {{Imaging dermal blood flow through the intact rat skin with an optical clearing method}},
    year = {2010},
    journal = {Journal of Biomedical Optics},
    author = {Zhu, Dan and Wang, Jing and Zhi, Zhongwei and Wen, Xiang and Luo, Qingming},
    number = {2},
    pages = {026008},
    volume = {15},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.3369739},
    isbn = {8627877920},
    doi = {10.1117/1.3369739},
    issn = {10833668},
    keywords = {12, 2009, 2010, 23, 26, accepted for publication jan, dermal blood flow, laser speckle contrast imaging, monitoring, optical clearing, optical properties, paper 09246prr received jun, published online apr, revised manuscript received jan, thiazone}
}

@article{Ripoll2004,
    title = {{Imaging in scattering media from a distance: Theory and applications of noncontact optical tomography}},
    year = {2004},
    journal = {Modern Physics Letters B},
    author = {Ripoll, J. and Ntziachristos, V.},
    number = {28n29},
    month = {12},
    pages = {1403--1431},
    volume = {18},
    publisher = {CRC Press},
    url = {http://www.crcnetbase.com/doi/10.1201/9780203501962.ch7 http://www.worldscientific.com/doi/abs/10.1142/S0217984904007864 https://www.worldscientific.com/doi/abs/10.1142/S0217984904007864},
    doi = {10.1142/S0217984904007864},
    issn = {0217-9849},
    keywords = {diffuse optical tomography, diffusion, imaging in scattering, media, noncontact tomography, pacs number, radiative transfer equation}
}

@article{Keller2013,
    title = {{Imaging Morphogenesis: Technological Advances and Biological Insights}},
    year = {2013},
    journal = {Science},
    author = {Keller, P. J.},
    number = {6137},
    month = {6},
    pages = {1234168--1234168},
    volume = {340},
    url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1234168},
    doi = {10.1126/science.1234168},
    issn = {0036-8075}
}

@article{kellner2012,
    title = {{Imaging of the mouse lung with scanning laser optical tomography (SLOT)}},
    year = {2012},
    journal = {Journal of Applied Physiology},
    author = {Kellner, Manuela and Heidrich, Marko and Beigel, Rebecca and Lorbeer, Raoul-Amadeus and Knudsen, Lars and Ripken, Tammo and Heisterkamp, Alexander and Meyer, Heiko and K{\"{u}}hnel, Mark Philipp and Ochs, Matthias},
    number = {6},
    pages = {975--983},
    volume = {113},
    doi = {10.1152/japplphysiol.00026.2012},
    issn = {8750-7587}
}

@article{Birk2011,
    title = {{Improved reconstructions and generalized filtered back projection for optical projection tomography}},
    year = {2011},
    journal = {Applied Optics},
    author = {Jochen Birk, Udo and Darrell, Alex and Konstantinides, Nikos and Sarasa-Renedo, Ana and Ripoll, Jorge},
    number = {4},
    month = {2},
    pages = {392},
    volume = {50},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/21283227 https://www.osapublishing.org/abstract.cfm?URI=ao-50-4-392},
    doi = {10.1364/AO.50.000392},
    pmid = {21283227},
    keywords = {Algorithms, Computer-Assisted, Computer-Assisted: methods, Image Enhancement, Image Enhancement: methods, Image Interpretation, Imaging, Optical Coherence, Optical Coherence: methods, Reproducibility of Results, Sensitivity and Specificity, Three-Dimensional, Three-Dimensional: methods, Tomography}
}

@article{Strobl2017,
    title = {{Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research}},
    year = {2017},
    journal = {Nature Protocols},
    author = {Strobl, Frederic and Schmitz, Alexander and Stelzer, Ernst H K},
    number = {6},
    month = {6},
    pages = {1103--1109},
    volume = {12},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nprot.2017.028 http://www.nature.com/doifinder/10.1038/nprot.2017.028 http://www.nature.com/articles/nprot.2017.028},
    doi = {10.1038/nprot.2017.028},
    issn = {1754-2189}
}

@article{DelRosal2016,
    title = {{In vivo autofluorescence in the biological windows: the role of pigmentation}},
    year = {2016},
    journal = {Journal of Biophotonics},
    author = {del Rosal, Blanca and Villa, Irene and Jaque, Daniel and Sanz-Rodr{\'{i}}guez, Francisco},
    number = {10},
    month = {10},
    pages = {1059--1067},
    volume = {9},
    url = {http://doi.wiley.com/10.1002/jbio.201500271},
    doi = {10.1002/jbio.201500271},
    issn = {1864063X},
    pmid = {26576035},
    keywords = {autofluorescence, bioimaging, infrared imaging, laser-induced heating}
}

@incollection{Hong2016,
    title = {{In Vivo Fluorescence Imaging in the Second Near-Infrared Window Using Carbon Nanotubes}},
    year = {2016},
    booktitle = {In Vivo Fluorescence Imaging: Methods and Protocols},
    author = {Hong, Guosong and Dai, Hongjie},
    editor = {Bai, Mingfeng},
    chapter = {15},
    pages = {167--181},
    series = {Methods in Molecular Biology},
    volume = {1444},
    publisher = {Springer New York},
    url = {http://link.springer.com/10.1007/978-1-4939-3721-9 http://link.springer.com/10.1007/978-1-4939-3721-9_15},
    address = {New York, NY},
    isbn = {978-1-4939-3719-6},
    doi = {10.1007/978-1-4939-3721-9{\_}15},
    keywords = {autofluorescence, carbon, nanotubes, near-infrared ii, nir-ii fluorescence imaging, photon scattering, second near-infrared window, tissue penetration}
}

@article{Vinegoni2008,
    title = {{In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography}},
    year = {2008},
    journal = {Nature methods},
    author = {Vinegoni, Claudio and Pitsouli, Chrysoula and Razansky, Daniel and Perrimon, Norbert and Ntziachristos, Vasilis},
    number = {1},
    month = {1},
    pages = {45--7},
    volume = {5},
    url = {http://www.nature.com/articles/nmeth1149 http://www.ncbi.nlm.nih.gov/pubmed/18066071},
    isbn = {1548-7091},
    doi = {10.1038/nmeth1149},
    issn = {1548-7105},
    pmid = {18066071}
}

@article{Bassi2011,
    title = {{In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography}},
    year = {2011},
    journal = {Journal of Biomedical Optics},
    author = {Bassi, Andrea and Fieramonti, Luca and D’Andrea, Cosimo and Mione, Marina and Valentini, Gianluca},
    number = {10},
    pages = {100502},
    volume = {16},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.3640808},
    isbn = {1560-2281 (Electronic){\textbackslash}r1083-3668 (Linking)},
    doi = {10.1117/1.3640808},
    issn = {10833668},
    pmid = {22029341},
    keywords = {Animals, Blood Vessels, Blood Vessels: anatomy {\&} histology, Genetically Modified, Green Fluorescent Proteins, Green Fluorescent Proteins: genetics, Imaging, Optical, Optical Phenomena, Optical: methods, Recombinant Proteins, Recombinant Proteins: genetics, Rheology, Rheology: methods, Three-Dimensional, Three-Dimensional: methods, Tomography, Zebrafish, Zebrafish: anatomy {\&} histology, Zebrafish: genetics}
}

@article{Bassi2011b,
    title = {{In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography}},
    year = {2011},
    journal = {Journal of Biomedical Optics},
    author = {Bassi, Andrea and Fieramonti, Luca and D’Andrea, Cosimo and Mione, Marina and Valentini, Gianluca},
    number = {10},
    pages = {100502},
    volume = {16},
    doi = {10.1117/1.3640808},
    issn = {10833668},
    keywords = {2011, 25, 26, 29, 3, accepted for publication aug, aug, label free, online oct, optical tomography, paper 11405lr received jul, published, revised manuscript received, vascular networks}
}

@article{Bassi2011c,
    title = {{In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography}},
    year = {2011},
    journal = {Journal of Biomedical Optics},
    author = {Bassi, Andrea and Fieramonti, Luca and D’Andrea, Cosimo and Mione, Marina and Valentini, Gianluca},
    number = {10},
    pages = {100502},
    volume = {16},
    doi = {10.1117/1.3640808},
    issn = {10833668},
    keywords = {2011, 25, 26, 29, 3, accepted for publication aug, aug, label free, online oct, optical tomography, paper 11405lr received jul, published, revised manuscript received, vascular networks}
}

@article{Frangioni2003,
    title = {{In vivo near-infrared fluorescence imaging}},
    year = {2003},
    journal = {Current Opinion in Chemical Biology},
    author = {Frangioni, John V.},
    number = {5},
    pages = {626--634},
    volume = {7},
    isbn = {1367-5931},
    doi = {10.1016/j.cbpa.2003.08.007},
    issn = {13675931},
    pmid = {14580568}
}

@article{Ripoll2009,
    title = {{In vivo optical tomography: From diffusion to ballistic}},
    year = {2009},
    journal = {Optical Materials},
    author = {Ripoll, Jorge and Meyer, Heiko and Garofalakis, Anikitos},
    number = {7},
    month = {5},
    pages = {1082--1085},
    volume = {31},
    publisher = {Elsevier B.V.},
    url = {http://dx.doi.org/10.1016/j.optmat.2007.12.021 http://linkinghub.elsevier.com/retrieve/pii/S0925346708000736},
    doi = {10.1016/j.optmat.2007.12.021},
    issn = {09253467}
}

@article{Horton2013,
    title = {{In vivo three-photon microscopy of subcortical structures within an intact mouse brain}},
    year = {2013},
    journal = {Nature Photonics},
    author = {Horton, Nicholas G. and Wang, Ke and Kobat, Demirhan and Clark, Catharine G. and Wise, Frank W. and Schaffer, Chris B. and Xu, Chris},
    number = {3},
    month = {3},
    pages = {205--209},
    volume = {7},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nphoton.2012.336 http://www.nature.com/articles/nphoton.2012.336},
    doi = {10.1038/nphoton.2012.336},
    issn = {1749-4885}
}

@article{Bech2013,
    title = {{In-vivo dark-field and phase-contrast x-ray imaging}},
    year = {2013},
    journal = {Scientific Reports},
    author = {Bech, M. and Tapfer, A. and Velroyen, A. and Yaroshenko, A. and Pauwels, B. and Hostens, J. and Bruyndonckx, P. and Sasov, A. and Pfeiffer, F.},
    month = {1},
    pages = {3209},
    volume = {3},
    url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3826096&tool=pmcentrez&rendertype=abstract},
    isbn = {0000000000000},
    doi = {10.1038/srep03209},
    issn = {20452322},
    pmid = {24220606}
}

@article{Arranz2014,
    title = {{In-vivo Optical Tomography of Small Scattering Specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster}},
    year = {2015},
    journal = {Scientific Reports},
    author = {Arranz, Alicia and Dong, Di and Zhu, Shouping and Savakis, Charalambos and Tian, Jie and Ripoll, Jorge},
    number = {1},
    month = {5},
    pages = {7325},
    volume = {4},
    url = {http://www.nature.com/articles/srep07325 http://www.ncbi.nlm.nih.gov/pubmed/25471694 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4255187},
    doi = {10.1038/srep07325},
    issn = {2045-2322},
    pmid = {25471694}
}

@article{Chen2012,
    title = {{Incorporation of an experimentally determined MTF for spatial frequency filtering and deconvolution during optical projection tomography reconstruction}},
    year = {2012},
    journal = {Optics Express},
    author = {Chen, Lingling and McGinty, James and Taylor, Harriet B. and Bugeon, Laurence and Lamb, Jonathan R. and Dallman, Margaret J. and French, Paul M. W.},
    number = {7},
    month = {3},
    pages = {7323},
    volume = {20},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-20-7-7323},
    doi = {10.1364/OE.20.007323},
    issn = {1094-4087}
}

@article{Starosolski2017,
    title = {{Indocyanine green fluorescence in second near-infrared (NIR-II) window}},
    year = {2017},
    journal = {PLOS ONE},
    author = {Starosolski, Zbigniew and Bhavane, Rohan and Ghaghada, Ketan B. and Vasudevan, Sanjeev A. and Kaay, Alexander and Annapragada, Ananth},
    editor = {Evans, Conor L.},
    number = {11},
    month = {11},
    pages = {e0187563},
    volume = {12},
    url = {http://dx.plos.org/10.1371/journal.pone.0187563},
    isbn = {1111111111},
    doi = {10.1371/journal.pone.0187563},
    issn = {1932-6203},
    pmid = {29121078}
}

@article{Emmons1975,
    title = {{Infrared Detectors: An Overview Overview}},
    year = {1975},
    journal = {Optical Engineering},
    author = {Emmons, R. B. and Hawkins, S. R. and Cuff, K. F.},
    number = {1},
    pages = {21--30},
    volume = {14},
    keywords = {focal plane arrays, photon detectors, thermal detectors, two-colour detectors}
}

@article{Wagner2019a,
    title = {{Instantaneous isotropic volumetric imaging of fast biological processes}},
    year = {2019},
    journal = {Nature Methods},
    author = {Wagner, Nils and Norlin, Nils and Gierten, Jakob and de Medeiros, Gustavo and Bal{\'{a}}zs, Bálint and Wittbrodt, Joachim and Hufnagel, Lars and Prevedel, Robert},
    number = {6},
    pages = {497--500},
    volume = {16},
    isbn = {4159201903},
    doi = {10.1038/s41592-019-0393-z},
    issn = {15487105}
}

@article{Kumar2018,
    title = {{Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging}},
    year = {2018},
    journal = {Optics Express},
    author = {Kumar, Manish and Kishore, Sandeep and Nasenbeny, Jordan and McLean, David L. and Kozorovitskiy, Yevgenia},
    number = {10},
    month = {5},
    pages = {13027},
    volume = {26},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-26-10-13027},
    doi = {10.1364/OE.26.013027},
    issn = {1094-4087}
}

@article{Cao2018,
    title = {{Integrating fluorescence computed tomography with optical sheet illumination for imaging of live single cells}},
    year = {2018},
    journal = {Optics Express},
    author = {Cao, Bin and Shetty, Rishabh and Smith, Dean and Kelbauskas, Laimonas and Meldrum, Deirdre R.},
    number = {18},
    month = {9},
    pages = {24020},
    volume = {26},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-26-18-24020},
    doi = {10.1364/OE.26.024020},
    issn = {1094-4087}
}

@article{Lauzier2012,
    title = {{Interior tomography in x-ray differential phase contrast CT imaging}},
    year = {2012},
    journal = {Physics in Medicine and Biology},
    author = {Lauzier, Pascal Thériault and Qi, Zhihua and Zambelli, Joseph and Bevins, Nicholas and Chen, Guang Hong},
    number = {9},
    month = {5},
    pages = {117--30},
    volume = {57},
    url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3746740&tool=pmcentrez&rendertype=abstract},
    isbn = {1361-6560},
    doi = {10.1088/0031-9155/57/9/N117},
    issn = {00319155},
    pmid = {22491072},
    arxivId = {NIHMS150003},
    keywords = {Absorption, Algorithms, Computer-Assisted, Image Processing, Imaging, Models, Phantoms, Theoretical, Tomography, X-Ray Computed, X-Ray Computed: methods}
}

@article{Wang2014,
    title = {{Introduction}},
    year = {2014},
    journal = {Jacques Ranci{\`{e}}re : An Introduction},
    author = {Wang, S and Han, H and Gao, K and Wang, Z and Zhang, C and Yang, M and Wu, Z and Marcelli, A},
    pages = {1--11},
    url = {http://www.bloomsburycollections.com/book/jacques-ranciere-an-introduction/introduction},
    isbn = {9781441167705},
    doi = {10.5040/9781472546968.0005},
    keywords = {labview, phase-contrast, software platform, x-ray imaging}
}

@article{Markel2001,
    title = {{Inverse problem in optical diffusion tomography I Fourier–Laplace inversion formulas}},
    year = {2001},
    journal = {Journal of the Optical Society of America A},
    author = {Markel, Vadim A. and Schotland, John C.},
    number = {6},
    month = {6},
    pages = {1336},
    volume = {18},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-20-5-903 http://www.ncbi.nlm.nih.gov/pubmed/11393626 https://www.osapublishing.org/abstract.cfm?URI=josaa-18-6-1336},
    doi = {10.1364/JOSAA.18.001336},
    issn = {1084-7529},
    pmid = {11393626}
}

@article{Wu2011,
    title = {{Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans}},
    year = {2011},
    journal = {Proceedings of the National Academy of Sciences of the United States of America},
    author = {Wu, Yicong and Ghitani, Alireza and Christensen, Ryan and Santella, Anthony and Du, Zhuo and Rondeau, Gary and Bao, Zhirong and Col{\'{o}}n-Ramos, Daniel and Shroff, Hari},
    number = {43},
    pages = {17708--17713},
    volume = {108},
    doi = {10.1073/pnas.1108494108},
    issn = {00278424},
    keywords = {Axon growth, Fast 4D imaging, Neuron migration}
}

@inproceedings{Flay2015,
    title = {{Investigation of the Focal Spot Drift in Industrial Cone-beam X-ray Computed Tomography}},
    year = {2015},
    booktitle = {Digital Industrial Radiology and Computed Tomography},
    author = {Flay, Nadia and Sun, Wenjuan and Brown, Stephen and Leach, Richard K and Blumensath, Thomas},
    number = {June},
    pages = {22--25},
    address = {Ghent, Belgium},
    keywords = {focal spot drift, xct}
}

@article{Bruce1995,
    title = {{Investigation of the temporal spread of an ultrashort light pulse on transmission through a highly scattering medium}},
    year = {1995},
    journal = {Applied Optics},
    author = {Bruce, N. C. and Schmidt, F. E. W. and Dainty, J. C. and Barry, N. P. and Hyde, S. C. W. and French, P. M. W.},
    number = {25},
    pages = {5823},
    volume = {34},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-34-25-5823},
    isbn = {0003-6935 (Print){\textbackslash}r0003-6935 (Linking)},
    doi = {10.1364/AO.34.005823},
    issn = {0003-6935},
    pmid = {21060416}
}

@inproceedings{Badea2012,
    title = {{Investigations on x-ray luminescence CT for small animal imaging}},
    year = {2012},
    booktitle = {Proc SPIE},
    author = {Badea, C. T. and Stanton, I. N. and Johnston, S. M. and Johnson, G. A. and Therien, M. J.},
    pages = {83130T},
    url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.911465},
    isbn = {9780819489623},
    doi = {10.1117/12.911465},
    issn = {1996-756X},
    pmid = {23227300},
    keywords = {dual energy, micro-ct, nanophosphor, small animal imaging}
}

@article{Ban2019,
    title = {{Label-free optical projection tomography for quantitative three-dimensional anatomy of mouse embryo}},
    year = {2019},
    journal = {Journal of Biophotonics},
    author = {Ban, Sungbea and Cho, Nam Hyun and Min, Eunjung and Bae, Jung Kweon and Ahn, Yujin and Shin, Sungwon and Park, Soo Ah and Lee, Yoonsung and Jung, Woonggyu},
    number = {7},
    pages = {1--6},
    volume = {12},
    doi = {10.1002/jbio.201800481},
    issn = {18640648},
    keywords = {embryonic imaging, label-free imaging, optical projection tomography, tissue atlas segmentation, tissue clearing technique}
}

@article{Gao2019,
    title = {{Lattice light sheet microscopy using tiling lattice light sheets}},
    year = {2019},
    journal = {Optics Express},
    author = {Gao, Liang and Tang, Wei-Chun and Tsai, Yun-Chi and Chen, Bi-Chang},
    number = {2},
    month = {1},
    pages = {1497},
    volume = {27},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-27-2-1497},
    doi = {10.1364/OE.27.001497},
    issn = {1094-4087}
}

@article{Chen2014,
    title = {{Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution}},
    year = {2014},
    journal = {Science},
    author = {Chen, Bi Chang and Legant, Wesley R. and Wang, Kai and Shao, Lin and Milkie, Daniel E. and Davidson, Michael W. and Janetopoulos, Chris and Wu, Xufeng S. and Hammer, John A. and Liu, Zhe and English, Brian P. and Mimori-Kiyosue, Yuko and Romero, Daniel P. and Ritter, Alex T. and Lippincott-Schwartz, Jennifer and Fritz-Laylin, Lillian and Mullins, R. Dyche and Mitchell, Diana M. and Bembenek, Joshua N. and Reymann, Anne Cecile and B{\"{o}}hme, Ralph and Grill, Stephan W. and Wang, Jennifer T. and Seydoux, Geraldine and Tulu, U. Serdar and Kiehart, Daniel P. and Betzig, Eric},
    number = {6208},
    volume = {346},
    doi = {10.1126/science.1257998},
    issn = {10959203}
}

