Journal papers

@article{kellman2020memory,

title = {Memory-efficient Learning for Large-Scale Computational Imaging},

author = { Michael Kellman and Kevin Zhang and Eric Markley and Jon Tamir and Emrah Bostan and Michael Lustig and Laura Waller},

url = {https://ieeexplore.ieee.org/document/9204455},

doi = {10.1109/TCI.2020.3025735},

year  = {2020},

date = {2020-10-14},

journal = {IEEE Transactions on Computational Imaging},

volume = {6},

pages = {1403-1414},

keywords = {algorithms, computational imaging, experimental design, learning-based, LED array, memory efficient, memory-efficient, physics-based},

pubstate = {published},

tppubtype = {article}

}

@article{yanny2020,

title = {Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy},

author = {Kyrollos Yanny and Nick Antipa and William Liberti and Sam Dehaeck and Kristina Monakhova and Fanglin Linda Liu and Konlin Shen and Ren Ng and Laura Waller},

url = {https://www.nature.com/articles/s41377-020-00403-7},

doi = {https://doi.org/10.1038/s41377-020-00403-7},

year  = {2020},

date = {2020-10-02},

journal = {Light: Science & Applications},

volume = {9},

number = {171},

abstract = {Miniature fluorescence microscopes are a standard tool in systems biology. However, widefield miniature microscopes capture only 2D information, and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth range. Here, we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective’s aperture stop. Placing the phase mask at the aperture stop significantly reduces the size of the device, and varying the focal lengths enables a uniform resolution across a wide depth range. The phase mask encodes the 3D fluorescence intensity into a single 2D measurement, and the 3D volume is recovered by solving a sparsity-constrained inverse problem. We provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the field-varying aberrations in miniature objectives. We demonstrate a prototype that is 17 mm tall and weighs 2.5 grams, achieving 2.76 μm lateral, and 15 μm axial resolution across most of the 900 × 700 × 390 μm3 volume at 40 volumes per second. The performance is validated experimentally on resolution targets, dynamic biological samples, and mouse brain tissue. Compared with existing miniature single-shot volume-capture implementations, our system is smaller and lighter and achieves a more than 2× better lateral and axial resolution throughout a 10× larger usable depth range. Our microscope design provides single-shot 3D imaging for applications where a compact platform matters, such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.},

keywords = {3D imaging, algorithms, diffuser, fluorescence imaging},

pubstate = {published},

tppubtype = {article}

}

@article{bostan2020deep,

title = {Deep Phase Decoder: Self-calibrating phase microscopy with an untrained deep neural network},

author = { Emrah Bostan and Reinhard Heckel and Michael Chen and Michael Kellman and Laura Waller},

url = {https://doi.org/10.1364/OPTICA.389314

https://arxiv.org/abs/2001.09803},

doi = {10.1364/OPTICA.389314},

year  = {2020},

date = {2020-05-21},

journal = {Optica},

volume = {7},

number = {6},

pages = {559-562},

keywords = {algorithms, learning-based, LED array, measurement diversity, phase imaging, physics-based, self-calibration},

pubstate = {published},

tppubtype = {article}

}

@article{ren2020multiple,

title = {A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography},

author = { David Ren and Colin Ophus and Michael Chen and Laura Waller},

url = {https://www.sciencedirect.com/science/article/pii/S030439911930052X},

year  = {2020},

date = {2020-01-01},

journal = {Ultramicroscopy},

volume = {208},

pages = {112860},

publisher = {North-Holland},

keywords = {3D imaging, algorithms, multiple-scattering, phase imaging, TEM},

pubstate = {published},

tppubtype = {article}

}

@article{pinkard2019deep,

title = {Deep learning for single-shot autofocus microscopy},

author = { Henry Pinkard and Zachary F Phillips and Arman Babakhani and Daniel A Fletcher and Laura Waller},