@book{lorenzo2012principles,
    title = {{Light Absorbers, Emitters and Scatterers: The Origins of Color in Nature}},
    year = {2012},
    booktitle = {Principles of diffuse light propagation: light propagation in tissues with applications in biology and medicine},
    author = {Lorenzo, Jorge Ripoll},
    pages = {3--51},
    publisher = {World Scientific},
    url = {www.worldscientific.com/doi/abs/10.1142/9789814293860_0001},
    isbn = {9814293768},
    doi = {10.1142/9789814293860{\_}0001}
}

@article{Jacques1998,
    title = {{Light Distributions from Point, Line and Plane Sources for Photochemical Reactions and Fluorescence in Turbid Biological Tissues}},
    year = {1998},
    journal = {Photochemistry and Photobiology},
    author = {Jacques, Steven L.},
    number = {1},
    month = {1},
    pages = {23--32},
    volume = {67},
    url = {http://doi.wiley.com/10.1111/j.1751-1097.1998.tb05161.x},
    doi = {10.1111/j.1751-1097.1998.tb05161.x},
    issn = {0031-8655},
    pmid = {9477762}
}

@article{Keijzer1989,
    title = {{Light distributions in artery tissue: Monte Carlo simulations for finite-diameter laser beams}},
    year = {1989},
    journal = {Lasers in Surgery and Medicine},
    author = {Keijzer, Marleen and Jacques, Steven L. and Prahl, Scott A. and Welch, Ashley J.},
    number = {2},
    pages = {148--154},
    volume = {9},
    url = {http://doi.wiley.com/10.1002/lsm.1900090210},
    doi = {10.1002/lsm.1900090210},
    issn = {01968092},
    keywords = {absorption, aorta, dosimetry, fiber optics, lasers, photometry, radiation, random walk, scattering}
}

@article{Schneckenburger2012,
    title = {{Light exposure and cell viability in fluorescence microscopy}},
    year = {2012},
    journal = {Journal of Microscopy},
    author = {Schneckenburger, H. and Weber, P. and Wagner, M. and Schickinger, S. and Richter, V. and Bruns, T. and Strauss, W. S.L. and Wittig, R.},
    number = {3},
    pages = {311--318},
    volume = {245},
    doi = {10.1111/j.1365-2818.2011.03576.x},
    issn = {00222720},
    keywords = {3D cell cultures, Cell viability, Fluorescence microscopy, Light dose}
}

@article{Fan2014,
    title = {{Light scattering and surface plasmons on small spherical particles}},
    year = {2014},
    journal = {Light: Science and Applications},
    author = {Fan, Xiaofeng and Zheng, Weitao and Singh, David J.},
    number = {November 2013},
    pages = {1--14},
    volume = {3},
    isbn = {2047-7538},
    doi = {10.1038/lsa.2014.60},
    issn = {20477538},
    pmid = {24522336},
    arxivId = {physics/0308016},
    keywords = {Mie theory, light scattering, nano-optics, small particles, surface plasmons}
}

@article{Sinclair1947,
    title = {{Light scattering by spherical particles}},
    year = {1947},
    journal = {Josa},
    author = {Sinclair, D},
    number = {6},
    pages = {475--480},
    volume = {37},
    url = {http://www.opticsinfobase.org/abstract.cfm?&id=77193}
}

@article{VanStaveren1991,
    title = {{Light scattering in lntralipid-10{\%} in the wavelength range of 400–1100 nm}},
    year = {1991},
    journal = {Applied Optics},
    author = {van Staveren, Hugo J. and Moes, Christian J. M. and van Marie, Jan and Prahl, Scott A. and van Gemert, Martin J. C.},
    number = {31},
    month = {11},
    pages = {4507},
    volume = {30},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-30-31-4507 http://www.ncbi.nlm.nih.gov/pubmed/20717241},
    doi = {10.1364/AO.30.004507},
    issn = {0003-6935},
    pmid = {20717241},
    arxivId = {arXiv:1011.1669v3}
}

@article{Gustavsson2018,
    title = {{Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells}},
    year = {2018},
    journal = {Optics Express},
    author = {Gustavsson, Anna-Karin and Petrov, Petar N. and Moerner, W. E.},
    number = {10},
    month = {5},
    pages = {13122},
    volume = {26},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-26-10-13122},
    doi = {10.1364/OE.26.013122},
    issn = {1094-4087}
}

@article{Santi2011,
    title = {{Light Sheet Fluorescence Microscopy}},
    year = {2011},
    journal = {Journal of Histochemistry {\&} Cytochemistry},
    author = {Santi, Peter A.},
    number = {2},
    month = {2},
    pages = {129--138},
    volume = {59},
    url = {http://journals.sagepub.com/doi/10.1369/0022155410394857},
    doi = {10.1369/0022155410394857},
    issn = {0022-1554},
    pmid = {21339178},
    keywords = {Light sheet microscopy, OPFOS, Optical sectioning, TSLIM}
}

@article{Berthet2016,
    title = {{Light sheet microscopy and live imaging of plants}},
    year = {2016},
    journal = {Journal of Microscopy},
    author = {Berthet, Bé;atrice and Maizel, Alexis},
    number = {2},
    month = {8},
    pages = {158--164},
    volume = {263},
    publisher = {Blackwell Publishing Ltd},
    doi = {10.1111/jmi.12393},
    issn = {13652818},
    keywords = {Fluorescence microscopy, light sheet microscopy, live imaging, plant}
}

@article{Poola2019,
    title = {{Light sheet microscopy for histopathology applications}},
    year = {2019},
    journal = {Biomedical Engineering Letters},
    author = {Poola, Praveen Kumar and Afzal, Muhammad Imran and Yoo, Youngseung and Kim, Ki Hean and Chung, Euiheon},
    number = {3},
    month = {8},
    pages = {279--291},
    volume = {9},
    publisher = {Springer Science and Business Media LLC},
    doi = {10.1007/s13534-019-00122-y},
    issn = {2093-9868}
}

@article{Weber2011,
    title = {{Light sheet microscopy for real-time developmental biology}},
    year = {2011},
    journal = {Current Opinion in Genetics and Development},
    author = {Weber, Michael and Huisken, Jan},
    number = {5},
    pages = {566--572},
    volume = {21},
    publisher = {Elsevier Ltd},
    url = {http://dx.doi.org/10.1016/j.gde.2011.09.009},
    isbn = {1879-0380 (Electronic){\textbackslash}n0959-437X (Linking)},
    doi = {10.1016/j.gde.2011.09.009},
    issn = {0959437X},
    pmid = {21963791}
}

@article{Weber2011a,
    title = {{Light sheet microscopy for real-time developmental biology}},
    year = {2011},
    journal = {Current Opinion in Genetics {\&} Development},
    author = {Weber, Michael and Huisken, Jan},
    number = {5},
    month = {10},
    pages = {566--572},
    volume = {21},
    url = {https://linkinghub.elsevier.com/retrieve/pii/S0959437X11001444},
    doi = {10.1016/j.gde.2011.09.009},
    issn = {0959437X}
}

@misc{Keller2012,
    title = {{Light sheet microscopy of living or cleared specimens}},
    year = {2012},
    booktitle = {Current Opinion in Neurobiology},
    author = {Keller, Philipp J. and Dodt, Hans Ulrich},
    number = {1},
    month = {2},
    pages = {138--143},
    volume = {22},
    doi = {10.1016/j.conb.2011.08.003},
    issn = {09594388}
}

@article{Rieckher2017,
    title = {{Light Sheet Microscopy to Measure Protein Dynamics}},
    year = {2017},
    journal = {Journal of Cellular Physiology},
    author = {Rieckher, Matthias},
    number = {1},
    month = {1},
    pages = {27--35},
    volume = {232},
    url = {http://doi.wiley.com/10.1002/jcp.25451},
    doi = {10.1002/jcp.25451},
    issn = {00219541}
}

@article{Yang2019,
    title = {{Light sheet microscopy with acoustic sample confinement}},
    year = {2019},
    journal = {Nature Communications},
    author = {Yang, Zhengyi and Cole, Katy L. H. and Qiu, Yongqiang and Somorjai, Ildikó M. L. and Wijesinghe, Philip and Nylk, Jonathan and Cochran, Sandy and Spalding, Gabriel C. and Lyons, David A. and Dholakia, Kishan},
    number = {1},
    month = {12},
    pages = {669},
    volume = {10},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41467-019-08514-5 http://www.nature.com/articles/s41467-019-08514-5},
    doi = {10.1038/s41467-019-08514-5},
    issn = {2041-1723}
}

@article{Migliori2018,
    title = {{Light sheet theta microscopy for rapid high-resolution imaging of large biological samples}},
    year = {2018},
    journal = {BMC Biology},
    author = {Migliori, Bianca and Datta, Malika S. and Dupre, Christophe and Apak, Mehmet C. and Asano, Shoh and Gao, Ruixuan and Boyden, Edward S. and Hermanson, Ola and Yuste, Rafael and Tomer, Raju},
    number = {1},
    pages = {1--19},
    volume = {16},
    publisher = {BMC Biology},
    doi = {10.1186/s12915-018-0521-8},
    issn = {17417007},
    keywords = {Calcium imaging, Expansion microscopy, Hydra, Light sheet microscopy, Quantitative imaging, Tissue clearing, Whole brain imaging}
}

@article{Pampaloni2015,
    title = {{Light sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues}},
    year = {2015},
    journal = {Cell and Tissue Research},
    author = {Pampaloni, Francesco and Chang, Bo Jui and Stelzer, Ernst H.K.},
    number = {1},
    pages = {129--141},
    volume = {360},
    doi = {10.1007/s00441-015-2144-5},
    issn = {14320878},
    keywords = {Cellular spheroids, Digitally scanned light sheet-based microscopy, High-throughput LSFM, Light sheet-based fluorescence microscopy (LSFM), Single/selective-plane illumination microscopy, Three-dimensional cell cultures}
}

@article{Chang2019a,
    title = {{Light-sheet engineering using the Field Synthesis theorem}},
    year = {2019},
    journal = {bioRxiv},
    author = {Chang, Bo-Jui and Fiolka, Reto and Biology, Cell and Southwestern, U T and Southwestern, U T},
    month = {1},
    pages = {700633},
    url = {http://biorxiv.org/content/early/2019/07/13/700633.1.abstract},
    doi = {10.1101/700633},
    keywords = {c-light-sheet, field synthesis, lattice light-sheet}
}

@article{Stelzer2014,
    title = {{Light-sheet fluorescence microscopy for quantitative biology}},
    year = {2014},
    journal = {Nature Methods},
    author = {Stelzer, Ernst H.K.},
    number = {1},
    pages = {23--26},
    volume = {12},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.3219},
    doi = {10.1038/nmeth.3219},
    issn = {15487105}
}

@article{Keller2014,
    title = {{Light-sheet imaging for systems neuroscience}},
    year = {2015},
    journal = {Nature Methods},
    author = {Keller, Philipp J. and Ahrens, Misha B. and Freeman, Jeremy},
    number = {1},
    month = {1},
    pages = {27--29},
    volume = {12},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.3214 http://www.nature.com/articles/nmeth.3214},
    doi = {10.1038/nmeth.3214},
    issn = {1548-7091}
}

@article{DeMedeiros2016,
    title = {{Light-sheet imaging of mammalian development}},
    year = {2016},
    journal = {Seminars in Cell and Developmental Biology},
    author = {de Medeiros, Gustavo and Bal{\'{a}}zs, Bálint and Hufnagel, Lars},
    pages = {148--155},
    volume = {55},
    publisher = {Elsevier Ltd},
    url = {http://dx.doi.org/10.1016/j.semcdb.2015.11.001},
    doi = {10.1016/j.semcdb.2015.11.001},
    issn = {10963634},
    keywords = {Light-sheet, Live-imaging, Microscopy, Mouse embryo}
}

@article{Wan2019,
    title = {{Light-Sheet Microscopy and Its Potential for Understanding Developmental Processes}},
    year = {2019},
    journal = {Annual Review of Cell and Developmental Biology},
    author = {Wan, Yinan and McDole, Katie and Keller, Philipp J.},
    number = {1},
    pages = {1--27},
    volume = {35},
    doi = {10.1146/annurev-cellbio-100818-125311},
    issn = {1081-0706},
    keywords = {cellular dynamics, embryonic development, fluorescence microscopy, image, light-sheet microscopy, live imaging, processing}
}

@article{Glaser2017,
    title = {{Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens}},
    year = {2017},
    journal = {Nature Biomedical Engineering},
    author = {Glaser, Adam K. and Reder, Nicholas P. and Chen, Ye and McCarty, Erin F. and Yin, Chengbo and Wei, Linpeng and Wang, Yu and True, Lawrence D. and Liu, Jonathan T.C.},
    number = {7},
    volume = {1},
    isbn = {4936551015},
    doi = {10.1038/s41551-017-0084},
    issn = {2157846X},
    pmid = {20944749},
    arxivId = {Figures, S., 2010. Supplementary information. Nature, 1(c), pp.1–7. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3006164{\&}tool=pmcentrez{\&}rendertype=abstract.}
}

@article{Hillman2019,
    title = {{Light-Sheet Microscopy in Neuroscience}},
    year = {2019},
    journal = {Annual Review of Neuroscience},
    author = {Hillman, Elizabeth M.C. and Voleti, Venkatakaushik and Li, Wenze and Yu, Hang},
    number = {1},
    pages = {295--313},
    volume = {42},
    doi = {10.1146/annurev-neuro-070918-050357},
    issn = {0147-006X},
    keywords = {functional imaging, gcamp, light sheet, microscopy, tissue clearing}
}

@article{Wang2019,
    title = {{Light-sheet microscopy in the near-infrared II window}},
    year = {2019},
    journal = {Nature Methods},
    author = {Wang, Feifei and Wan, Hao and Ma, Zhuoran and Zhong, Yeteng and Sun, Qinchao and Tian, Ye and Qu, Liangqiong and Du, Haotian and Zhang, Mingxi and Li, Lulin and Ma, Huilong and Luo, Jian and Liang, Yongye and Li, Wen Jung and Hong, Guosong and Liu, Lianqing and Dai, Hongjie},
    number = {6},
    month = {6},
    pages = {545--552},
    volume = {16},
    publisher = {Springer US},
    url = {http://www.nature.com/articles/s41592-019-0398-7},
    isbn = {4159201903},
    doi = {10.1038/s41592-019-0398-7},
    issn = {1548-7091}
}

@article{Fahrbach2013b,
    title = {{Light-sheet microscopy in thick media using scanned Bessel beams and two-photon fluorescence excitation}},
    year = {2013},
    journal = {Optics Express},
    author = {Fahrbach, Florian O. and Gurchenkov, Vasily and Alessandri, Kevin and Nassoy, Pierre and Rohrbach, Alexander},
    number = {11},
    month = {6},
    pages = {13824},
    volume = {21},
    publisher = {The Optical Society},
    doi = {10.1364/oe.21.013824}
}

@article{Chakraborty2019a,
    title = {{Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution}},
    year = {2019},
    journal = {Nature Methods},
    author = {Chakraborty, Tonmoy and Driscoll, Meghan K. and Jeffery, Elise and Murphy, Malea M. and Roudot, Philippe and Chang, Bo-Jui and Vora, Saumya and Wong, Wen Mai and Nielson, Cara D. and Zhang, Hua and Zhemkov, Vladimir and Hiremath, Chitkale and De La Cruz, Estanislao Daniel and Yi, Yating and Bezprozvanny, Ilya and Zhao, Hu and Tomer, Raju and Heintzmann, Rainer and Meeks, Julian P. and Marciano, Denise K. and Morrison, Sean J. and Danuser, Gaudenz and Dean, Kevin M. and Fiolka, Reto},
    number = {11},
    month = {11},
    pages = {1109--1113},
    volume = {16},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41592-019-0615-4 http://www.nature.com/articles/s41592-019-0615-4},
    doi = {10.1038/s41592-019-0615-4},
    issn = {1548-7091}
}

@article{Vettenburg2014,
    title = {{Light-sheet microscopy using an Airy beam}},
    year = {2014},
    journal = {Nature Methods},
    author = {Vettenburg, Tom and Dalgarno, Heather I.C. and Nylk, Jonathan and Coll-Llad{\'{o}}, Clara and Ferrier, David E.K. and {\v{C}}i{\v{z}}m{\'{a}}r, Tomáš and Gunn-Moore, Frank J. and Dholakia, Kishan},
    number = {5},
    pages = {541--544},
    volume = {11},
    doi = {10.1038/nmeth.2922},
    issn = {15487105}
}

@article{Nylk2018,
    title = {{Light-sheet microscopy with attenuation-compensated propagation-invariant beams}},
    year = {2018},
    journal = {Science Advances},
    author = {Nylk, Jonathan and McCluskey, Kaley and Preciado, Miguel A. and Mazilu, Michael and Yang, Zhengyi and Gunn-Moore, Frank J. and Aggarwal, Sanya and Tello, Javier A. and Ferrier, David E. K. and Dholakia, Kishan},
    number = {4},
    month = {4},
    pages = {eaar4817},
    volume = {4},
    publisher = {American Association for the Advancement of Science},
    url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aar4817},
    doi = {10.1126/sciadv.aar4817},
    issn = {2375-2548}
}

@article{Chakraborty2019,
    title = {{Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging}},
    year = {2019},
    journal = {bioRxiv (preprint)},
    author = {Chakraborty, Tonmoy and Driscoll, Meghan and Murphy, Malea and Roudot, Philippe and Chang, Bo-Jui and Vora, Saumya and Wong, Wen Mai and Nielson, Cara and Zhang, Hua and Zhemkov, Vladimir and Hiremath, Chitkale and Cruz, Estanislao Daniel De La and Bezprozvanny, Ilya and Zhao, Hu and Tomer, Raju and Heintzmann, Rainer and Meeks, Julian and Marciano, Denise and Morrison, Sean and Danuser, Gaudenz and Dean, Kevin M. and Fiolka, Reto},
    pages = {605493},
    url = {https://www.biorxiv.org/content/10.1101/605493v1},
    doi = {10.1101/605493}
}

@article{Meinert2019,
    title = {{Light-sheet microscopy with length-adaptive Bessel beams}},
    year = {2019},
    journal = {Biomedical Optics Express},
    author = {Meinert, Tobias and Rohrbach, Alexander},
    number = {2},
    pages = {670},
    volume = {10},
    doi = {10.1364/boe.10.000670},
    issn = {2156-7085}
}

@article{Olarte2018,
    title = {{Light-sheet microscopy: a tutorial}},
    year = {2018},
    journal = {Advances in Optics and Photonics},
    author = {Olarte, Omar E. and Andilla, Jordi and Gualda, Emilio J. and Loza-Alvarez, Pablo},
    number = {1},
    month = {3},
    pages = {111},
    volume = {10},
    url = {https://www.osapublishing.org/abstract.cfm?URI=aop-10-1-111},
    doi = {10.1364/AOP.10.000111},
    issn = {1943-8206}
}

@article{Roos2009,
    title = {{Linear refractive index and absorption measurements of nonlinear optical liquids in the visible and near-infrared spectral region}},
    year = {2012},
    journal = {Optical Materials Express},
    author = {Kedenburg, S. and Vieweg, M. and Gissibl, T. and Giessen, H.},
    number = {11},
    month = {11},
    pages = {1588},
    volume = {2},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ome-2-11-1588 https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-23/issue-09/091416/Measurement-of-tissue-optical-properties-in-the-context-of-tissue/10.1117/1.JBO.23.9.091416.ful},
    doi = {10.1364/OME.2.001588},
    issn = {2159-3930}
}

@article{Colas2009,
    title = {{Live optical projection tomography}},
    year = {2009},
    journal = {Organogenesis},
    author = {Colas, Jean-François and Sharpe, James},
    number = {4},
    month = {10},
    pages = {211--216},
    volume = {5},
    url = {www.landesbioscience.com http://www.tandfonline.com/doi/abs/10.4161/org.5.4.10426},
    doi = {10.4161/org.5.4.10426},
    issn = {1547-6278}
}