url = {https://www.osapublishing.org/optica/abstract.cfm?uri=optica-6-6-794},

year  = {2019},

date = {2019-06-20},

journal = {Optica},

volume = {6},

number = {6},

pages = {794--797},

publisher = {Optical Society of America},

keywords = {algorithms, high-throughput, LED array},

pubstate = {published},

tppubtype = {article}

}

@article{ophus2018linear,

title = {Linear and Nonlinear Reconstruction Algorithms for Atomic-Resolution Tomography Using Phase Contrast Electron Microscopy},

author = { Colin Ophus and David Ren and Michael Chen and Catherine Groschner and Mary C Scott and Laura Waller},

url = {https://doi.org/10.1017/S1431927618001046},

doi = {10.1017/S1431927618001046},

year  = {2018},

date = {2018-08-01},

journal = {Microscopy and Microanalysis},

volume = {24},

number = {S1},

pages = {110--111},

publisher = {Cambridge University Press},

keywords = {3D imaging, algorithms, phase imaging, TEM},

pubstate = {published},

tppubtype = {article}

}

@article{eckert2018efficient,

title = {Efficient illumination angle self-calibration in Fourier ptychography},

author = { Regina Eckert and Zachary F Phillips and Laura Waller},

url = {https://doi.org/10.1364/AO.57.005434},

year  = {2018},

date = {2018-06-28},

journal = {Applied Optics},

volume = {57},

number = {19},

pages = {5434--5442},

publisher = {Optical Society of America},

keywords = {algorithms, FPM, LED array, phase imaging, self-calibration},

pubstate = {published},

tppubtype = {article}

}

@article{bostan2018learning,

title = {Learning-based image reconstruction via parallel proximal algorithm},

author = { Emrah Bostan and Ulugbek S Kamilov and Laura Waller},

url = {https://doi.org/10.1109/LSP.2018.2833812},

doi = {10.1109/LSP.2018.2833812},

year  = {2018},

date = {2018-05-07},

journal = {IEEE Signal Processing Letters},

volume = {25},

number = {7},

pages = {989--993},

publisher = {IEEE},

keywords = {algorithms, fluorescence imaging, learning-based, regularization},

pubstate = {published},

tppubtype = {article}

}

@article{liu2017seagle,

title = {SEAGLE: Sparsity-driven image reconstruction under multiple scattering},

author = { Hsiou-Yuan Liu and Dehong Liu and Hassan Mansour and Petros T Boufounos and Laura Waller and Ulugbek S Kamilov},

url = {https://doi.org/10.1109/TCI.2017.2764461},

doi = {10.1109/TCI.2017.2764461},

year  = {2017},

date = {2017-10-19},

journal = {IEEE Transactions on Computational Imaging},

volume = {4},

number = {1},

pages = {73--86},

publisher = {IEEE},

keywords = {algorithms, multiple-scattering, optical models},

pubstate = {published},

tppubtype = {article}

}

@article{zhang20173d,

title = {3D computer-generated holography by non-convex optimization},

author = { Jingzhao Zhang and Nicolas C Pégard and Jingshan Zhong and Hillel Adesnik and Laura Waller},

url = {https://doi.org/10.1364/OPTICA.4.001306},

doi = {10.1364/OPTICA.4.001306},

year  = {2017},

date = {2017-10-19},

journal = {Optica},

volume = {4},

number = {10},

pages = {1306--1313},

publisher = {Optical Society of America},

keywords = {3D imaging, algorithms, digital holography, fluorescence imaging, neural imaging},

pubstate = {published},

tppubtype = {article}

}

@article{yeh2017structured,

title = {Structured illumination microscopy with unknown patterns and a statistical prior},

author = { Li-Hao Yeh and Lei Tian and Laura Waller},

url = {https://doi.org/10.1364/BOE.8.000695},

doi = {10.1364/BOE.8.000695},

year  = {2017},

date = {2017-02-01},

journal = {Biomedical optics express},

volume = {8},

number = {2},

pages = {695--711},

publisher = {Optical Society of America},

keywords = {algorithms, self-calibration, structured illumination},

pubstate = {published},

tppubtype = {article}

}

@article{zhong2016nonlinear,

title = {Nonlinear optimization algorithm for partially coherent phase retrieval and source recovery},