@article{Ntziachristos2005,
    title = {{Looking and listening to light: The evolution of whole-body photonic imaging}},
    year = {2005},
    journal = {Nature Biotechnology},
    author = {Ntziachristos, Vasilis and Ripoll, Jorge and Wang, Lihong V. and Weissleder, Ralph},
    number = {3},
    pages = {313--320},
    volume = {23},
    doi = {10.1038/nbt1074},
    issn = {10870156}
}

@article{Thoms2013,
    title = {{Low-cost experiments on infrared phenomena}},
    year = {2013},
    journal = {Physics Education},
    author = {Thoms, L. J. and Colicchia, G. and Girwidz, R.},
    number = {1},
    pages = {16--19},
    volume = {48},
    doi = {10.1088/0031-9120/48/1/F05},
    issn = {00319120}
}

@article{Hagen2014,
    title = {{Low-dose phase contrast tomography with conventional x-ray sources}},
    year = {2014},
    journal = {Medical Physics},
    author = {Hagen, C. K. and Munro, P. R.T. and Endrizzi, M. and Diemoz, P. C. and Olivo, A.},
    number = {7},
    month = {7},
    pages = {070701},
    volume = {41},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/24989369 http://scitation.aip.org/content/aapm/journal/medphys/41/7/10.1118/1.4884297},
    isbn = {0094-2405 (Print) 0094-2405 (Linking)},
    doi = {10.1118/1.4884297},
    issn = {00942405},
    pmid = {24989369},
    keywords = {phase contrast, tomography, x-rays}
}

@inproceedings{Badea2013,
    title = {{Lung imaging in rodents using dual energy micro-CT}},
    year = {2013},
    booktitle = {Proc SPIE},
    author = {Badea, CT and Guo, X and Clark, D and Johnston, SM and Marshal, C and Piantadosi, CA},
    pages = {1--12},
    isbn = {9780819489661},
    doi = {10.1117/12.912155.Lung},
    issn = {1996-756X},
    pmid = {24027623},
    keywords = {dual energy, lung, micro-ct, small animal imaging}
}

@article{Lee2017,
    title = {{Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity}},
    year = {2017},
    journal = {Journal of Experimental Botany},
    author = {Lee, Karen J.I. and Calder, Grant M. and Hindle, Christopher R. and Newman, Jacob L. and Robinson, Simon N. and Avondo, Jerome J.H.Y. and Coen, Enrico S.},
    number = {3},
    pages = {527--538},
    volume = {68},
    doi = {10.1093/jxb/erw452},
    issn = {14602431},
    pmid = {28025317},
    keywords = {3D, Development, Gene activity, Imaging, M-OPT, Macro optical projection tomography, Macroscopic, Plant-insect interactions, Tomography, Whole plant}
}

@article{Lee2017a,
    title = {{Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity}},
    year = {2017},
    journal = {Journal of Experimental Botany},
    author = {Lee, Karen J.I. and Calder, Grant M. and Hindle, Christopher R. and Newman, Jacob L. and Robinson, Simon N. and Avondo, Jerome J.H.Y. and Coen, Enrico S.},
    number = {3},
    pages = {527--538},
    volume = {68},
    doi = {10.1093/jxb/erw452},
    issn = {14602431},
    keywords = {3D, Development, Gene activity, Imaging, M-OPT, Macro optical projection tomography, Macroscopic, Plant-insect interactions, Tomography, Whole plant}
}

@article{Yang2015,
    title = {{Macro-optical trapping for sample confinement in light sheet microscopy}},
    year = {2015},
    journal = {Biomedical Optics Express},
    author = {Yang, Zhengyi and Piksarv, Peeter and Ferrier, David E.K. and Gunn-Moore, Frank J. and Dholakia, Kishan},
    number = {8},
    pages = {2778},
    volume = {6},
    doi = {10.1364/boe.6.002778},
    issn = {2156-7085}
}

@article{WangJacquesZheng1995,
    title = {{MCML—Monte Carlo modeling of light transport in multi-layered tissues}},
    year = {1995},
    journal = {Computer Methods and Programs in Biomedicine},
    author = {Wang, Lihong and Jacques, Steven L. and Zheng, Liqiong},
    number = {2},
    month = {7},
    pages = {131--146},
    volume = {47},
    publisher = {Springer US},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/7587160 http://link.springer.com/10.1007/978-1-4757-6092-7_4 http://linkinghub.elsevier.com/retrieve/pii/016926079501640F https://linkinghub.elsevier.com/retrieve/pii/016926079501640F},
    address = {Boston, MA},
    isbn = {978-1-4757-6094-1},
    doi = {10.1016/0169-2607(95)01640-F},
    issn = {01692607},
    pmid = {7587160}
}

@article{Bashkatov2018,
    title = {{Measurement of tissue optical properties in the context of tissue optical clearing}},
    year = {2018},
    journal = {Journal of Biomedical Optics},
    author = {Bashkatov, Alexey N. and Berezin, Kirill V. and Dvoretskiy, Konstantin N. and Chernavina, Maria L. and Genina, Elina A. and Genin, Vadim D. and Kochubey, Vyacheslav I.},
    number = {09},
    month = {8},
    pages = {1},
    volume = {23},
    url = {https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-23/issue-09/091416/Measurement-of-tissue-optical-properties-in-the-context-of-tissue/10.1117/1.JBO.23.9.091416.full},
    doi = {10.1117/1.JBO.23.9.091416},
    issn = {1083-3668},
    keywords = {12, 2012, 2013, 6, 9, accepted for publication feb, kidney, oxygenation, paper 12432rr received jul, published online, revised manuscript received feb, swine, visible reflectance spectroscopy}
}

@article{Fang2010a,
    title = {{Mesh-based Monte Carlo method using fast ray-tracing in Pl{\"{u}}cker coordinates}},
    year = {2010},
    journal = {Biomedical Optics Express},
    author = {Fang, Qianqian},
    number = {1},
    pages = {165},
    volume = {1},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-1-1-165},
    isbn = {2156-7085},
    doi = {10.1364/BOE.1.000165},
    issn = {2156-7085},
    pmid = {21170299},
    keywords = {Light propagation in tissues, Photon migration, Turbid media}
}

@misc{Ripoll2016,
    title = {{Microscope and method for generating 3D images of a collection of samples}},
    year = {2016},
    author = {Ripoll, Jorge and Arranz, Alicia}
}

@article{Rieckher2011,
    title = {{Microscopic optical projection tomography in vivo}},
    year = {2011},
    journal = {PLoS ONE},
    author = {Rieckher, Matthias and Birk, Udo Jochen and Meyer, Heiko and Ripoll, Jorge and Tavernarakis, Nektarios},
    number = {4},
    pages = {2--7},
    volume = {6},
    isbn = {2006041827},
    doi = {10.1371/journal.pone.0018963},
    issn = {19326203},
    pmid = {21559481}
}

@article{Fahrbach2010,
    title = {{Microscopy with self-reconstructing beams}},
    year = {2010},
    journal = {Nature Photonics},
    author = {Fahrbach, Florian O. and Simon, Philipp and Rohrbach, Alexander},
    number = {11},
    pages = {780--785},
    volume = {4},
    publisher = {Nature Publishing Group},
    url = {http://www.nature.com/doifinder/10.1038/nphoton.2010.204},
    isbn = {1749-4885},
    doi = {10.1038/nphoton.2010.204},
    issn = {17494885},
    pmid = {16883278}
}

@article{Fahrbach2010b,
    title = {{Microscopy with self-reconstructing beams}},
    year = {2010},
    journal = {Nature Photonics},
    author = {Fahrbach, Florian O. and Simon, Philipp and Rohrbach, Alexander},
    number = {11},
    month = {11},
    pages = {780--785},
    volume = {4},
    url = {http://www.nature.com/articles/nphoton.2010.204},
    doi = {10.1038/nphoton.2010.204},
    issn = {1749-4885}
}

@article{Marx2016,
    title = {{Microscopy: OpenSPIM 2.0}},
    year = {2016},
    journal = {Nature Methods},
    author = {Marx, Vivien},
    number = {12},
    month = {12},
    pages = {979--982},
    volume = {13},
    publisher = {Nature Publishing Group},
    url = {http://www.nature.com/articles/nmeth.4070},
    doi = {10.1038/nmeth.4070},
    issn = {1548-7091}
}

@incollection{Wriedt2012,
    title = {{Mie Theory: A Review}},
    year = {2012},
    author = {Wriedt, Thomas},
    editor = {Hergert, Wolfram and Wriedt, Thomas},
    pages = {53--71},
    series = {Springer Series in Optical Sciences},
    volume = {169},
    publisher = {Springer Berlin Heidelberg},
    url = {http://link.springer.com/10.1007/978-3-642-28738-1 http://link.springer.com/10.1007/978-3-642-28738-1_2},
    address = {Berlin, Heidelberg},
    isbn = {978-3-642-28737-4},
    doi = {10.1007/978-3-642-28738-1{\_}2},
    issn = {978-3-642-28737-4},
    pmid = {25246403},
    arxivId = {arXiv:1011.1669v3}
}

@article{Kashekodi2018,
    title = {{Miniature scanning light-sheet illumination implemented in a conventional microscope}},
    year = {2018},
    journal = {Biomedical Optics Express},
    author = {Kashekodi, Anjan Bhat and Meinert, Tobias and Michiels, Rebecca and Rohrbach, Alexander},
    number = {9},
    pages = {4263},
    volume = {9},
    doi = {10.1364/boe.9.004263},
    issn = {2156-7085}
}

@article{Al-Saeed2019,
    title = {{Modeling Gaussian beam focusing by the Poynting vector in Monte Carlo simulation and a concise review}},
    year = {2019},
    journal = {Optik},
    author = {Al-Saeed, Tarek A.},
    number = {September 2018},
    pages = {71--82},
    volume = {177},
    publisher = {Elsevier},
    url = {https://doi.org/10.1016/j.ijleo.2018.09.072},
    doi = {10.1016/j.ijleo.2018.09.072},
    issn = {00304026},
    keywords = {Imaging through turbid media, Light propagation in tissues, Turbid media}
}

@article{DiRocco2013,
    title = {{Modeling transition diffusive-nondiffusive transport in a turbid media and application to time-resolved reflectance}},
    year = {2013},
    journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
    author = {Di Rocco, Héctor O. and Carbone, Nicolás A. and Iriarte, Daniela I. and Pomarico, Juan A. and Ranea Sandoval, Héctor F.},
    pages = {6--22},
    volume = {120},
    doi = {10.1016/j.jqsrt.2013.02.013},
    issn = {00224073},
    keywords = {Ballistic photons, Biomedical optics, Diffusive photons, Snake photons, Turbid media}
}

@article{Jiang2018a,
    title = {{Molecular Fluorescence and Photoacoustic Imaging in the Second Near-Infrared Optical Window Using Organic Contrast Agents}},
    year = {2018},
    journal = {Advanced Biosystems},
    author = {Jiang, Yuyan and Pu, Kanyi},
    number = {5},
    month = {5},
    pages = {1700262},
    volume = {2},
    url = {http://doi.wiley.com/10.1002/adbi.201700262},
    doi = {10.1002/adbi.201700262},
    issn = {23667478}
}

@article{Fang2009,
    title = {{Monte Carlo Simulation of Photon Migration in 3D Turbid Media Accelerated by Graphics Processing Units}},
    year = {2009},
    journal = {Optics Express},
    author = {Fang, Qianqian and Boas, David A.},
    number = {22},
    month = {10},
    pages = {20178},
    volume = {17},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-17-22-20178},
    doi = {10.1364/OE.17.020178},
    issn = {1094-4087},
    pmid = {19997242},
    arxivId = {NIHMS150003}
}

@incollection{Staelens2009,
    title = {{Monte Carlo Simulations in Nuclear Medicine Imaging}},
    year = {2009},
    booktitle = {Advances in Biomedical Engineering},
    author = {Staelens, Steven and Buvat, Irène},
    pages = {177--209},
    publisher = {Elsevier},
    url = {https://linkinghub.elsevier.com/retrieve/pii/B9780444530752000058},
    isbn = {9780444530752},
    doi = {10.1016/B978-0-444-53075-2.00005-8}
}

@article{Glaser2019,
    title = {{Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues}},
    year = {2019},
    journal = {Nature Communications},
    author = {Glaser, Adam K. and Reder, Nicholas P. and Chen, Ye and Yin, Chengbo and Wei, Linpeng and Kang, Soyoung and Barner, Lindsey A. and Xie, Weisi and McCarty, Erin F. and Mao, Chenyi and Halpern, Aaron R. and Stoltzfus, Caleb R. and Daniels, Jonathan S. and Gerner, Michael Y. and Nicovich, Philip R. and Vaughan, Joshua C. and True, Lawrence D. and Liu, Jonathan T.C.},
    number = {1},
    pages = {1--8},
    volume = {10},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41467-019-10534-0},
    isbn = {4146701910},
    doi = {10.1038/s41467-019-10534-0},
    issn = {20411723}
}

@article{Swoger2007,
    title = {{Multi-view image fusion improves resolution in three-dimensional microscopy}},
    year = {2007},
    journal = {Optics Express},
    author = {Swoger, Jim and Verveer, Peter and Greger, Klaus and Huisken, Jan and Stelzer, Ernst H.K.},
    number = {13},
    pages = {8029},
    volume = {15},
    doi = {10.1364/oe.15.008029}
}

@article{Manuscript2013,
    title = {{Multifunctional in vivo vascular imaging using near-infrared II fluorescence}},
    year = {2012},
    journal = {Nature Medicine},
    author = {Hong, Guosong and Lee, Jerry C and Robinson, Joshua T and Raaz, Uwe and Xie, Liming and Huang, Ngan F and Cooke, John P and Dai, Hongjie},
    number = {12},
    month = {12},
    pages = {1841--1846},
    volume = {18},
    url = {http://www.nature.com/articles/nm.2995},
    doi = {10.1038/nm.2995},
    issn = {1078-8956}
}

@article{Kaufmann2012,
    title = {{Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope}},
    year = {2012},
    journal = {Development},
    author = {Kaufmann, A. and Mickoleit, M. and Weber, M. and Huisken, J.},
    number = {17},
    pages = {3242--3247},
    volume = {139},
    url = {http://dev.biologists.org/cgi/doi/10.1242/dev.082586},
    isbn = {1477-9129 (Electronic){\textbackslash}r0950-1991 (Linking)},
    doi = {10.1242/dev.082586},
    issn = {0950-1991},
    pmid = {22872089},
    keywords = {in vivo imaging, light sheet microscopy, materials and methods, mounting, spim, time-lapse microscopy, zebrafish}
}

@article{Kaufmann2012a,
    title = {{Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope}},
    year = {2012},
    journal = {Development},
    author = {Kaufmann, Anna and Mickoleit, Michaela and Weber, Michael and Huisken, Jan},
    number = {17},
    month = {9},
    pages = {3242--3247},
    volume = {139},
    url = {http://dev.biologists.org/cgi/doi/10.1242/dev.082586},
    doi = {10.1242/dev.082586},
    issn = {0950-1991},
    keywords = {In vivo imaging, Light sheet microscopy, Mounting, SPIM, Time-lapse microscopy, Zebrafish}
}

@article{Bertolotti2015,
    title = {{Multiple scattering: Unravelling the tangle}},
    year = {2015},
    journal = {Nature Physics},
    author = {Bertolotti, Jacopo},
    number = {8},
    pages = {622--623},
    volume = {11},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nphys3389},
    doi = {10.1038/nphys3389},
    issn = {17452481}
}

@article{Krzic2012,
    title = {{Multiview light-sheet microscope for rapid in toto imaging}},
    year = {2012},
    journal = {Nature Methods},
    author = {Krzic, Uros and Gunther, Stefan and Saunders, Timothy E. and Streichan, Sebastian J. and Hufnagel, Lars},
    number = {7},
    pages = {730--733},
    volume = {9},
    doi = {10.1038/nmeth.2064},
    issn = {15487091}
}

@article{Hielscher2002,
    title = {{Near-Infrared Diffuse Optical Tomography}},
    year = {2002},
    journal = {Disease Markers},
    author = {Hielscher, A. H. and Bluestone, A. Y. and Abdoulaev, G. S. and Klose, A. D. and Lasker, J. and Stewart, M. and Netz, U. and Beuthan, J.},
    number = {5-6},
    pages = {313--337},
    volume = {18},
    url = {http://www.hindawi.com/journals/dm/2002/164252/abs/},
    address = {Department of Biomedical Engineering, Columbia University, New York, NY 10027-6623, USA. ahh2004@columbia.edu},
    doi = {10.1155/2002/164252},
    issn = {0278-0240},
    pmid = {14646043},
    keywords = {Optics and Photonics},
    language = {eng}
}

@article{Hong2017,
    title = {{Near-infrared fluorophores for biomedical imaging}},
    year = {2017},
    journal = {Nature Biomedical Engineering},
    author = {Hong, Guosong and Antaris, Alexander L. and Dai, Hongjie},
    number = {1},
    month = {1},
    pages = {0010},
    volume = {1},
    url = {http://www.nature.com/articles/s41551-016-0010},
    doi = {10.1038/s41551-016-0010},
    issn = {2157-846X}
}

@article{Zhao2018,
    title = {{NIR-I-to-NIR-II fluorescent nanomaterials for biomedical imaging and cancer therapy}},
    year = {2018},
    journal = {Journal of Materials Chemistry B},
    author = {Zhao, Jingya and Zhong, Dian and Zhou, Shaobing},
    number = {3},
    pages = {349--365},
    volume = {6},
    publisher = {Royal Society of Chemistry},
    url = {http://dx.doi.org/10.1039/C7TB02573D},
    isbn = {8628876340},
    doi = {10.1039/c7tb02573d},
    issn = {2050750X}
}

@article{Bertolotti2012,
    title = {{Non-invasive imaging through opaque scattering layers}},
    year = {2012},
    journal = {Nature},
    author = {Bertolotti, Jacopo and Van Putten, Elbert G. and Blum, Christian and Lagendijk, Ad and Vos, Willem L. and Mosk, Allard P.},
    number = {7423},
    pages = {232--234},
    volume = {491},
    publisher = {Nature Publishing Group},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/23135468},
    isbn = {1476-4687 (Electronic){\textbackslash}r0028-0836 (Linking)},
    doi = {10.1038/nature11578},
    issn = {00280836},
    pmid = {23135468},
    arxivId = {1403.3316},
    keywords = {Convallaria, Diffusion, Fluorescence, Lasers, Plant Stems, Tomography, Optical, Tomography, Optical: methods}
}

@article{Katz2014,
    title = {{Non-invasive single-shot imaging through scattering layers and around corners via speckle correlations}},
    year = {2014},
    journal = {Nature Photonics},
    author = {Katz, Ori and Heidmann, Pierre and Fink, Mathias and Gigan, Sylvain},
    number = {10},
    pages = {784--790},
    volume = {8},
    publisher = {Nature Publishing Group},
    url = {http://www.nature.com/doifinder/10.1038/nphoton.2014.189%5Cnpapers3://publication/doi/10.1038/nphoton.2014.189%5Cnhttp://arxiv.org/abs/1403.3316%5Cnhttp://dx.doi.org/10.1038/nphoton.2014.189},
    isbn = {1749-4885},
    doi = {10.1038/nphoton.2014.189},
    issn = {17494893},
    pmid = {23135468},
    arxivId = {1403.3316}
}

@article{Weitz1989,
    title = {{Nondiffusive Brownian motion studied by diffusing-wave spectroscopy}},
    year = {1989},
    journal = {Physical Review Letters},
    author = {Weitz, D. A. and Pine, D. J. and Pusey, P. N. and Tough, R. J. A.},
    number = {16},
    month = {10},
    pages = {1747--1750},
    volume = {63},
    url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.63.1747 https://link.aps.org/doi/10.1103/PhysRevLett.63.1747},
    doi = {10.1103/PhysRevLett.63.1747},
    issn = {0031-9007},
    pmid = {10040660}
}

@article{Vinegoni2009,
    title = {{Normalized Born ratio for fluorescence optical projection tomography}},
    year = {2009},
    journal = {Optics Letters},
    author = {Vinegoni, Claudio and Razansky, Daniel and Figueiredo, Jose-Luiz and Nahrendorf, Matthias and Ntziachristos, Vasilis and Weissleder, Ralph},
    number = {3},
    month = {2},
    pages = {319},
    volume = {34},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-34-3-319},
    doi = {10.1364/OL.34.000319},
    issn = {0146-9592}
}

@article{Shin2018,
    title = {{Oblique scanning 2-photon light-sheet fluorescence microscopy for rapid volumetric imaging}},
    year = {2018},
    journal = {Journal of Biophotonics},
    author = {Shin, Younghoon and Kim, Dongmok and Kwon, Hyuk-Sang},
    number = {5},
    month = {5},
    pages = {e201700270},
    volume = {11},
    url = {http://doi.wiley.com/10.1002/jbio.201700270},
    doi = {10.1002/jbio.201700270},
    issn = {1864063X},
    keywords = {fluorescence microscopy, light-sheet microscopy, multiphoton, oblique plane microscopy, time-lapse imaging}
}

@article{Jeongmin2019,
    title = {{Oblique-plane single-molecule localization microscopy for tissues and small intact animals}},
    year = {2019},
    journal = {Nature Methods},
    author = {Kim, Jeongmin and Wojcik, Michal and Wang, Yuan and Moon, Seonah and Zin, Emilia A. and Marnani, Nadia and Newman, Zachary L. and Flannery, John G. and Xu, Ke and Zhang, Xiang},
    number = {9},
    pages = {853--857},
    volume = {16},
    doi = {10.1038/s41592-019-0510-z},
    issn = {1548-7091}
}

@article{Dierick2004,
    title = {{Octopus, a fast and user-friendly tomographic reconstruction package developed in LabView}},
    year = {2004},
    journal = {Measurement Science and Technology},
    author = {Dierick, M. and Masschaele, B. and Van Hoorebeke, L.},
    number = {7},
    month = {7},
    pages = {1366--1370},
    volume = {15},
    url = {http://stacks.iop.org/0957-0233/15/i=7/a=020?key=crossref.45a838b30c1293c653b9c763f5abc4d6},
    isbn = {0957-0233},
    doi = {10.1088/0957-0233/15/7/020},
    issn = {09570233},
    keywords = {Cluster, Software, Tomographic reconstruction}
}

@article{Miura2018,
    title = {{On-chip light-sheet fluorescence imaging flow cytometry at a high flow speed of 1 m/s}},
    year = {2018},
    journal = {Biomedical Optics Express},
    author = {Miura, Taichi and Mikami, Hideharu and Isozaki, Akihiro and Ito, Takuro and Ozeki, Yasuyuki and Goda, Keisuke},
    number = {7},
    pages = {3424},
    volume = {9},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-9-7-3424},
    doi = {10.1364/BOE.9.003424},
    issn = {2156-7085}
}

@article{Mcgorty2015,
    title = {{Open-top selective plane illumination microscope for conventionally mounted specimens}},
    year = {2015},
    journal = {Optics Express},
    author = {McGorty, Ryan and Liu, Harrison and Kamiyama, Daichi and Dong, Zhiqiang and Guo, Su and Huang, Bo},
    number = {12},
    pages = {16142},
    volume = {23},
    doi = {10.1364/oe.23.016142}
}

@article{Pitrone2013,
    title = {{OpenSPIM: An open-access light-sheet microscopy platform}},
    year = {2013},
    journal = {Nature Methods},
    author = {Pitrone, Peter G. and Schindelin, Johannes and Stuyvenberg, Luke and Preibisch, Stephan and Weber, Michael and Eliceiri, Kevin W. and Huisken, Jan and Tomancak, Pavel},
    number = {7},
    pages = {598--599},
    volume = {10},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.2507},
    doi = {10.1038/nmeth.2507},
    issn = {15487091}
}

@article{Gualda2013,
    title = {{OpenSpinMicroscopy: An open-source integrated microscopy platform}},
    year = {2013},
    journal = {Nature Methods},
    author = {Gualda, Emilio J. and Vale, Tiago and Almada, Pedro and Feij{\'{o}}, José A. and Martins, Gabriel G. and Moreno, Nuno},
    number = {7},
    pages = {599--600},
    volume = {10},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.2508},
    doi = {10.1038/nmeth.2508},
    issn = {15487091}
}

@article{Kelbauskas2017,
    title = {{Optical computed tomography for spatially isotropic four-dimensional imaging of live single cells}},
    year = {2017},
    journal = {Science Advances},
    author = {Kelbauskas, Laimonas and Shetty, Rishabh and Cao, Bin and Wang, Kuo-Chen and Smith, Dean and Wang, Hong and Chao, Shi-Hui and Gangaraju, Sandhya and Ashcroft, Brian and Kritzer, Margaret and Glenn, Honor and Johnson, Roger H. and Meldrum, Deirdre R.},
    number = {12},
    month = {12},
    pages = {e1602580},
    volume = {3},
    url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1602580},
    doi = {10.1126/sciadv.1602580},
    issn = {2375-2548}
}

@article{Sani2014,
    title = {{Optical constants of ethylene glycol over an extremely wide spectral range}},
    year = {2014},
    journal = {Optical Materials},
    author = {Sani, Elisa and Dell’Oro, Aldo},
    number = {C},
    month = {11},
    pages = {36--41},
    volume = {37},
    publisher = {Elsevier B.V.},
    url = {http://dx.doi.org/10.1016/j.optmat.2014.04.035 https://linkinghub.elsevier.com/retrieve/pii/S092534671400202X},
    doi = {10.1016/j.optmat.2014.04.035},
    issn = {09253467},
    keywords = {Ethylene glycol, Liquid phase, Optical constants, Optical properties, Solar energy}
}

@article{Hale1973,
    title = {{Optical Constants of Water in the 200-nm to 200-{$\mu$}m Wavelength Region}},
    year = {1973},
    journal = {Applied Optics},
    author = {Hale, George M. and Querry, Marvin R.},
    number = {3},
    month = {3},
    pages = {555},
    volume = {12},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-12-3-555},
    doi = {10.1364/AO.12.000555},
    issn = {0003-6935}
}

@article{Hebden1997,
    title = {{Optical imaging in medicine .2. Modelling and reconstruction}},
    year = {1997},
    journal = {Physics in medicine and biology},
    author = {{Arridge} and Hebden, Jc},
    number = {5},
    pages = {841--853},
    volume = {42},
    url = {http://discovery.ucl.ac.uk/98942/},
    isbn = {0031-9155},
    doi = {10.1088/0031-9155/42/5/008},
    issn = {0031-9155},
    pmid = {9172263},
    keywords = {FINITE-ELEMENT-METHOD, MEASUREMENT DENSITY-FUNCTIO}
}

@article{Oliveira2013,
    title = {{Optical measurements of rat muscle samples under treatment with ethylene glycol and glucose}},
    year = {2013},
    journal = {Journal of Innovative Optical Health Sciences},
    author = {Oliveira, Luís and Carvalho, Maria Inês and Nogueira, Elisabete and Tuchin, Valery V.},
    number = {2},
    pages = {1--15},
    volume = {6},
    doi = {10.1142/S1793545813500120},
    issn = {17935458},
    keywords = {Tissue optical clearing, agent diffusivity, optical absorbance, optical reflectance, optical transmittance}
}

@article{Sharpe2002,
    title = {{Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies}},
    year = {2002},
    journal = {Science},
    author = {Sharpe, James},
    number = {5567},
    month = {4},
    pages = {541--545},
    volume = {296},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/11964482 http://www.sciencemag.org/cgi/doi/10.1126/science.1068206},
    doi = {10.1126/science.1068206},
    issn = {00368075},
    pmid = {11964482},
    keywords = {Anatomy, Animals, Computer-Assisted, Cross-Sectional, DNA-Binding Proteins, DNA-Binding Proteins: analysis, Embryo, Embryonic and Fetal Development, Fluorescence, Fluorescence: instrumentation, Fluorescence: methods, Fluorescent Antibody Technique, Gene Expression, Gene Expression Profiling, Gene Expression Profiling: instrumentation, Gene Expression Profiling: methods, Hepatocyte Nuclear Factor 3-beta, Image Processing, Immunohistochemistry, In Situ Hybridization, Magnetic Resonance Imaging, Mammalian, Mammalian: anatomy {\&} histology, Mammalian: metabolism, Mice, Microscopy, Microscopy: instrumentation, Microscopy: methods, Mutation, Nervous System, Nervous System: embryology, Neurofilament Proteins, Neurofilament Proteins: analysis, Nuclear Proteins, Nuclear Proteins: analysis, Software, Stomach, Stomach: embryology, Tomography, Transcription Factors}
}

@article{Nguyen2017,
    title = {{Optical projection tomography for rapid whole mouse brain imaging}},
    year = {2017},
    journal = {Biomedical Optics Express},
    author = {Nguyen, David and Marchand, Paul J. and Planchette, Arielle L. and Nilsson, Julia and Sison, Miguel and Extermann, Jérôme and Lopez, Antonio and Sylwestrzak, Marcin and Sordet-Dessimoz, Jessica and Schmidt-Christensen, Anja and Holmberg, Dan and Van De Ville, Dimitri and Lasser, Theo},
    number = {12},
    pages = {5637},
    volume = {8},
    doi = {10.1364/boe.8.005637},
    issn = {2156-7085}
}

@article{Ancora2018,
    title = {{Optical projection tomography via phase retrieval algorithms}},
    year = {2018},
    journal = {Methods},
    author = {Ancora, Daniele and Di Battista, Diego and Giasafaki, Georgia and Psycharakis, Stylianos E. and Liapis, Evangelos and Ripoll, Jorge and Zacharakis, Giannis},
    pages = {81--89},
    volume = {136},
    publisher = {Elsevier Inc.},
    url = {https://doi.org/10.1016/j.ymeth.2017.10.009},
    doi = {10.1016/j.ymeth.2017.10.009},
    issn = {10959130},
    keywords = {Autocorrelation imaging, Hidden object tomography, Optical projection tomography, Phase retrieval, Registration-free imaging}
}

@article{Jacques2013,
    title = {{Optical properties of biological tissues: a review}},
    year = {2013},
    journal = {Physics in medicine and biology},
    author = {Jacques, Steven L.},
    number = {11},
    month = {6},
    pages = {37--61},
    volume = {58},
    url = {http://stacks.iop.org/0031-9155/58/i=14/a=5007?key=crossref.c531ac37cfa1f77bbc0d33a8e92de8c9 http://www.ncbi.nlm.nih.gov/pubmed/23666068},
    doi = {10.1088/0031-9155/58/11/R37},
    issn = {1361-6560},
    pmid = {23666068}
}

@inproceedings{Bashkatov2014,
    title = {{Optical properties of human cranial bone in the spectral range from 800 to 2000 nm}},
    year = {2006},
    booktitle = {Saratov Fall Meeting 2005: Optical Technologies in Biophysics and Medicine VII},
    author = {Bashkatov, Alexey N. and Genina, Elina A. and Kochubey, Vyacheslav I. and Tuchin, Valery V.},
    editor = {Tuchin, Valery V.},
    month = {8},
    pages = {616310},
    volume = {6163},
    url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1280792},
    organization = {International Society for Optics and Photonics},
    address = {Saratov},
    doi = {10.1117/12.697305},
    keywords = {absorption, bone, in vitro, infrared, optical properties, scattering, spectroscopy}
}

@article{Bashkatov2005,
    title = {{Optical properties of human skin, subcutaneos and mucous tissues in the wavelength range from 400 tol 2000 nm}},
    year = {2005},
    journal = {Journal of Physics D: Applied Physics},
    author = {Bashkatov, Alexey N. and Genina, Elina A. and Kochubey, V I and Tuchin, Valery V.},
    number = {15},
    pages = {2543--2555},
    volume = {38},
    url = {http://stacks.iop.org/0022-3727/38/i=15/a=004},
    doi = {10.1088/0022-3727/38/15/004},
    issn = {0022-3727},
    pmid = {16}
}

@article{Flock1992,
    title = {{Optical properties of Intralipid: a phantom medium for light propagation studies.}},
    year = {1992},
    journal = {Lasers in surgery and medicine},
    author = {Flock, Stephen T. and Jacques, Steven L. and Wilson, Brian C and Star, Willem M and van Gemert, M J},
    number = {5},
    pages = {510--9},
    volume = {12},
    url = {http://doi.wiley.com/10.1002/lsm.1900120510 http://www.ncbi.nlm.nih.gov/pubmed/1406004},
    doi = {10.1002/lsm.1900120510},
    issn = {0196-8092},
    pmid = {1406004},
    keywords = {intralipid, light-dosimetry, optical-interaction-coefficients, phantom, radiative-transfer, similarity}
}

@article{Moy2015,
    title = {{Optical properties of mouse brain tissue after optical clearing with FocusClear™}},
    year = {2015},
    journal = {Journal of Biomedical Optics},
    author = {Moy, Austin J. and Capulong, Bernard V. and Saager, Rolf B. and Wiersma, Matthew P. and Lo, Patrick C. and Durkin, Anthony J. and Choi, Bernard},
    number = {9},
    month = {9},
    pages = {095010},
    volume = {20},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.20.9.095010},
    doi = {10.1117/1.JBO.20.9.095010},
    issn = {1083-3668},
    keywords = {12, 2015, 21, 8, accepted for publication aug, optical clearing, optical properties, paper 150237r received apr, published online sep, scattering, tissue optics}
}

@article{Bashkatov2011,
    title = {{Optical properties of skin, subcutaneous, and muscle tissues: A review}},
    year = {2011},
    journal = {Journal of Innovative Optical Health Sciences},
    author = {Bashkatov, Alexey N. and Genina, Elina A. and Tuchin, Valery V.},
    number = {01},
    month = {1},
    pages = {9--38},
    volume = {04},
    url = {http://www.worldscientific.com/doi/abs/10.1142/S1793545811001319},
    doi = {10.1142/S1793545811001319},
    issn = {1793-5458}
}

@incollection{Marcos-Vidal2019,
    title = {{Optical properties of tissues in the near infrared: Their relevance for optical bioimaging}},
    year = {2019},
    booktitle = {Near-Infrared-Emitting Nanoparticles for Biomedical Applications},
    author = {Marcos-Vidal, Asier and Vaquero, Juan José and Ripoll, Jorge},
    editor = {Benayas, Antonio and Hemmer, Eva and Hong, Guosong and Jaque, Daniel},
    chapter = {1},
    edition = {1},
    publisher = {Springer International Publishing},
    doi = {10.1007/978-3-030-32036-2}
}

@article{Palmer1974,
    title = {{Optical properties of water in the near infrared*}},
    year = {1974},
    journal = {Journal of the Optical Society of America},
    author = {Palmer, Kent F. and Williams, Dudley},
    number = {8},
    month = {8},
    pages = {1107},
    volume = {64},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josa-64-8-1107},
    doi = {10.1364/JOSA.64.001107},
    issn = {0030-3941}
}

@article{SuchandSandeep2019,
    title = {{Optical sectioning and high resolution visualization of trabecular meshwork using Bessel beam assisted light sheet fluorescence microscopy}},
    year = {2019},
    journal = {Journal of Biophotonics},
    author = {Suchand Sandeep, C. S. and Sarangapani, Sreelatha and Hong, Xun J. J. and Aung, Tin and Baskaran, Mani and Murukeshan, Vadakke M.},
    number = {July},
    pages = {1--6},
    doi = {10.1002/jbio.201900048},
    issn = {1864-063X},
    keywords = {aqueous outflow system, bessel beam, centre for optical and, glaucoma, laser engineering, light sheet, lsfm, ocular imaging, optical sectioning, trabecular meshwork}
}

@article{Huisken2004,
    title = {{Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy}},
    year = {2004},
    journal = {Science},
    author = {Huisken, Jan},
    number = {5686},
    month = {8},
    pages = {1007--1009},
    volume = {305},
    url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1100035 http://www.ncbi.nlm.nih.gov/pubmed/15310904},
    doi = {10.1126/science.1100035},
    issn = {0036-8075},
    pmid = {15310904}
}

@article{Wang2018,
    title = {{Optical Sectioning of Live Mammal with Near-Infrared Light Sheet}},
    year = {2018},
    journal = {BioarXiv},
    author = {Wang, Feifei and Wan, Hao and Yue, Jingying and Zhang, Mingxi and Ma, Zhuoran and Sun, Qinchao},
    doi = {10.1101/447433}
}

@article{Bassi2015,
    title = {{Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development}},
    year = {2015},
    journal = {Development},
    author = {Bassi, A. and Schmid, B. and Huisken, J.},
    number = {5},
    month = {3},
    pages = {1016--1020},
    volume = {142},
    url = {http://dev.biologists.org/cgi/doi/10.1242/dev.116970},
    doi = {10.1242/dev.116970},
    issn = {0950-1991},
    pmid = {25655702},
    keywords = {Animals, Embryo, Microscopy, Nonmammalian, Optical, Tomography, Zebrafish}
}

@article{Arridge1999,
    title = {{Optical tomography in medical imaging}},
    year = {1999},
    journal = {Inverse Problems},
    author = {Arridge, Simon R},
    number = {2},
    pages = {R41-R93},
    volume = {15},
    url = {http://stacks.iop.org/0266-5611/15/i=2/a=022},
    isbn = {02665611 (ISSN)},
    doi = {10.1088/0266-5611/15/2/022},
    issn = {0266-5611}
}

@article{Arridge2009,
    title = {{Optical tomography: forward and inverse problems}},
    year = {2009},
    journal = {Inverse Problems},
    author = {Arridge, Simon R. and Schotland, John C.},
    number = {12},
    month = {12},
    pages = {123010},
    volume = {25},
    url = {http://stacks.iop.org/0266-5611/25/i=12/a=123010?key=crossref.f11916d483a3f159d89cc0d87c982047},
    doi = {10.1088/0266-5611/25/12/123010},
    issn = {0266-5611},
    arxivId = {0907.2586}
}

@article{Haidekker2005,
    title = {{Optical transillumination tomography with tolerance against refraction mismatch}},
    year = {2005},
    journal = {Computer Methods and Programs in Biomedicine},
    author = {Haidekker, Mark A.},
    number = {3},
    month = {12},
    pages = {225--235},
    volume = {80},
    url = {https://linkinghub.elsevier.com/retrieve/pii/S0169260705001914},
    doi = {10.1016/j.cmpb.2005.09.002},
    issn = {01692607},
    pmid = {16257081},
    keywords = {Algebraic reconstruction technique, Computed tomography, Reconstruction, Refraction}
}

@article{Dunsby2009,
    title = {{Optically sectioned imaging by oblique plane microscopy}},
    year = {2008},
    journal = {Optics Express},
    author = {Dunsby, C.},
    number = {25},
    month = {12},
    pages = {20306},
    volume = {16},
    isbn = {9780819476432},
    doi = {10.1364/OE.16.020306},
    issn = {1094-4087},
    keywords = {Fluorescence microscopy, Selective plane illumination microscopy, Three-dimensional microscopy}
}

@article{VallejoRamirez2019,
    title = {{OptiJ: Open-source optical projection tomography of large organ samples}},
    year = {2019},
    journal = {bioRxiv},
    author = {Vallejo Ramirez, Pedro P and Zammit, Joseph and Vanderpoorten, Oliver and Riche, Fergus and Bl{\'{e}}, François-Xavier and Zhou, Xiao-Hong and Spiridon, Bogdan and Valentine, Christopher and Spasov, Simeon P and Oluwasanya, Pelumi W and Goodfellow, Gemma and Fantham, Marcus J and Siddiqui, Omid and Alimagham, Farah and Robbins, Miranda and Stretton, Andrew and Simatos, Dimitrios and Hadeler, Oliver and Rees, Eric J and Str{\"{o}}hl, Florian and Laine, Romain F and Kaminski, Clemens F},
    pages = {1--8},
    url = {http://dx.doi.org/10.1101/656488},
    doi = {10.1101/656488}
}

@article{Watson2017,
    title = {{OPTiM: Optical projection tomography integrated microscope using open-source hardware and software}},
    year = {2017},
    journal = {PLoS ONE},
    author = {Watson, Thomas and Andrews, Natalie and Davis, Samuel and Bugeon, Laurence and Dallman, Margaret D. and McGinty, James},
    number = {7},
    pages = {1--13},
    volume = {12},
    isbn = {1111111111},
    doi = {10.1371/journal.pone.0180309},
    issn = {19326203}
}

@article{Gao2015,
    title = {{Optimization of the excitation light sheet in selective plane illumination microscopy}},
    year = {2015},
    journal = {Biomedical Optics Express},
    author = {Gao, Liang},
    number = {3},
    month = {3},
    pages = {881},
    volume = {6},
    publisher = {The Optical Society},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-6-3-881},
    doi = {10.1364/BOE.6.000881},
    issn = {2156-7085}
}