author = { Jingshan Zhong and Lei Tian and Paroma Varma and Laura Waller},

url = {https://doi.org/10.1109/TCI.2016.2571669},

doi = {10.1109/TCI.2016.2571669},

year  = {2016},

date = {2016-05-23},

journal = {IEEE Transactions on Computational Imaging},

volume = {2},

number = {3},

pages = {310--322},

publisher = {IEEE},

keywords = {algorithms, LED array, nonlinear optimization, partial coherence, phase from defocus, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{dardikman2016video,

title = {Video-rate processing in tomographic phase microscopy of biological cells using CUDA},

author = { Gili Dardikman and Mor Habaza and Laura Waller and Natan T Shaked},

url = {https://doi.org/10.1364/OE.24.011839},

doi = {10.1364/OE.24.011839},

year  = {2016},

date = {2016-05-23},

journal = {Optics express},

volume = {24},

number = {11},

pages = {11839--11854},

publisher = {Optical Society of America},

keywords = {3D imaging, algorithms},

pubstate = {published},

tppubtype = {article}

}

@article{yeh2015experimental,

title = {Experimental robustness of Fourier ptychography phase retrieval algorithms},

author = { Li-Hao Yeh and Jonathan Dong and Jingshan Zhong and Lei Tian and Michael Chen and Gongguo Tang and Mahdi Soltanolkotabi and Laura Waller},

url = {https://doi.org/10.1364/OE.23.033214},

doi = {10.1364/OE.23.033214},

year  = {2015},

date = {2015-12-16},

journal = {Optics express},

volume = {23},

number = {26},

pages = {33214--33240},

publisher = {Optical Society of America},

keywords = {algorithms, FPM, high-resolution, high-throughput, LED array, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{claus2015quantitative,

title = {Quantitative phase retrieval with arbitrary pupil and illumination},

author = { Rene A Claus and Patrick P Naulleau and Andrew R Neureuther and Laura Waller},

url = {https://doi.org/10.1364/OE.23.026672},

doi = {10.1364/OE.23.026672},

year  = {2015},

date = {2015-10-02},

journal = {Optics express},

volume = {23},

number = {20},

pages = {26672--26682},

publisher = {Optical Society of America},

keywords = {algorithms, EUV, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{ma2015motion,

title = {Motion deblurring with temporally coded illumination in an LED array microscope},

author = { Chenguang Ma and Ziji Liu and Lei Tian and Qionghai Dai and Laura Waller},

url = {https://doi.org/10.1364/OL.40.002281},

doi = {10.1364/OL.40.002281},

year  = {2015},

date = {2015-05-07},

journal = {Optics letters},

volume = {40},

number = {10},

pages = {2281--2284},

publisher = {Optical Society of America},

keywords = {algorithms, coded illumination, LED array, motion deblur},

pubstate = {published},

tppubtype = {article}

}

@article{tian20153db,

title = {3D intensity and phase imaging from light field measurements in an LED array microscope},

author = { Lei Tian and Laura Waller},

url = {https://doi.org/10.1364/OPTICA.2.000104},

doi = {10.1364/OPTICA.2.000104},

year  = {2015},

date = {2015-01-28},

journal = {optica},

volume = {2},

number = {2},

pages = {104--111},

publisher = {Optical Society of America},

keywords = {3D imaging, algorithms, FPM, LED array, light field},

pubstate = {published},

tppubtype = {article}

}

@article{shanker2014transport,

title = {Transport of intensity phase imaging in the presence of curl effects induced by strongly absorbing photomasks},

author = { Aamod Shanker and Lei Tian and Martin Sczyrba and Brid Connolly and Andrew R Neureuther and Laura Waller},

url = {https://doi.org/10.1364/AO.53.0000J1},

doi = {10.1364/AO.53.0000J1},

year  = {2014},

date = {2014-10-23},

journal = {Applied optics},

volume = {53},

number = {34},

pages = {J1--J6},

publisher = {Optical Society of America},

keywords = {algorithms, EUV, physics-based, TIE},

pubstate = {published},

tppubtype = {article}

}

@article{tian2014multiplexed,

title = {Multiplexed coded illumination for Fourier Ptychography with an LED array microscope},