@article{Mayer2014,
    title = {{OPTiSPIM: integrating optical projection tomography in light sheet microscopy extends specimen characterization to nonfluorescent contrasts}},
    year = {2014},
    journal = {Optics Letters},
    author = {Mayer, Jürgen and Robert-Moreno, Alexandre and Danuser, Renzo and Stein, Jens V. and Sharpe, James and Swoger, Jim},
    number = {4},
    pages = {1053},
    volume = {39},
    doi = {10.1364/ol.39.001053},
    issn = {0146-9592}
}

@article{VOIE1993,
    title = {{Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens.}},
    year = {1993},
    journal = {Journal of microscopy},
    author = {Voie, A H and Burns, D H and Spelman, F A},
    number = {Pt 3},
    month = {6},
    pages = {229--36},
    volume = {170},
    url = {http://doi.wiley.com/10.1111/j.1365-2818.1993.tb03346.x http://www.ncbi.nlm.nih.gov/pubmed/8371260},
    doi = {10.1111/j.1365-2818.1993.tb03346.x},
    issn = {0022-2720},
    pmid = {8371260},
    keywords = {cochlea, fluorescence, imaging, optical sectioning, reconstruction, three-dimensional}
}

@article{Hansen2008,
    title = {{Overview of SWIR detectors, cameras, and applications}},
    year = {2008},
    author = {Hansen, Marc P. and Malchow, Douglas S.},
    number = {March 2008},
    pages = {69390I},
    url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.777776},
    isbn = {978-0-8194-7130-7},
    doi = {10.1117/12.777776},
    issn = {0277786X},
    keywords = {biological, imaging, ingaas, inspection, near infrared, night vision, nir, oct, optical coherence tomography, photodiode arrays, short-wave infrared, sorting, swir, vein imaging}
}

@article{Alerstam2008,
    title = {{Parallel computing with graphics processing units for high-speed Monte Carlo simulation of photon migration}},
    year = {2008},
    journal = {Journal of Biomedical Optics},
    author = {Alerstam, Erik and Svensson, Tomas and Andersson-Engels, Stefan},
    number = {6},
    pages = {060504},
    volume = {13},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.3041496},
    doi = {10.1117/1.3041496},
    issn = {10833668},
    keywords = {15, 16, 2008, 8, accepted for publication oct, biomedical optics, monte carlo, oct, paper 08231lrr received jul, published on-, revised manuscript received, scattering, simulations}
}

@article{Zhang2016,
    title = {{Penetration depth of photons in biological tissues from hyperspectral imaging in shortwave infrared in transmission and reflection geometries}},
    year = {2016},
    journal = {Journal of Biomedical Optics},
    author = {Zhang, Hairong and Salo, Daniel and Kim, David M. and Komarov, Sergey and Tai, Yuan-Chuan and Berezin, Mikhail Y.},
    number = {12},
    month = {12},
    pages = {126006},
    volume = {21},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.21.12.126006},
    doi = {10.1117/1.JBO.21.12.126006},
    issn = {1083-3668},
    pmid = {27930773},
    keywords = {carlo, deep tissue imaging, extended nir, hyperspectral imaging, michelson contrast, monte, shortwave infrared}
}

@article{Palenstijn2011,
    title = {{Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)}},
    year = {2011},
    journal = {Journal of Structural Biology},
    author = {Palenstijn, W. J. and Batenburg, K. J. and Sijbers, J.},
    number = {2},
    pages = {250--253},
    volume = {176},
    publisher = {Elsevier Inc.},
    url = {http://dx.doi.org/10.1016/j.jsb.2011.07.017},
    isbn = {1047-8477},
    doi = {10.1016/j.jsb.2011.07.017},
    issn = {10478477},
    pmid = {21840398},
    keywords = {Electron tomography, GPU, Reconstruction}
}

@article{Pogue2018,
    title = {{Perspective review of what is needed for molecular-specific fluorescence-guided surgery.}},
    year = {2018},
    journal = {Journal of Biomedical Optics},
    author = {Pogue, Brian W and Rosenthal, Eben L and Dam, Gooitzen M Van},
    number = {10},
    volume = {23},
    url = {http://doi.org/10.1117/1.JBO.23.10.100601},
    doi = {10.1117/1.JBO.23.10.100601},
    issn = {1083-3668},
    keywords = {2018, 23, 5, 7, accepted for publication sep, active, cancer, emerged as a very, fluorescent, molecular image-guided surgery has, paper 180464-per received jul, potential to allow surgeons, published online oct, research field with transformative, resection, surgical, therapy, to}
}

@article{Momose2006,
    title = {{Phase Imaging With an X-Ray Talbot Interferometer}},
    year = {2006},
    journal = {Citeseer},
    author = {Momose, Atsushi and Yashiro, Wataru and Takeda, Yoshihiro and Yashiro, Aw W and Takeda, Ay Y and Suzuki, Y and Hattori, T},
    pages = {21--30},
    url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.296.791&rep=rep1&type=pdf},
    isbn = {0255-5476},
    doi = {10.1143/JJAP.45.5254},
    issn = {0021-4922},
    pmid = {548},
    arxivId = {10.1107/S0021889892004084}
}

@article{Shechtman2015,
    title = {{Phase Retrieval with Application to Optical Imaging: A contemporary overview}},
    year = {2015},
    journal = {IEEE Signal Processing Magazine},
    author = {Shechtman, Yoav and Eldar, Yonina C. and Cohen, Oren and Chapman, Henry Nicholas and Miao, Jianwei and Segev, Mordechai},
    number = {3},
    month = {5},
    pages = {87--109},
    volume = {32},
    url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=7078985},
    isbn = {1053-5888},
    doi = {10.1109/MSP.2014.2352673},
    issn = {1053-5888},
    arxivId = {1402.7350}
}

@article{Naraghi2016,
    title = {{Phase Transitions in Diffusion of Light}},
    year = {2016},
    journal = {Physical Review Letters},
    author = {Naraghi, Roxana Rezvani and Dogariu, Aristide},
    number = {26},
    pages = {1--5},
    volume = {117},
    isbn = {9781943580279},
    doi = {10.1103/PhysRevLett.117.263901},
    issn = {10797114}
}

@article{Ancora2017,
    title = {{Phase-Retrieved Tomography enables Mesoscopic imaging of Opaque Tumor Spheroids}},
    year = {2017},
    journal = {Scientific Reports},
    author = {Ancora, Daniele and Di Battista, Diego and Giasafaki, Georgia and Psycharakis, Stylianos E. and Liapis, Evangelos and Ripoll, Jorge and Zacharakis, Giannis},
    number = {1},
    month = {12},
    pages = {11854},
    volume = {7},
    url = {http://www.nature.com/articles/s41598-017-12193-x},
    doi = {10.1038/s41598-017-12193-x},
    issn = {20452322}
}

@article{Aronson1999,
    title = {{Photon diffusion coefficient in an absorbing medium}},
    year = {1999},
    journal = {Journal of the Optical Society of America A},
    author = {Aronson, Raphael and Corngold, Noel},
    number = {5},
    month = {5},
    pages = {1066},
    volume = {16},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-16-5-1066},
    doi = {10.1364/JOSAA.16.001066},
    issn = {1084-7529},
    pmid = {10234856},
    keywords = {Co-design, Food manufacturing, Food waste, Resource efficiency, Stakeholder engagement, Sustainability tool, True cost of waste}
}

@article{Pierrat2006,
    title = {{Photon diffusion coefficient in scattering and absorbing media}},
    year = {2006},
    journal = {Journal of the Optical Society of America A},
    author = {Pierrat, Romain and Greffet, Jean-Jacques and Carminati, Rémi},
    number = {5},
    month = {5},
    pages = {1106},
    volume = {23},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-23-5-1106},
    doi = {10.1364/JOSAA.23.001106},
    issn = {1084-7529},
    pmid = {16642188},
    keywords = {Diffusion, Light propagation in tissues, Multiple scattering, Photon migration, Turbid media}
}

@article{Vollmer2017,
    title = {{Photonics in nature: Yellowstone National Park in IR}},
    year = {2017},
    journal = {14th Conference on Education and Training in Optics and Photonics: ETOP 2017},
    author = {Vollmer, Michael and Shaw, Jospeh A. and Nugent, Paul W. and Harris, Wilson and Gillis, Kendra and Weiss, William and Carpenter, Logan and Carpenter, Amy and Scherrer, Bryan},
    number = {August 2017},
    pages = {73},
    url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10452/2266677/Photonics-in-nature-Yellowstone-National-Park-in-IR/10.1117/12.2266677.full},
    isbn = {9781510613812},
    doi = {10.1117/12.2266677},
    issn = {1996756X}
}

@article{Abdellah2015,
    title = {{Physically-based in silico light sheet microscopy for visualizing fluorescent brain models}},
    year = {2015},
    journal = {BMC Bioinformatics},
    author = {Abdellah, Marwan and Bilgili, Ahmet and Eilemann, Stefan and Markram, Henry and Sch{\"{u}}rmann, Felix},
    number = {11},
    pages = {S8},
    volume = {16},
    publisher = {BioMed Central Ltd},
    url = {http://www.biomedcentral.com/1471-2105/16/S11/S8},
    isbn = {0962-8479 (Print){\textbackslash}n0962-8479 (Linking)},
    doi = {10.1186/1471-2105-16-S11-S8},
    issn = {14712105},
    pmid = {26329404},
    keywords = {Fluorescence rendering and visualization, In silico neuroscience, Light sheet fluorescence microscopy, Modelling and simulation, Neocortical brain models}
}

@article{Bonanno2018,
    title = {{Physics meets fine arts: A project-based learning path on infrared imaging}},
    year = {2018},
    journal = {European Journal of Physics},
    author = {Bonanno, A. and Bozzo, G. and Sapia, P.},
    number = {2},
    volume = {39},
    publisher = {IOP Publishing},
    doi = {10.1088/1361-6404/aa9cac},
    issn = {13616404},
    keywords = {color, fine arts, infrared radiation, low cost devices, problem based learning, reflectography}
}

@article{Trull2017,
    title = {{Point spread function based image reconstruction in optical projection tomography}},
    year = {2017},
    journal = {Physics in Medicine and Biology},
    author = {Trull, Anna K. and Van Der Horst, Jelle and Palenstijn, Willem Jan and Van Vliet, Lucas J. and Van Leeuwen, Tristan and Kalkman, Jeroen},
    number = {19},
    pages = {7784--7797},
    volume = {62},
    publisher = {IOP Publishing},
    doi = {10.1088/1361-6560/aa8945},
    issn = {13616560},
    keywords = {image reconstruction techniques, inverse problems, tomographic image processing}
}

@article{Reidt2016,
    title = {{Polarised light sheet tomography}},
    year = {2016},
    journal = {Optics Express},
    author = {Reidt, Sascha L. and O’Brien, Daniel J. and Wood, Kenneth and MacDonald, Michael P.},
    number = {10},
    month = {5},
    pages = {11239},
    volume = {24},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-24-10-11239},
    doi = {10.1364/OE.24.011239},
    issn = {1094-4087}
}

@article{Fang2016,
    title = {{Polarization-sensitive optical projection tomography for muscle fiber imaging}},
    year = {2016},
    journal = {Scientific Reports},
    author = {Fang, Mengjie and Dong, Di and Zeng, Chaoting and Liang, Xiao and Yang, Xin and Arranz, Alicia and Ripoll, Jorge and Hui, Hui and Tian, Jie},
    number = {December 2015},
    pages = {1--8},
    volume = {6},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/srep19241},
    doi = {10.1038/srep19241},
    issn = {20452322}
}

@article{Jacques2004,
    title = {{Polarized Light imaging of tissues}},
    year = {2004},
    journal = {Lasers and Current Optical Techniques in Biology},
    author = {Jacques, Steven L and Ramella-Roman, Jessica C},
    number = {Anderson 1991},
    pages = {649--670},
    publisher = {Royal Society of Chemistry}
}

@article{Tuchin2016,
    title = {{Polarized light interaction with tissues}},
    year = {2016},
    journal = {Journal of Biomedical Optics},
    author = {Tuchin, Valery V.},
    number = {7},
    pages = {071114},
    volume = {21},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.21.7.071114},
    isbn = {1083-3668},
    doi = {10.1117/1.JBO.21.7.071114},
    issn = {1083-3668},
    pmid = {27121763},
    keywords = {2016, 22, 28, 4, accepted for publication mar, biomedical optics, birefringence, medical imaging, optical properties, paper 160010sstr received jan, polarization, published online apr, tissues}
}

@inproceedings{Vogeler2011,
    title = {{Positional stability of 2D X-ray images for computer tomography}},
    year = {2011},
    booktitle = {International Symposium on Digital Industrial Radiology and Computed Tomography},
    author = {Vogeler, Frederik and Verheecke, Wesley and Voet, André and Kruth, Jean-pierre},
    pages = {9},
    address = {Berlin, Germany}
}

@book{Kak1988,
    title = {{Principles of Computerized Tomographic Imaging}},
    year = {2001},
    author = {Kak, Avinash C. and Slaney, Malcolm},
    month = {1},
    publisher = {Society for Industrial and Applied Mathematics},
    url = {http://epubs.siam.org/doi/book/10.1137/1.9780898719277},
    isbn = {978-0-89871-494-4},
    doi = {10.1137/1.9780898719277}
}

@book{Lorenzo2012,
    title = {{Principles of Diffuse Light Propagation: Light Propagation in Tissues with Applications in Biology and Medicine}},
    year = {2012},
    booktitle = {World Scientific},
    author = {Ripoll, Jorge},
    pages = {336},
    publisher = {World Scientific},
    url = {http://www.tandfonline.com/doi/abs/10.1080/00107514.2013.810670},
    isbn = {9789814293761},
    doi = {10.1080/00107514.2013.810670},
    issn = {0010-7514}
}

@book{Born1999,
    title = {{Principles of Optics}},
    year = {1999},
    author = {Born, Max and Wolf, Emil and Bhatia, A. B. and Clemmow, P. C. and Gabor, D. and Stokes, A. R. and Taylor, A. M. and Wayman, P. A. and Wilcock, W. L.},
    publisher = {Cambridge University Press},
    url = {http://ebooks.cambridge.org/ref/id/CBO9781139644181},
    address = {Cambridge},
    isbn = {9781139644181},
    doi = {10.1017/CBO9781139644181}
}

@inproceedings{Marcos-Vidal2018,
    title = {{Projection tomography in the NIR-IIa window: Challenges, advantages, and comparison with classical optical approach}},
    year = {2018},
    booktitle = {Progress in Biomedical Optics and Imaging - Proceedings of SPIE},
    author = {Marcos-Vidal, A. and Ancora, D. and Zacharakis, G. and Vaquero, J.J. and Ripoll, J.},
    volume = {10573},
    isbn = {9781510616356},
    doi = {10.1117/12.2293708},
    issn = {16057422},
    keywords = {OPT, Optical Imaging, near-infrared-filtered-backprojection}
}

@article{Ping2019,
    title = {{Propagating-path uniformly scanned light sheet excitation microscopy for isotropic volumetric imaging of large specimens}},
    year = {2019},
    journal = {Journal of Biomedical Optics},
    author = {Ping, Junyu and Zhao, Fang and Nie, Jun and Yu, Tingting and Zhu, Dan and Liu, Mugen and Fei, Peng},
    number = {08},
    pages = {1},
    volume = {24},
    doi = {10.1117/1.jbo.24.8.086501},
    keywords = {biomedical optics, imaging systems, isotropic resolution, light-sheet microscopy, optical design, three-dimensional}
}

@article{Fahrbach2012,
    title = {{Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media}},
    year = {2012},
    journal = {Nature Communications},
    author = {Fahrbach, Florian O. and Rohrbach, Alexander},
    number = {1},
    month = {1},
    pages = {632},
    volume = {3},
    url = {http://www.nature.com/articles/ncomms1646},
    doi = {10.1038/ncomms1646},
    issn = {2041-1723}
}

@article{Madrid-Wolff2019,
    title = {{Protocol for the Design and Assembly of a Light Sheet Light Field Microscope}},
    year = {2019},
    journal = {Methods and Protocols},
    author = {Madrid-Wolff, Jorge and Forero-Shelton, Manu},
    number = {3},
    pages = {56},
    volume = {2},
    doi = {10.3390/mps2030056},
    keywords = {3d imaging, fast, imaging, light field microscopy, light sheet fluorescence microscopy, lsfm, open science}
}

@article{Tuchina2015,
    title = {{Quantification of glucose and glycerol diffusion in myocardium}},
    year = {2015},
    journal = {Journal of Innovative Optical Health Sciences},
    author = {Tuchina, Daria K. and Bashkatov, Alexey N. and Genina, Elina A. and Tuchin, Valery V.},
    number = {03},
    month = {5},
    pages = {1541006},
    volume = {08},
    url = {https://www.worldscientific.com/doi/abs/10.1142/S1793545815410060},
    doi = {10.1142/S1793545815410060},
    issn = {1793-5458},
    keywords = {Diffusion coefficient, dehydration, optical clearing, scattering}
}

@article{Tomer2012,
    title = {{Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy}},
    year = {2012},
    journal = {Nature Methods},
    author = {Tomer, Raju and Khairy, Khaled and Amat, Fernando and Keller, Philipp J.},
    number = {7},
    pages = {755--763},
    volume = {9},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nmeth.2062},
    doi = {10.1038/nmeth.2062},
    issn = {15487091}
}

@article{Hu2017,
    title = {{Quantum Dots Emitting in the Third Biological Window as Bimodal Contrast Agents for Cardiovascular Imaging}},
    year = {2017},
    journal = {Advanced Functional Materials},
    author = {Hu, Jie and Ortgies, Dirk H. and Aguliar Torres, Rio and Fern{\'{a}}ndez, Nuria and Porto, Lucas and Mart{\'{i}}n Rodr{\'{i}}guez, Emma and Garc{\'{i}}a Sol{\'{e}}, José and Jaque, Daniel and Alfonso, Fernando and Rivero, Fernando},
    number = {41},
    pages = {1--9},
    volume = {27},
    doi = {10.1002/adfm.201703276},
    issn = {16163028},
    keywords = {cardiovascular imaging, coronary artery disease, infrared imaging, molecular imaging, optical coherence tomography, quantum dots}
}

@article{Granot2006,
    title = {{Quasi-ballistic imaging through a dynamic scattering medium with optical-field averaging using Spectral-Ballistic-Imaging.}},
    year = {2006},
    journal = {Optics Express},
    author = {Granot, Er'el and Sternklar, Shmuel and Ben-Aderet, Yossi and Schermann, Dan},
    number = {19},
    pages = {8598--8603},
    volume = {14},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/19529239},
    doi = {10.1364/OE.14.008598},
    issn = {1094-4087},
    pmid = {19529239}
}

@article{Fahrbach2013,
    title = {{Rapid 3D light-sheet microscopy with a tunable lens}},
    year = {2013},
    journal = {Optics Express},
    author = {Fahrbach, Florian O. and Voigt, Fabian F. and Schmid, Benjamin and Helmchen, Fritjof and Huisken, Jan},
    number = {18},
    month = {9},
    pages = {21010},
    volume = {21},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-21-18-21010},
    doi = {10.1364/OE.21.021010},
    issn = {1094-4087},
    pmid = {24103973}
}

@article{Fahrbach2013a,
    title = {{Rapid 3D light-sheet microscopy with a tunable lens}},
    year = {2013},
    journal = {Optics Express},
    author = {Fahrbach, Florian O. and Voigt, Fabian F. and Schmid, Benjamin and Helmchen, Fritjof and Huisken, Jan},
    number = {18},
    pages = {21010},
    volume = {21},
    doi = {10.1364/oe.21.021010}
}

@article{Planchon2011,
    title = {{Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination}},
    year = {2011},
    journal = {Nature Methods},
    author = {Planchon, Thomas A. and Gao, Liang and Milkie, Daniel E. and Davidson, Michael W. and Galbraith, James A. and Galbraith, Catherine G. and Betzig, Eric},
    number = {5},
    pages = {417--423},
    volume = {8},
    doi = {10.1038/nmeth.1586},
    issn = {15487091}
}

@misc{NASANAOJ,
    title = {{Rayleigh scattering in exoplanet atmospheres}},
    author = {{NASA NAOJ}},
    url = {https://exoplanets.nasa.gov/resources/168/rayleigh-scattering-in-exoplanet-atmospheres/}
}

@article{Yang2016,
    title = {{Real-time Imaging of Mycobacterium tuberculosis , Using a Novel Near-Infrared Fluorescent Substrate}},
    year = {2016},
    journal = {Journal of Infectious Diseases},
    author = {Yang, Hee-Jeong and Kong, Ying and Cheng, Yunfeng and Janagama, Harish and Hassounah, Hany and Xie, Hexin and Rao, Jianghong and Cirillo, Jeffrey D.},
    pages = {jiw298},
    url = {http://jid.oxfordjournals.org/lookup/doi/10.1093/infdis/jiw298},
    doi = {10.1093/infdis/jiw298},
    issn = {0022-1899},
    keywords = {antimicrobials, fl uorescence, in vivo imaging, infection, mycobacterium}
}

@article{Voleti2019,
    title = {{Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0}},
    year = {2019},
    journal = {Nature Methods},
    author = {Voleti, Venkatakaushik and Patel, Kripa B. and Li, Wenze and Perez Campos, Citlali and Bharadwaj, Srinidhi and Yu, Hang and Ford, Caitlin and Casper, Malte J. and Yan, Richard Wenwei and Liang, Wenxuan and Wen, Chentao and Kimura, Koutarou D. and Targoff, Kimara L. and Hillman, Elizabeth M. C. and Zuckerman, Mortimer B and Voleti, Venkatakaushik and Patel, Kripa B. and Li, Wenze and Campos, Citlali Perez and Bharadwaj, Srinidhi and Yu, Hang and Ford, Caitlin and Casper, Malte J. and Yan, Richard Wenwei and Liang, Wenxuan and Wen, Chentao and Kimura, Koutarou D. and Targoff, Kimara L. and Hillman, Elizabeth M. C.},
    number = {10},
    month = {10},
    pages = {1054--1062},
    volume = {16},
    url = {https://doi.org/10.1038/s41592-019-0579-4 http://www.nature.com/articles/s41592-019-0579-4},
    doi = {10.1038/s41592-019-0579-4},
    issn = {1548-7091}
}

@article{Ding2018,
    title = {{Recent advances in near-infrared II fluorophores for multifunctional biomedical imaging}},
    year = {2018},
    journal = {Chemical Science},
    author = {Ding, Feng and Zhan, Yibei and Lu, Xiaoju and Sun, Yao},
    number = {19},
    pages = {4370--4380},
    volume = {9},
    publisher = {Royal Society of Chemistry},
    url = {http://dx.doi.org/10.1039/C8SC01153B},
    doi = {10.1039/c8sc01153b},
    issn = {20416539}
}

@article{Duan2018,
    title = {{Recent Advances of Optical Imaging in the Second Near-Infrared Window}},
    year = {2018},
    journal = {Advanced Materials},
    author = {{Kenry} and Duan, Yukun and Liu, Bin},
    number = {47},
    month = {11},
    pages = {1802394},
    volume = {30},
    url = {https://doi.org/10.1002/adma.201802394. http://doi.wiley.com/10.1002/adma.201802394},
    doi = {10.1002/adma.201802394},
    issn = {09359648},
    pmid = {30182451}
}

@article{Chatterjee2018,
    title = {{Recent Progress in Light Sheet Microscopy for Biological Applications}},
    year = {2018},
    journal = {Applied Spectroscopy},
    author = {Chatterjee, Krishnendu and Pratiwi, Feby Wijaya and Wu, Frances Camille M. and Chen, Peilin and Chen, Bi Chang},
    number = {8},
    pages = {1137--1169},
    volume = {72},
    doi = {10.1177/0003702818778851},
    issn = {19433530},
    keywords = {Light sheet microscopy, cellular imaging, optical imaging, super-resolution microscopy}
}

@article{Keller2008,
    title = {{Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy}},
    year = {2008},
    journal = {Science},
    author = {Keller, Philipp J. and Schmidt, Annette D. and Wittbrodt, Joachim and Stelzer, Ernst H.K.},
    number = {5904},
    month = {11},
    pages = {1065--1069},
    volume = {322},
    url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1162493},
    doi = {10.1126/science.1162493},
    issn = {0036-8075},
    pmid = {18845710},
    arxivId = {arXiv:1011.1669v3}
}

@inproceedings{Kratz2015,
    title = {{Relevance of the Focal Spot in High-Resolution CT}},
    year = {2015},
    booktitle = {Digital Industrial Radiology and Computed Tomography},
    author = {Kratz, Bärbel and Herold, Frank and Niemann, Wilhelm},
    number = {June},
    pages = {22--25},
    address = {Ghent, Belgium},
    keywords = {computed tomography, focal spot drift, high-resolution, thermal in-, x-ray tube}
}

@article{Chen2014a,
    title = {{Remote focal scanning optical projection tomography with an electrically tunable lens}},
    year = {2014},
    journal = {Biomedical Optics Express},
    author = {Chen, Lingling and Kumar, Sunil and Kelly, Douglas and Andrews, Natalie and Dallman, Margaret J. and French, Paul M. W. and McGinty, James},
    number = {10},
    pages = {3367},
    volume = {5},
    doi = {10.1364/boe.5.003367},
    issn = {2156-7085}
}

@article{Windows,
    title = {{Remote refocus enables class-leading spatiotemporal resolution in 4D optical microscopy}},
    author = {Millett-Sikking, Alfred and Thayer, Nathaniel H. and Bohnert, Adam and York, Andrew G.},
    doi = {10.5281/zenodo.1146083}
}

@article{Sadi2010,
    title = {{Removal of ring artifacts in computed tomographic imaging using iterative center weighted median filter}},
    year = {2010},
    journal = {Computers in Biology and Medicine},
    author = {Sadi, Fazle and Lee, Soo Yeol and Hasan, Md Kamrul},
    number = {1},
    pages = {109--118},
    volume = {40},
    publisher = {Elsevier},
    url = {http://linkinghub.elsevier.com/retrieve/pii/S0010482509002029},
    isbn = {0010-4825},
    doi = {10.1016/j.compbiomed.2009.11.007},
    issn = {00104825},
    pmid = {20031123},
    keywords = {Iterative center weighted median filter, Ring artifact, {$\mu$} -CT imaging}
}

@article{Anas2010,
    title = {{Removal of ring artifacts in CT imaging through detection and correction of stripes in the sinogram}},
    year = {2010},
    journal = {Physics in Medicine and Biology},
    author = {Abu Anas, Emran Mohammad and Lee, Soo Yeol and Hasan, Md Kamrul},
    number = {22},
    pages = {6911--6930},
    volume = {55},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/21048294},
    isbn = {0031-9155},
    doi = {10.1088/0031-9155/55/22/020},
    issn = {00319155},
    pmid = {21048294},
    keywords = {Algorithms, Animals, Artifacts, Cattle, Computer-Assisted, Computer-Assisted: methods, Image Processing, Imaging, Phantoms, Rats, Tomography, X-Ray Computed, X-Ray Computed: methods}
}

@article{Walls2007,
    title = {{Resolution improvement in emission optical projection tomography}},
    year = {2007},
    journal = {Physics in Medicine and Biology},
    author = {Walls, Johnathon R. and Sled, John G. and Sharpe, James and Henkelman, R. Mark},
    number = {10},
    month = {5},
    pages = {2775--2790},
    volume = {52},
    url = {http://stacks.iop.org/0031-9155/52/i=10/a=010?key=crossref.b3438f857bc9b5dccacbfe58e72cf5de},
    doi = {10.1088/0031-9155/52/10/010},
    issn = {0031-9155}
}

@article{Miao2010,
    title = {{Resolution improvement in optical projection tomography by the focal scanning method.}},
    year = {2010},
    journal = {Optics letters},
    author = {Miao, Qin and Hayenga, Jon and Meyer, Michael G and Neumann, Thomas and Nelson, Alan C and Seibel, Eric J},
    number = {20},
    pages = {3363--5},
    volume = {35},
    url = {papers2://publication/uuid/90C75875-585A-4454-BF78-35F68354ED63%5Cnhttp://www.ncbi.nlm.nih.gov/pubmed/20967067},
    doi = {10.1364/OL.35.003363},
    issn = {1539-4794},
    pmid = {20967067}
}

@article{Smith2011,
    title = {{Resolution of oblique-plane images in sectioning microscopy}},
    year = {2011},
    journal = {Optics Express},
    author = {Smith, C. W. and Botcherby, E. J. and Wilson, T.},
    number = {3},
    month = {1},
    pages = {2662},
    volume = {19},
    url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-19-3-2662},
    doi = {10.1364/OE.19.002662},
    issn = {1094-4087}
}

@article{Fiolka2019,
    title = {{Resolution upgrades for light-sheet microscopy}},
    year = {2019},
    journal = {Nature Methods},
    author = {Fiolka, Reto},
    number = {9},
    pages = {813--814},
    volume = {16},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41592-019-0542-4},
    doi = {10.1038/s41592-019-0542-4},
    issn = {1548-7091}
}

@article{Matson2000,
    title = {{Resolved object imaging and localization with the use of a backpropagation algorithm}},
    year = {2000},
    journal = {Optics Express},
    author = {Matson, Charles L. and Liu, Hanli},
    number = {9},
    month = {4},
    pages = {168},
    volume = {6},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-6-9-168},
    doi = {10.1364/OE.6.000168},
    issn = {1094-4087},
    pmid = {19404348}
}

@article{Grosenick2016,
    title = {{Review of optical breast imaging and spectroscopy}},
    year = {2016},
    journal = {Journal of Biomedical Optics},
    author = {Grosenick, Dirk and Rinneberg, Herbert and Cubeddu, Rinaldo and Taroni, Paola},
    number = {9},
    pages = {091311},
    volume = {21},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.21.9.091311},
    isbn = {1083-3668},
    doi = {10.1117/1.JBO.21.9.091311},
    issn = {1083-3668},
    pmid = {27403837},
    keywords = {breast cancer, diffuse correlation, multimodality techniques, near-infrared spectroscopy, optical mammography}
}

@article{VonWangenheim2016,
    title = {{Rules and self-organizing properties of post-embryonic plant organ cell division patterns}},
    year = {2016},
    journal = {Current Biology},
    author = {Von Wangenheim, Daniel and Fangerau, Jens and Schmitz, Alexander and Smith, Richard S. and Leitte, Heike and Stelzer, Ernst H.K. and Maizel, Alexis},
    number = {4},
    pages = {439--449},
    volume = {26},
    publisher = {Elsevier Ltd},
    url = {http://dx.doi.org/10.1016/j.cub.2015.12.047},
    doi = {10.1016/j.cub.2015.12.047},
    issn = {09609822}
}

@article{Smith2009a,
    title = {{Second window for in vivo imaging}},
    year = {2009},
    journal = {Nature Nanotechnology},
    author = {Smith, Andrew M. and Mancini, Michael C. and Nie, Shuming},
    number = {11},
    month = {11},
    pages = {710--711},
    volume = {4},
    url = {http://www.nature.com/articles/nnano.2009.326},
    doi = {10.1038/nnano.2009.326},
    issn = {1748-3387},
    pmid = {19898521},
    arxivId = {NIHMS150003}
}

@article{Duocastella2017a,
    title = {{Selectable light-sheet uniformity using tuned axial scanning}},
    year = {2017},
    journal = {Microscopy Research and Technique},
    author = {Duocastella, Martí and Arnold, Craig B. and Puchalla, Jason},
    number = {2},
    month = {2},
    pages = {250--259},
    volume = {80},
    url = {http://doi.wiley.com/10.1002/jemt.22795},
    doi = {10.1002/jemt.22795},
    issn = {1059910X},
    keywords = {(180.2520) fluorescence microscopy, (180.6900) three-dimensional microscopy, OCIS codes: (110.1080) active or adaptive optics}
}

@article{Frangioni2003a,
    title = {{Selection of Quantum Dot Wavelengths for Biomedical Assays and Imaging}},
    year = {2003},
    journal = {Molecular Imaging},
    author = {Frangioni, J. V. and Nakayama, A. and Lim, Y. T. and Kim, S. and Stott, N. E. and Bawendi, M. G.},
    number = {1},
    pages = {50--64},
    volume = {2},
    url = {http://molecularimaging.deckerpublishing.com/index.php/article/selection-of-quantum-dot-wavelengths-for-biomedical-assays-and-imaging},
    keywords = {blood assays, fluorescent semiconductor nanocrystals, imaging, in vivo, quantum dots, wavelength selection}
}

@article{Paie2016,
    title = {{Selective plane illumination microscopy on a chip}},
    year = {2016},
    journal = {Lab on a Chip},
    author = {Pai{\`{e}}, Petra and Bragheri, Francesca and Bassi, Andrea and Osellame, Roberto},
    number = {9},
    pages = {1556--1560},
    volume = {16},
    publisher = {Royal Society of Chemistry},
    doi = {10.1039/c6lc00084c},
    issn = {14730189},
    pmid = {27030116}
}

@article{Meinert2016,
    title = {{Separation of ballistic and diffusive fluorescence photons in confocal Light-Sheet Microscopy of Arabidopsis roots}},
    year = {2016},
    journal = {Scientific Reports},
    author = {Meinert, Tobias and Tietz, Olaf and Palme, Klaus J. and Rohrbach, Alexander},
    number = {April},
    pages = {1--14},
    volume = {6},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/srep30378},
    doi = {10.1038/srep30378},
    issn = {20452322},
    pmid = {27553506}
}

@article{Tomer2011,
    title = {{Shedding light on the system: Studying embryonic development with light sheet microscopy}},
    year = {2011},
    journal = {Current Opinion in Genetics and Development},
    author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J.},
    number = {5},
    pages = {558--565},
    volume = {21},
    publisher = {Elsevier Ltd},
    url = {http://dx.doi.org/10.1016/j.gde.2011.07.003},
    doi = {10.1016/j.gde.2011.07.003},
    issn = {0959437X}
}

@article{Weissleder2003,
    title = {{Shedding light onto live molecular targets}},
    year = {2003},
    journal = {Nature Medicine},
    author = {Weissleder, Ralph and Ntziachristos, Vasilis},
    number = {1},
    pages = {123--128},
    volume = {9},
    url = {http://www.nature.com/nm/journal/v9/n1/abs/nm0103-123.html},
    isbn = {1078-8956},
    doi = {10.1038/nm0103-123},
    issn = {10788956},
    pmid = {12514725}
}

@article{Sordillo2017,
    title = {{Short wavelength infrared optical windows for evaluation of benign and malignant tissues}},
    year = {2017},
    journal = {Journal of Biomedical Optics},
    author = {Sordillo, Diana C. and Sordillo, Laura A. and Sordillo, Peter P. and Shi, Lingyan and Alfano, Robert R.},
    number = {4},
    pages = {045002},
    volume = {22},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.22.4.045002},
    doi = {10.1117/1.JBO.22.4.045002},
    issn = {1083-3668},
    pmid = {28384701},
    keywords = {18, 2016, 2017, 3, accepted for publication mar, collagen, fourth nir window, light scattering, paper 160708pr received oct, published online apr, short wavelength infrared, third optical window}
}

@article{Carr2018a,
    title = {{Shortwave infrared fluorescence imaging with the clinically approved near-infrared dye indocyanine green}},
    year = {2018},
    journal = {Proceedings of the National Academy of Sciences},
    author = {Carr, Jessica A. and Franke, Daniel and Caram, Justin R. and Perkinson, Collin F. and Saif, Mari and Askoxylakis, Vasileios and Datta, Meenal and Fukumura, Dai and Jain, Rakesh K. and Bawendi, Moungi G. and Bruns, Oliver T.},
    number = {17},
    month = {4},
    pages = {4465--4470},
    volume = {115},
    url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1718917115},
    doi = {10.1073/pnas.1718917115},
    issn = {0027-8424},
    pmid = {29626132}
}

@article{Wyman1989,
    title = {{Similarity relations for hte interaction parameters in radiation transport}},
    year = {1989},
    journal = {Applied optics},
    author = {Wyman, Douglas R and Patterson, Michael S and Wilson, Brian C},
    number = {24},
    pages = {5243--5249},
    volume = {28},
    isbn = {0003-6935},
    doi = {10.1364/AO.28.005243},
    issn = {0003-6935},
    pmid = {20556035}
}

@article{Vogt2018,
    title = {{Simulating the imaging process in scattering tissue}},
    year = {2018},
    journal = {Nature Methods},
    author = {Vogt, Nina},
    number = {6},
    pages = {406},
    volume = {15},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41592-018-0031-1},
    doi = {10.1038/s41592-018-0031-1},
    issn = {15487105}
}

@article{Meddens2016,
    title = {{Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution}},
    year = {2016},
    journal = {Biomedical Optics Express},
    author = {Meddens, Marjolein B. M. and Liu, Sheng and Finnegan, Patrick S. and Edwards, Thayne L. and James, Conrad D. and Lidke, Keith A.},
    number = {6},
    month = {6},
    pages = {2219},
    volume = {7},
    url = {https://www.osapublishing.org/abstract.cfm?URI=boe-7-6-2219},
    doi = {10.1364/BOE.7.002219},
    issn = {2156-7085}
}

@article{Wohland2010,
    title = {{Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments}},
    year = {2010},
    journal = {Optics Express},
    author = {Wohland, Thorsten and Shi, Xianke and Sankaran, Jagadish and Stelzer, Ernst H.K.},
    number = {10},
    pages = {10627},
    volume = {18},
    doi = {10.1364/oe.18.010627}
}

@article{Gebhardt2013,
    title = {{Single-molecule imaging of transcription factor binding to DNA in live mammalian cells}},
    year = {2013},
    journal = {Nature Methods},
    author = {Gebhardt, J. Christof M. and Suter, David M. and Roy, Rahul and Zhao, Ziqing W. and Chapman, Alec R. and Basu, Srinjan and Maniatis, Tom and Xie, X. Sunney},
    number = {5},
    pages = {421--426},
    volume = {10},
    doi = {10.1038/nmeth.2411},
    issn = {15487091}
}

@article{Davis2018,
    title = {{Slice-illuminated optical projection tomography}},
    year = {2018},
    journal = {Optics Letters},
    author = {Davis, Samuel P. X. and Wisniewski, Laura and Kumar, Sunil and Correia, Teresa and Arridge, Simon R. and Frankel, Paul and McGinty, James and French, Paul M. W.},
    number = {22},
    pages = {5555},
    volume = {43},
    doi = {10.1364/ol.43.005555},
    issn = {0146-9592}
}

@article{Huisken2012,
    title = {{Slicing embryos gently with laser light sheets}},
    year = {2012},
    journal = {BioEssays},
    author = {Huisken, Jan},
    number = {5},
    pages = {406--411},
    volume = {34},
    isbn = {1521-1878 (Electronic){\textbackslash}n0265-9247 (Linking)},
    doi = {10.1002/bies.201100120},
    issn = {02659247},
    pmid = {22396246},
    keywords = {Cell biology, Developmental biology, Light sheet microscopy, Selective plane illumination microscopy (SPIM), Zebrafish}
}

@article{Darne2014a,
    title = {{Small animal fluorescence and bioluminescence tomography: A review of approaches, algorithms and technology update}},
    year = {2014},
    journal = {Physics in Medicine and Biology},
    author = {Darne, Chinmay and Lu, Yujie and Sevick-Muraca, Eva M.},
    number = {1},
    volume = {59},
    isbn = {0031-9155},
    doi = {10.1088/0031-9155/59/1/R1},
    issn = {00319155},
    pmid = {24334634},
    keywords = {Cerenkov tomography, bioluminescence tomography, exogenous contrast agents, fluorescence tomography, fluorescent gene reporters, time-domain and frequency-domain measurements}
}

@article{Darne2014,
    title = {{Small animal fluorescence and bioluminescence tomography: A review of approaches, algorithms and technology update}},
    year = {2014},
    journal = {Physics in Medicine and Biology},
    author = {Darne, Chinmay and Lu, Yujie and Sevick-Muraca, Eva M.},
    number = {1},
    volume = {59},
    isbn = {0031-9155},
    doi = {10.1088/0031-9155/59/1/R1},
    issn = {00319155},
    pmid = {24334634},
    keywords = {Cerenkov tomography, bioluminescence tomography, exogenous contrast agents, fluorescence tomography, fluorescent gene reporters, time-domain and frequency-domain measurements}
}

@article{Barner2019,
    title = {{Solid immersion meniscus lens (SIMlens) for open-top light-sheet microscopy}},
    year = {2019},
    journal = {Optics Letters},
    author = {Barner, Lindsey A. and Glaser, Adam K. and True, Lawrence D. and Reder, Nicholas P. and Liu, Jonathan T. C.},
    number = {18},
    pages = {4451},
    volume = {44},
    doi = {10.1364/ol.44.004451},
    issn = {0146-9592}
}