author = { Lei Tian and Xiao Li and Kannan Ramchandran and Laura Waller},

url = {https://doi.org/10.1364/BOE.5.002376},

doi = {10.1364/BOE.5.002376},

year  = {2014},

date = {2014-06-19},

journal = {Biomedical optics express},

volume = {5},

number = {7},

pages = {2376--2389},

publisher = {Optical Society of America},

keywords = {algorithms, experimental design, FPM, high-resolution, high-throughput, LED array, multiplexed illumination},

pubstate = {published},

tppubtype = {article}

}

@article{jingshan2013sparse,

title = {Sparse ACEKF for phase reconstruction},

author = { Zhong Jingshan and Justin Dauwels and Manuel A Vázquez and Laura Waller},

url = {https://doi.org/10.1364/OE.21.018125},

doi = {10.1364/OE.21.018125},

year  = {2013},

date = {2013-07-22},

journal = {Optics express},

volume = {21},

number = {15},

pages = {18125--18137},

publisher = {Optical Society of America},

keywords = {algorithms, phase from defocus, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{waller2013quantitative,

title = {Quantitative amplification of weak images by nonlinear propagation},

author = { Laura Waller and Dmitry V Dylov and Jason W Fleischer},

url = {https://doi.org/10.1364/OL.38.000082},

doi = {10.1364/OL.38.000082},

year  = {2013},

date = {2013-01-04},

journal = {Optics letters},

volume = {38},

number = {2},

pages = {82--84},

publisher = {Optical Society of America},

keywords = {algorithms, partial coherence, TIE},

pubstate = {published},

tppubtype = {article}

}

@article{kou2011quantitative,

title = {Quantitative phase restoration by direct inversion using the optical transfer function},

author = { Shan Shan Kou and Laura Waller and George Barbastathis and Pierre Marquet and Christian Depeursinge and Colin JR Sheppard},

url = {https://doi.org/10.1364/OL.36.002671},

doi = {10.1364/OL.36.002671},

year  = {2011},

date = {2011-07-13},

journal = {Optics letters},

volume = {36},

number = {14},

pages = {2671--2673},

publisher = {Optical Society of America},

keywords = {algorithms, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{waller2011phase,

title = {Phase and amplitude imaging from noisy images by Kalman filtering},

author = { Laura Waller and Mankei Tsang and Sameera Ponda and Se Young Yang and George Barbastathis},

url = {https://doi.org/10.1364/OE.19.002805},

doi = {10.1364/OE.19.002805},

year  = {2011},

date = {2011-01-28},

journal = {Optics express},

volume = {19},

number = {3},

pages = {2805--2815},

publisher = {Optical Society of America},

keywords = {algorithms, phase from defocus, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{waller2010transportb,

title = {Transport of intensity phase-amplitude imaging with higher order intensity derivatives},

author = { Laura Waller and Lei Tian and George Barbastathis},

url = {https://doi.org/10.1364/OE.18.012552},

doi = {10.1364/OE.18.012552},

year  = {2010},

date = {2010-05-27},

journal = {Optics express},

volume = {18},

number = {12},

pages = {12552--12561},

publisher = {Optical Society of America},

keywords = {algorithms, phase imaging, TIE},

pubstate = {published},

tppubtype = {article}

}

@article{kou2010transport,

title = {Transport-of-intensity approach to differential interference contrast (TI-DIC) microscopy for quantitative phase imaging},

author = { Shan Shan Kou and Laura Waller and George Barbastathis and Colin JR Sheppard},

url = {https://doi.org/10.1364/OL.35.000447},

doi = {10.1364/OL.35.000447},

year  = {2010},

date = {2010-01-29},

journal = {Optics letters},

volume = {35},

number = {3},

pages = {447--449},

publisher = {Optical Society of America},

keywords = {algorithms, DIC, phase imaging, TIE},

pubstate = {published},

tppubtype = {article}

}