@article{Ripoll1999,
    title = {{Spatial resolution of diffuse photon density waves}},
    year = {1999},
    journal = {Journal of the Optical Society of America A},
    author = {Ripoll, J. and Nieto-Vesperinas, M. and Carminati, Rémi},
    number = {6},
    month = {6},
    pages = {1466},
    volume = {16},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-16-6-1466},
    doi = {10.1364/JOSAA.16.001466},
    issn = {1084-7529},
    keywords = {Diffusion, Photon density waves, Superresolution, Turbid media}
}

@article{Wu2013a,
    title = {{Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy}},
    year = {2013},
    journal = {Nature Biotechnology},
    author = {Wu, Yicong and Wawrzusin, Peter and Senseney, Justin and Fischer, Robert S. and Christensen, Ryan and Santella, Anthony and York, Andrew G. and Winter, Peter W. and Waterman, Clare M. and Bao, Zhirong and Col{\'{o}}n-Ramos, Daniel A. and McAuliffe, Matthew and Shroff, Hari},
    number = {11},
    month = {11},
    pages = {1032--1038},
    volume = {31},
    url = {http://www.nature.com/articles/nbt.2713},
    doi = {10.1038/nbt.2713},
    issn = {1087-0156}
}

@article{Granot2003,
    title = {{Spectral ballistic imaging: a novel technique for viewing through turbid or obstructing media.}},
    year = {2003},
    journal = {Journal of the Optical Society of America. A, Optics, image science, and vision},
    author = {Granot, Er'el and Sternklar, Shmuel},
    number = {8},
    pages = {1595--1599},
    volume = {20},
    isbn = {1084-7529},
    doi = {10.1364/JOSAA.20.001595},
    issn = {1084-7529},
    pmid = {12938916}
}

@article{Zubkovs2018,
    title = {{Spinning-disc confocal microscopy in the second near-infrared window (NIR-II)}},
    year = {2018},
    journal = {Scientific Reports},
    author = {Zubkovs, Vitalijs and Antonucci, Alessandra and Schuergers, Nils and Lambert, Benjamin and Latini, Andrea and Ceccarelli, Raino and Santinelli, Andrea and Rogov, Andrii and Ciepielewski, Daniel and Boghossian, Ardemis A.},
    number = {1},
    month = {12},
    pages = {13770},
    volume = {8},
    url = {http://www.nature.com/articles/s41598-018-31928-y},
    doi = {10.1038/s41598-018-31928-y},
    issn = {2045-2322}
}

@article{Aakhte2018,
    title = {{SSPIM: A beam shaping toolbox for structured selective plane illumination microscopy}},
    year = {2018},
    journal = {Scientific Reports},
    author = {Aakhte, Mostafa and Akhlaghi, Ehsan A. and M{\"{u}}ller, H. Arno J.},
    number = {1},
    pages = {1--12},
    volume = {8},
    doi = {10.1038/s41598-018-28389-8},
    issn = {20452322}
}

@article{Friedrich2011,
    title = {{STED-SPIM: Stimulated emission depletion improves sheet illumination microscopy resolution}},
    year = {2011},
    journal = {Biophysical Journal},
    author = {Friedrich, Mike and Gan, Qiang and Ermolayev, Vladimir and Harms, Gregory S.},
    number = {8},
    pages = {L43-L45},
    volume = {100},
    publisher = {Biophysical Society},
    url = {http://dx.doi.org/10.1016/j.bpj.2010.12.3748},
    doi = {10.1016/j.bpj.2010.12.3748},
    issn = {15420086}
}

@article{Ben2016,
    title = {{Study of a simple model for the transition between the ballistic and the diffusive regimes in diffusive media}},
    year = {2016},
    journal = {Journal of Biomedical Optics},
    author = {Ben, Igor and Layosh, Yonatan Y. and Granot, Er’el},
    number = {6},
    month = {6},
    pages = {066004},
    volume = {21},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.JBO.21.6.066004},
    doi = {10.1117/1.JBO.21.6.066004},
    issn = {1083-3668},
    keywords = {Absorption, Photons, Scattering, Simulations}
}

@article{Fei2019,
    title = {{Subvoxel light-sheet microscopy for high-resolution high-throughput volumetric imaging of large biomedical specimens}},
    year = {2019},
    journal = {Advanced Photonics},
    author = {Fei, Peng and Nie, Jun and Lee, Juhyun and Ding, Yichen and Li, Shuoran and Zhang, Hao and Hagiwara, Masaya and Yu, Tingting and Segura, Tatiana and Ho, Chih-Ming and Zhu, Dan and Hsiai, Tzung K.},
    number = {01},
    pages = {1},
    volume = {1},
    doi = {10.1117/1.ap.1.1.016002},
    keywords = {0 unported license, 17, 18, 2018, 2019, 28, accepted for publication oct, clp under a creative, commons attribution 4, distribution or, high-throughput volumetric imaging, in whole or in, including its doi, large tissue imaging, light-sheet microscopy, of the original publication, part requires full attribution, published by spie and, published online jan, received jul, reproduction of this work, subvoxel-resolving reconstruction, the authors}
}

@article{Bouchard2015,
    title = {{Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms}},
    year = {2015},
    journal = {Nature Photonics},
    author = {Bouchard, Matthew B. and Voleti, Venkatakaushik and Mendes, César S. and Lacefield, Clay and Grueber, Wesley B. and Mann, Richard S. and Bruno, Randy M. and Hillman, Elizabeth M.C.},
    number = {2},
    pages = {113--119},
    volume = {9},
    doi = {10.1038/nphoton.2014.323},
    issn = {17494893}
}

@article{DiGiovanna2019,
    title = {{Tailored sample mounting for light-sheet fluorescence microscopy of clarified specimens by polydimethylsiloxane casting}},
    year = {2019},
    journal = {Frontiers in Neuroanatomy},
    author = {Di Giovanna, Antonino Paolo and Credi, Caterina and Franceschini, Alessandra and M{\"{u}}llenbroich, Marie Caroline and Silvestri, Ludovico and Pavone, Francesco Saverio},
    number = {March},
    pages = {1--10},
    volume = {13},
    doi = {10.3389/fnana.2019.00035},
    issn = {16625129},
    keywords = {Brain, Light-sheet microscopy, PDMS, Sample mounting, Tissue clearing}
}

@article{Elisa2018,
    title = {{Technical implementations of light sheet microscopy}},
    year = {2018},
    journal = {Microscopy Research and Technique},
    author = {Elisa, Zagato and Toon, Brans and De Smedt, Stefaan C. and Katrien, Remaut and Kristiaan, Neyts and Kevin, Braeckmans},
    editor = {Cella Zanacchi, Francesca},
    number = {9},
    month = {9},
    pages = {941--958},
    volume = {81},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jemt.22981},
    doi = {10.1002/jemt.22981},
    issn = {1059-910X},
    keywords = {SPIM, light sheet microscopy}
}

@article{Johnston2012,
    title = {{Temporal and spectral imaging with micro-CT}},
    year = {2012},
    journal = {Med Phys},
    author = {Johnston, Samuel M and Johnson, G Allan and Badea, Cristian T},
    number = {8},
    pages = {4943--4958},
    volume = {39},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/22894420},
    isbn = {0094-2405 (Print){\textbackslash}n0094-2405 (Linking)},
    doi = {10.1118/1.4736809},
    issn = {0094-2405},
    pmid = {22894420},
    keywords = {Algorithms, Animals, Computer Graphics, Computer Simulation, Computer-Assist, Computer-Assisted, Computers, Image Processing, Inbred C57BL, Iodine, Iodine/chemistry/*pharmacology, Iodine: chemistry, Iodine: pharmacology, Mice, Models, Normal Distribution, Radiographic Image Interpretation, Reproducibility of Results, Retrospective Studies, Statistical, Time Factors, Water, Water/chemistry, Water: chemistry, X-Ray Microtomography, X-Ray Microtomography/*methods, X-Ray Microtomography: methods}
}

@article{VanAarle2015,
    title = {{The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography.}},
    year = {2015},
    journal = {Ultramicroscopy},
    author = {van Aarle, Wim and Palenstijn, Willem Jan and De Beenhouwer, Jan and Altantzis, Thomas and Bals, Sara and Batenburg, K. Joost and Sijbers, Jan},
    month = {10},
    pages = {35--47},
    volume = {157},
    publisher = {Elsevier},
    url = {http://dx.doi.org/10.1016/j.ultramic.2015.05.002 http://www.ncbi.nlm.nih.gov/pubmed/26057688},
    doi = {10.1016/j.ultramic.2015.05.002},
    issn = {1879-2723},
    pmid = {26057688},
    keywords = {ASTRA Toolbox, Dual-axis, Electron tomography, Reconstruction}
}

@article{Mappes2012,
    title = {{The invention of immersion ultramicroscopy in 1912-The birth of nanotechnology?}},
    year = {2012},
    journal = {Angewandte Chemie - International Edition},
    author = {Mappes, Timo and Jahr, Norbert and Csaki, Andrea and Vogler, Nadine and Popp, Jürgen and Fritzsche, Wolfgang},
    number = {45},
    pages = {11208--11212},
    volume = {51},
    doi = {10.1002/anie.201204688},
    issn = {14337851},
    keywords = {history of science, nanoparticles, nanotechnology, ultramicroscopy}
}

@article{Girkin2018,
    title = {{The light-sheet microscopy revolution}},
    year = {2018},
    journal = {Journal of Optics},
    author = {Girkin, J M and Carvalho, M T},
    number = {5},
    month = {5},
    pages = {053002},
    volume = {20},
    url = {https://doi.org/10.1088/2040-8986/aab58a http://stacks.iop.org/2040-8986/20/i=5/a=053002?key=crossref.f388fde27b264ecf7a7c58ec9fd0e62f},
    doi = {10.1088/2040-8986/aab58a},
    issn = {2040-8978},
    keywords = {3D biological imaging, SPIM, in vivo imaging, light-sheet microscopy, optical microscopy, selective plane illumination microscopy}
}

@article{Voigt2019a,
    title = {{The mesoSPIM initiative: open-source light-sheet mesoscopes for imaging in cleared tissue}},
    year = {2019},
    journal = {bioRxiv},
    author = {Voigt, Fabian F. and Kirschenbaum, Daniel and Platonova, Evgenia and Pag{\`{e}}s, Stéphane and Campbell, Robert A. A. and K{\"{a}}stli, Rahel and Schaettin, Martina and Egolf, Ladan and Bourg, Alexander van der and Bethge, Philipp and Haenraets, Karen and Fr{\'{e}}zel, Noémie and Topilko, Thomas and Perin, Paola and Hillier, Daniel and Hildebrand, Sven and Schueth, Anna and Roebroeck, Alard and Roska, Botond and Stoeckli, Esther and Pizzala, Roberto and Renier, Nicolas and Zeilhofer, Hanns Ulrich and Karayannis, Theofanis and Ziegler, Urs and Batti, Laura and Holtmaat, Anthony and L{\"{u}}scher, Christian and Aguzzi, Adriano and Helmchen, Fritjof},
    pages = {577122},
    url = {https://www.biorxiv.org/content/10.1101/577122v1},
    doi = {10.1101/577122}
}

@article{Voigt2019,
    title = {{The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue}},
    year = {2019},
    journal = {Nature Methods},
    author = {Voigt, Fabian F. and Kirschenbaum, Daniel and Platonova, Evgenia and Pag{\`{e}}s, Stéphane and Campbell, Robert A. A. and Kastli, Rahel and Schaettin, Martina and Egolf, Ladan and van der Bourg, Alexander and Bethge, Philipp and Haenraets, Karen and Fr{\'{e}}zel, Noémie and Topilko, Thomas and Perin, Paola and Hillier, Daniel and Hildebrand, Sven and Schueth, Anna and Roebroeck, Alard and Roska, Botond and Stoeckli, Esther T. and Pizzala, Roberto and Renier, Nicolas and Zeilhofer, Hanns Ulrich and Karayannis, Theofanis and Ziegler, Urs and Batti, Laura and Holtmaat, Anthony and L{\"{u}}scher, Christian and Aguzzi, Adriano and Helmchen, Fritjof},
    month = {9},
    pages = {577122},
    url = {https://www.biorxiv.org/content/10.1101/577122v1 http://www.nature.com/articles/s41592-019-0554-0},
    doi = {10.1038/s41592-019-0554-0},
    issn = {1548-7091}
}

@article{Owens2017b,
    title = {{The microscope makers}},
    year = {2017},
    journal = {Nature},
    author = {Owens, B},
    number = {7682},
    month = {11},
    pages = {659--662},
    volume = {551},
    url = {http://www.nature.com/doifinder/10.1038/d41586-017-07528-7},
    doi = {10.1038/d41586-017-07528-7},
    issn = {0028-0836}
}

@article{Sabino2016,
    title = {{The optical properties of mouse skin in the visible and near infrared spectral regions}},
    year = {2016},
    journal = {Journal of Photochemistry and Photobiology B: Biology},
    author = {Sabino, Caetano P. and Deana, Alessandro M. and Yoshimura, Tania M. and Da Silva, Daniela F.T. and Fran{\c{c}}a, Cristiane M. and Hamblin, Michael R. and Ribeiro, Martha S.},
    month = {7},
    pages = {72--78},
    volume = {160},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/27101274 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4899976},
    doi = {10.1016/j.jphotobiol.2016.03.047},
    issn = {18732682},
    pmid = {27101274},
    keywords = {Biophotonics, Photodiagnosis, Phototherapy, Radiative transfer, Skin optics, Tissue spectroscopy}
}

@article{Mangold2013,
    title = {{The physics of near-infrared photography}},
    year = {2013},
    journal = {European Journal of Physics},
    author = {Mangold, Klaus and Shaw, Joseph A. and Vollmer, Michael},
    number = {6},
    pages = {51--71},
    volume = {34},
    doi = {10.1088/0143-0807/34/6/S51},
    issn = {01430807}
}

@article{Patterson1991,
    title = {{The propagation of optical radiation in tissue I. Models of radiation transport and their application}},
    year = {1991},
    journal = {Lasers in Medical Science},
    author = {Patterson, Michael S. and Wilson, Brian C. and Wyman, Douglas R.},
    number = {2},
    month = {6},
    pages = {155--168},
    volume = {6},
    url = {http://link.springer.com/10.1007/BF02032543},
    isbn = {0268-8921},
    doi = {10.1007/BF02032543},
    issn = {0268-8921},
    keywords = {Absorption, Fluence distribution, Scattering, Tissue optics}
}

@article{Patterson1991a,
    title = {{The propagation of optical radiation in tissue. II: Optical properties of tissues and resulting fluence distributions}},
    year = {1991},
    journal = {Lasers in Medical Science},
    author = {Patterson, Michael S. and Wilson, Brian C. and Wyman, Douglas R.},
    number = {4},
    month = {12},
    pages = {379--390},
    volume = {6},
    url = {http://link.springer.com/10.1007/BF02042460},
    isbn = {0268-8921},
    doi = {10.1007/BF02042460},
    issn = {0268-8921}
}

@article{Fuchs2002a,
    title = {{Thin laser light sheet microscope for microbial oceanography}},
    year = {2002},
    journal = {Optics Express},
    author = {Fuchs, Eran and Jaffe, Jules and Long, Richard and Azam, Farooq},
    number = {2},
    month = {1},
    pages = {145},
    volume = {10},
    url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-10-2-145},
    doi = {10.1364/OE.10.000145},
    issn = {1094-4087},
    keywords = {(0100110) Imaging systems, (1802520) Fluorescence microscopy, OCIS codes: (0100010) Atmospheric and ocean optics}
}

@article{Fauver2005,
    title = {{Three-dimensional imaging of single isolated cell nuclei using optical projection tomography}},
    year = {2005},
    journal = {Optics Express},
    author = {Fauver, Mark and Seibel, Eric J. and Rahn, J. Richard and Meyer, Michael G. and Patten, Florence W. and Neumann, Thomas and Nelson, Alan C.},
    number = {11},
    month = {5},
    pages = {4210},
    volume = {13},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-13-11-4210},
    doi = {10.1364/OPEX.13.004210},
    issn = {1094-4087}
}

@article{Tran2014,
    title = {{Three-dimensional transillumination image reconstruction for small animal with new scattering suppression technique}},
    year = {2014},
    journal = {Biomedical Optics Express},
    author = {Tran, Trung Nghia and Yamamoto, Kohei and Namita, Takeshi and Kato, Yuji and Shimizu, Koichi},
    number = {5},
    pages = {1321},
    volume = {5},
    publisher = {OSA},
    url = {https://www.osapublishing.org/boe/abstract.cfm?uri=boe-5-5-1321},
    doi = {10.1364/BOE.5.001321},
    issn = {2156-7085},
    pmid = {24876998},
    keywords = {Deconvolution, Image reconstruction techniques, Medical and biological imaging, Tomography, Turbid media}
}

@article{Escobet-Montalban2018,
    title = {{Three-photon light-sheet fluorescence microscopy}},
    year = {2018},
    journal = {Optics Letters},
    author = {Escobet-Montalb{\'{a}}n, Adrià and Gasparoli, Federico M. and Nylk, Jonathan and Liu, Pengfei and Yang, Zhengyi and Dholakia, Kishan},
    number = {21},
    month = {11},
    pages = {5484},
    volume = {43},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-43-21-5484},
    doi = {10.1364/OL.43.005484},
    issn = {0146-9592}
}

@article{Hong2014,
    title = {{Through-skull fluorescence imaging of the brain in a new near-infrared window}},
    year = {2014},
    journal = {Nature Photonics},
    author = {Hong, Guosong and Diao, Shuo and Chang, Junlei and Antaris, Alexander L and Chen, Changxin and Zhang, Bo and Zhao, Su and Atochin, Dmitriy N and Huang, Paul L and Andreasson, Katrin I and Kuo, Calvin J and Dai, Hongjie},
    number = {9},
    month = {9},
    pages = {723--730},
    volume = {8},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/nphoton.2014.166 http://www.nature.com/articles/nphoton.2014.166},
    doi = {10.1038/nphoton.2014.166},
    issn = {1749-4885}
}

@article{Gao2018,
    title = {{Tiling light sheet selective plane illumination microscopy using discontinuous light sheets}},
    year = {2018},
    journal = {bioRxiv},
    author = {Gao, Liang},
    number = {23},
    pages = {378232},
    volume = {27},
    url = {https://www.biorxiv.org/content/10.1101/378232v1},
    doi = {10.1101/378232}
}

@article{Kumar2019,
    title = {{Tilt-invariant scanned oblique plane illumination microscopy for large-scale volumetric imaging}},
    year = {2019},
    journal = {Optics Letters},
    author = {Kumar, Manish and Kozorovitskiy, Yevgenia},
    number = {7},
    pages = {1706},
    volume = {44},
    doi = {10.1364/ol.44.001706},
    issn = {0146-9592}
}

@article{Ortiz-Rascon2016,
    title = {{Time of flight dependent linearity in diffuse imaging: how effective is it to evaluate the spatial resolution by measuring the edge response function?}},
    year = {2016},
    journal = {Applied Optics},
    author = {Ortiz-Rasc{\'{o}}n, E. and Bruce, N. C. and Rodr{\'{i}}guez-Rosales, A. A. and Gardu{\~{n}}o-Mej{\'{i}}a, J.},
    number = {7},
    pages = {1613},
    volume = {55},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-55-7-1613},
    isbn = {1539-4522},
    doi = {10.1364/AO.55.001613},
    issn = {0003-6935}
}

@article{Bassi2010a,
    title = {{Time-gated optical projection tomography}},
    year = {2010},
    journal = {Optics Letters},
    author = {Bassi, Andrea and Brida, Daniele and D’Andrea, Cosimo and Valentini, Gianluca and Cubeddu, Rinaldo and De Silvestri, Sandro and Cerullo, Giulio},
    number = {16},
    month = {8},
    pages = {2732--2734},
    volume = {35},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-35-16-2732},
    doi = {10.1364/OL.35.002732},
    issn = {0146-9592},
    pmid = {20717439}
}

@article{Fieramonti2012,
    title = {{Time-Gated Optical Projection Tomography Allows Visualization of Adult Zebrafish Internal Structures}},
    year = {2012},
    journal = {PLoS ONE},
    author = {Fieramonti, Luca and Bassi, Andrea and Foglia, Efrem Alessandro and Pistocchi, Anna and D'Andrea, Cosimo and Valentini, Gianluca and Cubeddu, Rinaldo and De Silvestri, Sandro and Cerullo, Giulio and Cotelli, Franco},
    editor = {Bene, Filippo Del},
    number = {11},
    month = {11},
    pages = {e50744},
    volume = {7},
    url = {https://dx.plos.org/10.1371/journal.pone.0050744},
    doi = {10.1371/journal.pone.0050744},
    issn = {1932-6203},
    pmid = {23185643}
}

@article{Rocha2019,
    title = {{Tissue clearing and light sheet microscopy: Imaging the unsectioned adult zebra finch brain at cellular resolution}},
    year = {2019},
    journal = {Frontiers in Neuroanatomy},
    author = {Rocha, Mariana Diales and D{\"{u}}ring, Daniel Normen and Bethge, Philipp and Voigt, Fabian F. and Hildebrand, Staffan and Helmchen, Fritjof and Pfeifer, Alexander and Hahnloser, Richard Hans Robert and Gahr, Manfred},
    number = {February},
    pages = {1--7},
    volume = {13},
    isbn = {2154253215020},
    doi = {10.3389/fnana.2019.00013},
    issn = {16625129},
    keywords = {Large volume imaging, Light sheet microscopy, Song system, Tissue clearing, Zebra finch}
}

@article{Owens2016,
    title = {{Tissue-Specific Near-Infrared Fluorescence Imaging}},
    year = {2016},
    journal = {Accounts of Chemical Research},
    author = {Owens, Eric A. and Henary, Maged and El Fakhri, Georges and Choi, Hak Soo},
    number = {9},
    pages = {1731--1740},
    volume = {49},
    isbn = {0001-4842 (ISSNLinking)},
    doi = {10.1021/acs.accounts.6b00239},
    issn = {15204898}
}

@article{Soloviev2012,
    title = {{Tomographic imaging with polarized light}},
    year = {2012},
    journal = {Journal of the Optical Society of America A},
    author = {Soloviev, Vadim Y. and Zacharakis, Giannis and Spiliopoulos, George and Favicchio, Rosy and Correia, Teresa and Arridge, Simon R. and Ripoll, Jorge},
    number = {6},
    pages = {980},
    volume = {29},
    url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-29-6-980},
    doi = {10.1364/JOSAA.29.000980},
    issn = {1084-7529},
    pmid = {22673429},
    keywords = {Image Processing, Computer-Assisted, Light, Optical Processes, Phantoms, Imaging, Scattering, Radiation, Tomography, Tomography: methods}
}

@article{Amat2013a,
    title = {{Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy}},
    year = {2013},
    journal = {Development Growth and Differentiation},
    author = {Amat, Fernando and Keller, Philipp J.},
    number = {4},
    pages = {563--578},
    volume = {55},
    doi = {10.1111/dgd.12063},
    issn = {00121592},
    keywords = {Cell lineage reconstruction, Cell tracking, Data visualization, Embryonic development, Light-sheet microscopy, Quantitative developmental biology}
}

@article{Amat2013,
    title = {{Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy}},
    year = {2013},
    journal = {Development Growth and Differentiation},
    author = {Amat, Fernando and Keller, Philipp J.},
    number = {4},
    pages = {563--578},
    volume = {55},
    doi = {10.1111/dgd.12063},
    issn = {00121592},
    keywords = {Cell lineage reconstruction, Cell tracking, Data visualization, Embryonic development, Light-sheet microscopy, Quantitative developmental biology}
}

@article{Ferrucci2015,
    title = {{Towards geometrical calibration of x-ray computed tomography systems - A review}},
    year = {2015},
    journal = {Measurement Science and Technology},
    author = {Ferrucci, Massimiliano and Leach, Richard K. and Giusca, Claudiu and Carmignato, Simone and Dewulf, Wim},
    number = {9},
    volume = {26},
    doi = {10.1088/0957-0233/26/9/092003},
    issn = {13616501},
    keywords = {dimensional metrology, geometrical calibration, x-ray computed tomography}
}

@article{Yaroshevsky2011,
    title = {{Transition from the ballistic to the diffusive regime in a turbid medium}},
    year = {2011},
    journal = {Optics Letters},
    author = {Yaroshevsky, Andre and Glasser, Ziv and Granot, Er’el and Sternklar, Shmuel},
    number = {8},
    month = {4},
    pages = {1395},
    volume = {36},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-36-8-1395},
    doi = {10.1364/OL.36.001395},
    issn = {0146-9592},
    pmid = {21499368}
}

@article{White2008,
    title = {{Transparent Adult Zebrafish as a Tool for In Vivo Transplantation Analysis}},
    year = {2008},
    journal = {Cell Stem Cell},
    author = {White, Richard Mark and Sessa, Anna and Burke, Christopher and Bowman, Teresa and LeBlanc, Jocelyn and Ceol, Craig and Bourque, Caitlin and Dovey, Michael and Goessling, Wolfram and Burns, Caroline Erter and Zon, Leonard I.},
    number = {2},
    pages = {183--189},
    volume = {2},
    doi = {10.1016/j.stem.2007.11.002},
    issn = {19345909},
    keywords = {DEVBIO, STEMCELL}
}

@article{Landry2019,
    title = {{Tunable structured illumination light sheet microscopy for background rejection and imaging depth in minimally processed tissues}},
    year = {2019},
    journal = {Journal of Biomedical Optics},
    author = {Landry, Joseph R.},
    number = {04},
    pages = {1},
    volume = {24},
    doi = {10.1117/1.jbo.24.4.046501},
    keywords = {2, 2019, 22, 9, accepted for publication mar, image reconstruction, microscopy, paper 180660r received jan, published online apr, spatial light modulators}
}

@article{Jacques2008,
    title = {{Tutorial on diffuse light transport}},
    year = {2008},
    journal = {Journal of Biomedical Optics},
    author = {Jacques, Steven L. and Pogue, Brian W.},
    number = {4},
    pages = {041302},
    volume = {13},
    url = {http://biomedicaloptics.spiedigitallibrary.org/article.aspx?doi=10.1117/1.2967535},
    doi = {10.1117/1.2967535},
    issn = {10833668},
    keywords = {18, 2007, 2008, 21, 26, accepted for publication feb, diffuse, imaging, light transport, optical properties, paper 07395ssr received sep, published online aug, revised manuscript received feb, spectroscopy, tissue}
}

@article{Zsigmondy1902,
    title = {{Uber Sichtbarmachung und Gr{\"{o}}{\ss}enbestimmung ultramikoskopischer Teilchen, mit besonderer Anwendung auf Goldrubingl{\"{a}}ser}},
    year = {1902},
    journal = {Annalen der Physik},
    author = {Siedentopf, H. and Zsigmondy, R.},
    number = {1},
    pages = {1--39},
    volume = {315},
    url = {http://doi.wiley.com/10.1002/andp.19023150102},
    doi = {10.1002/andp.19023150102},
    issn = {00033804}
}

@article{Dodt2007,
    title = {{Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain}},
    year = {2007},
    journal = {Nature Methods},
    author = {Dodt, Hans-Ulrich and Leischner, Ulrich and Schierloh, Anja and J{\"{a}}hrling, Nina and Mauch, Christoph Peter and Deininger, Katrin and Deussing, Jan Michael and Eder, Matthias and Zieglg{\"{a}}nsberger, Walter and Becker, Klaus},
    number = {4},
    month = {4},
    pages = {331--336},
    volume = {4},
    url = {http://www.nature.com/articles/nmeth1036},
    doi = {10.1038/nmeth1036},
    issn = {1548-7091}
}

@article{Dean2014,
    title = {{Uniform and scalable light-sheets generated by extended focusing}},
    year = {2014},
    journal = {Optics Express},
    author = {Dean, Kevin M. and Fiolka, Reto},
    number = {21},
    month = {10},
    pages = {26141},
    volume = {22},
    url = {https://www.osapublishing.org/abstract.cfm?URI=oe-22-21-26141},
    doi = {10.1364/OE.22.026141},
    issn = {1094-4087}
}

@article{Chang2019,
    title = {{Universal light-sheet generation with field synthesis}},
    year = {2019},
    journal = {Nature Methods},
    author = {Chang, Bo-Jui and Kittisopikul, Mark and Dean, Kevin M. and Roudot, Philippe and Welf, Erik S. and Fiolka, Reto},
    number = {3},
    month = {3},
    pages = {235--238},
    volume = {16},
    publisher = {Springer US},
    url = {http://dx.doi.org/10.1038/s41592-019-0327-9 http://www.nature.com/articles/s41592-019-0327-9},
    doi = {10.1038/s41592-019-0327-9},
    issn = {1548-7091}
}

@article{Ripoll2015,
    title = {{Unleashing Optics and Optoacoustics for Developmental Biology}},
    year = {2015},
    journal = {Trends in Biotechnology},
    author = {Ripoll, J. and Koberstein-Schwarz, B. and Ntziachristos, V.},
    number = {11},
    pages = {679--691},
    volume = {33},
    publisher = {Elsevier Ltd},
    url = {http://dx.doi.org/10.1016/j.tibtech.2015.08.002},
    isbn = {0167-7799},
    doi = {10.1016/j.tibtech.2015.08.002},
    issn = {18793096},
    pmid = {26435161}
}

@article{Alonso2001,
    title = {{Using rays better . II . Ray families}},
    year = {2001},
    author = {Alonso, M A and Forbes, G W},
    number = {5},
    pages = {1146--1159},
    volume = {18}
}

@article{Forbes2001,
    title = {{Using rays better I Theory for smoothly varying media}},
    year = {2001},
    journal = {Journal of the Optical Society of America A},
    author = {Forbes, G. W. and Alonso, M. A.},
    number = {5},
    pages = {1132},
    volume = {18},
    doi = {10.1364/josaa.18.001132},
    issn = {1084-7529}
}

@article{Chen2001,
    title = {{Validity of the diffusion approximation in bio-optical imaging}},
    year = {2001},
    journal = {Applied Optics},
    author = {Chen, Bingquan and Stamnes, Knut and Stamnes, Jakob J.},
    number = {34},
    month = {12},
    pages = {6356},
    volume = {40},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-40-34-6356},
    doi = {10.1364/AO.40.006356},
    issn = {0003-6935}
}

@article{Kim2014,
    title = {{Vectorial point spread function and optical transfer function in oblique plane imaging}},
    year = {2014},
    journal = {Optics Express},
    author = {Kim, Jeongmin and Li, Tongcang and Wang, Yuan and Zhang, Xiang},
    number = {9},
    pages = {11140},
    volume = {22},
    doi = {10.1364/oe.22.011140},
    issn = {1094-4087}
}

@article{Andrews2016,
    title = {{Visualising apoptosis in live zebrafish using fluorescence lifetime imaging with optical projection tomography to map FRET biosensor activity in space and time}},
    year = {2016},
    journal = {Journal of Biophotonics},
    author = {Andrews, Natalie and Ramel, Marie Christine and Kumar, Sunil and Alexandrov, Yuriy and Kelly, Douglas J. and Warren, Sean C. and Kerry, Louise and Lockwood, Nicola and Frolov, Antonina and Frankel, Paul and Bugeon, Laurence and Mcginty, James and Dallman, Margaret J. and French, Paul M.W.},
    number = {4},
    pages = {414--424},
    volume = {9},
    doi = {10.1002/jbio.201500258},
    issn = {18640648},
    keywords = {Caspase 3, FLIM, FRET, OPT, Zebrafish}
}

@article{Keller2015,
    title = {{Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy}},
    year = {2015},
    journal = {Neuron},
    author = {Keller, Philipp J. and Ahrens, Misha B.},
    number = {3},
    pages = {462--483},
    volume = {85},
    publisher = {Elsevier Inc.},
    url = {http://dx.doi.org/10.1016/j.neuron.2014.12.039},
    doi = {10.1016/j.neuron.2014.12.039},
    issn = {10974199}
}

@misc{Fang2010,
    title = {{Voxel- and mesh-based Monte Carlo methods for 3D photon transport simulations}},
    year = {2010},
    booktitle = {Virtual Photonics},
    author = {Fang, Qianqian}
}

@book{Ishimaru1978,
    title = {{Wave Propagation and Scattering in Random Media}},
    year = {1978},
    author = {Ishimaru, Akira},
    pages = {272},
    publisher = {Elsevier},
    url = {http://linkinghub.elsevier.com/retrieve/pii/B9780123747013X50017},
    isbn = {9780123747013},
    doi = {10.1016/B978-0-12-374701-3.X5001-7}
}

@article{Zhang1999,
    title = {{Wave transport in random media: The ballistic to diffusive transition}},
    year = {1999},
    journal = {Physical Review E},
    author = {Zhang, Z. Q. and Jones, I. P. and Schriemer, H. P. and Page, J. H. and Weitz, D. A. and Sheng, Ping},
    number = {4},
    month = {10},
    pages = {4843--4850},
    volume = {60},
    url = {https://link.aps.org/doi/10.1103/PhysRevE.60.4843},
    doi = {10.1103/PhysRevE.60.4843},
    issn = {1063-651X},
    pmid = {11970349}
}

@article{Darrell2008,
    title = {{Weighted filtered backprojection for quantitative fluorescence optical projection tomography}},
    year = {2008},
    journal = {Physics in Medicine and Biology},
    author = {Darrell, A. and Meyer, H. and Marias, K. and Brady, M. and Ripoll, J.},
    number = {14},
    month = {7},
    pages = {3863--3881},
    volume = {53},
    url = {http://stacks.iop.org/0031-9155/53/i=14/a=010?key=crossref.f9bf1054d06d9f1e1e3e5367f84b1a17%5Cnhttp://www.ncbi.nlm.nih.gov/pubmed/18583727 http://stacks.iop.org/0031-9155/53/i=14/a=010?key=crossref.f9bf1054d06d9f1e1e3e5367f84b1a17},
    doi = {10.1088/0031-9155/53/14/010},
    issn = {0031-9155},
    pmid = {18583727}
}

@article{Yoo1990,
    title = {{When does the diffusion approximation fail to describe photon transport in random media?}},
    year = {1990},
    journal = {Physical Review Letters},
    author = {Yoo, K. M. and Liu, Feng and Alfano, R. R.},
    number = {22},
    month = {5},
    pages = {2647--2650},
    volume = {64},
    url = {https://link.aps.org/doi/10.1103/PhysRevLett.64.2647},
    doi = {10.1103/PhysRevLett.64.2647},
    issn = {0031-9007},
    pmid = {10041774}
}

@article{Chhetri2015,
    title = {{Whole-animal functional and developmental imaging with isotropic spatial resolution}},
    year = {2015},
    journal = {Nature Methods},
    author = {Chhetri, Raghav K. and Amat, Fernando and Wan, Yinan and H{\"{o}}ckendorf, Burkhard and Lemon, William C. and Keller, Philipp J.},
    number = {12},
    pages = {1171--1178},
    volume = {12},
    doi = {10.1038/nmeth.3632},
    issn = {15487105}
}

@article{Susaki2016,
    title = {{Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals}},
    year = {2016},
    journal = {Cell Chemical Biology},
    author = {Susaki, Etsuo A. and Ueda, Hiroki R.},
    number = {1},
    pages = {137--157},
    volume = {23},
    publisher = {Elsevier Ltd},
    url = {http://dx.doi.org/10.1016/j.chembiol.2015.11.009},
    doi = {10.1016/j.chembiol.2015.11.009},
    issn = {24519448}
}

@article{Tainaka2014,
    title = {{Whole-body imaging with single-cell resolution by tissue decolorization}},
    year = {2014},
    journal = {Cell},
    author = {Tainaka, Kazuki and Kubota, Shimpei I. and Suyama, Takeru Q. and Susaki, Etsuo A. and Perrin, Dimitri and Ukai-Tadenuma, Maki and Ukai, Hideki and Ueda, Hiroki R.},
    number = {4},
    pages = {911--924},
    volume = {159},
    publisher = {Elsevier Inc.},
    url = {http://dx.doi.org/10.1016/j.cell.2014.10.034},
    doi = {10.1016/j.cell.2014.10.034},
    issn = {10974172}
}

@article{Kienle1996,
    title = {{Why do veins appear blue? A new look at an old question}},
    year = {1996},
    journal = {Applied Optics},
    author = {Kienle, Alwin and Lilge, Lothar and Vitkin, I. Alex and Patterson, Michael S. and Wilson, Brian C. and Hibst, Raimund and Steiner, Rudolf},
    number = {7},
    month = {3},
    pages = {1151},
    volume = {35},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ao-35-7-1151},
    doi = {10.1364/AO.35.001151},
    issn = {0003-6935}
}

@article{Ntziachristos2002,
    title = {{Would near-infrared fluorescence signals propagate through large human organs for clinical studies?}},
    year = {2002},
    journal = {Optics Letters},
    author = {Ntziachristos, Vasilis and Ripoll, Jorge and Weissleder, Ralph},
    number = {5},
    month = {3},
    pages = {333},
    volume = {27},
    url = {https://www.osapublishing.org/abstract.cfm?URI=ol-27-5-333 http://www.ncbi.nlm.nih.gov/pubmed/18007794},
    doi = {10.1364/OL.27.000333},
    issn = {0146-9592},
    pmid = {18007794}
}

@phdthesis{Bech2009,
    title = {{X-ray imaging with a grating interferometer}},
    year = {2009},
    booktitle = {Journal of Synchrotron Radiation},
    author = {Bech, Martin},
    pages = {155},
    school = {University of Copenhagen},
    doi = {10.1107/S0909049509017920},
    issn = {1600-5775},
    pmid = {19535872}
}

@article{Chen2010,
    title = {{X-ray Phase Sensitive Imaging Methods: Basic Physical Principles and Potential Medical Applications}},
    year = {2010},
    journal = {Current Medical Imaging Reviews},
    author = {Chen, Guang-Hong and Zambelli, Joseph and Bevins, Nicholas and Qi, Zhihua and Li, Ke},
    number = {2},
    pages = {90--99},
    volume = {6},
    url = {http://www.eurekaselect.com/openurl/content.php?genre=article&issn=1573-4056&volume=6&issue=2&spage=90},
    isbn = {1573-4056 (Print) 1573-4056 (Linking)},
    doi = {10.2174/157340510791268533},
    issn = {15734056},
    pmid = {23970846},
    arxivId = {NIHMS150003},
    keywords = {ct, dei, in-line holography, phase contrast, x-ray interferometry}
}

@book{Flood2013,
    title = {{ZEISS Lightsheet Z.1 Sample Preparation}},
    year = {2013},
    author = {Flood, PM and Kelly, R and Guti{\'{e}}rrez-Heredia, L and Reynaud, EG},
    publisher = {Carl Zeiss Microscopy GmbH;},
    url = {https://www.med.upenn.edu/cdbmicroscopycore/assets/user-content/documents/Zeiss_White_Paper_LightsheetZ1_Sample-Preparation.pdf},
    address = {Jena, Germany}
}

@article{Theer2016,
    title = {{{$\pi$}sPIM: High NA high resolution isotropic light-sheet imaging in cell culture dishes}},
    year = {2016},
    journal = {Scientific Reports},
    author = {Theer, Patrick and Dragneva, Denitsa and Knop, Michael},
    number = {September},
    pages = {1--9},
    volume = {6},
    publisher = {Nature Publishing Group},
    url = {http://dx.doi.org/10.1038/srep32880},
    doi = {10.1038/srep32880},
    issn = {20452322}
}

@misc{28_Vectorial_OTF_Optik_1997.pdf,
    title = {{28{\_}Vectorial{\_}OTF{\_}Optik{\_}1997.pdf}}
}

@misc{Ding2018Light-SheetRepair,
    title = {{Light-Sheet Imaging to Elucidate Cardiovascular Injury and Repair}},
    year = {2018},
    booktitle = {Current Cardiology Reports},
    author = {Ding, Yichen and Lee, Juhyun and Hsu, Jeffrey J. and Chang, Chih Chiang and Baek, Kyung In and Ranjbarvaziri, Sara and Ardehali, Reza and Packard, René R.Sevag and Hsiai, Tzung K.},
    number = {5},
    month = {5},
    volume = {20},
    publisher = {Current Medicine Group LLC 1},
    doi = {10.1007/s11886-018-0979-6},
    issn = {15343170},
    keywords = {Cardiovascular injury, Doxorubicin, Light-sheet imaging, Regeneration}
}

@article{BesselSelf-suppressionSheet,
    title = {{Self-suppression of Bessel Beam Side Lobes for High-Contrast Light Sheet}},
    author = {Bessel, Both},
    pages = {51--59},
    isbn = {9783030231897},
    doi = {10.1007/978-3-030-23189-7}
}