Journal papers

@article{kuo2020chip,

title = {On-chip fluorescence microscopy with a random microlens diffuser},

author = { Grace Kuo and Fanglin Linda Liu and Irene Grossrubatscher and Ren Ng and Laura Waller},

url = {https://doi.org/10.1364/OE.382055},

doi = {10.1364/OE.382055},

year  = {2020},

date = {2020-03-09},

journal = {Optics Express},

volume = {28},

number = {6},

pages = {8384--8399},

publisher = {Optical Society of America},

keywords = {3D imaging, diffuser, fluorescence imaging, lensless imaging, on-chip},

pubstate = {published},

tppubtype = {article}

}

@article{10.1145/3386569.3392414,

title = {High Resolution éTendue Expansion for Holographic Displays},

author = {Grace Kuo and Laura Waller and Ren Ng and Andrew Maimone},

url = {https://doi.org/10.1145/3386569.3392414},

doi = {10.1145/3386569.3392414},

issn = {0730-0301},

year  = {2020},

date = {2020-01-01},

journal = {ACM Trans. Graph.},

volume = {39},

number = {4},

publisher = {Association for Computing Machinery},

address = {New York, NY, USA},

abstract = {Holographic displays can create high quality 3D images while maintaining a small form factor suitable for head-mounted virtual and augmented reality systems. However, holographic displays have limited étendue based on the number of pixels in their spatial light modulators, creating a tradeoff between the eyebox size and the field-of-view. Scattering-based étendue expansion, in which coherent light is focused into an image after being scattered by a static mask, is a promising avenue to break this tradeoff. However, to date, this approach has been limited to very sparse content consisting of, for example, only tens of spots.In this work, we introduce new algorithms to scattering-based étendue expansion that support dense, photorealistic imagery at the native resolution of the spatial light modulator, offering up to a 20 dB improvement in peak signal to noise ratio over baseline methods. We propose spatial and frequency constraints to optimize performance for human perception, and performance is characterized both through simulation and a preliminary benchtop prototype. We further demonstrate the ability to generate content at multiple depths, and we provide a path for the miniaturization of our benchtop prototype into a sunglasses-like form factor.},

keywords = {augmented reality, computational displays, computer generated holography, near-eye displays},

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{phillips2020high,

title = {High-throughput fluorescence microscopy using multi-frame motion deblurring},

author = { Zachary F Phillips and Sarah Dean and Benjamin Recht and Laura Waller},

url = {https://doi.org/10.1364/BOE.11.000281},

doi = {10.1364/BOE.11.000281},

year  = {2019},

date = {2019-12-16},

journal = {Biomedical Optics Express},

volume = {11},

number = {1},

pages = {281--300},

publisher = {Optical Society of America},

keywords = {deconvolution, fluorescence imaging, high-throughput, motion deblur},

pubstate = {published},

tppubtype = {article}

}

@article{monakhova2019learned,

title = {Learned reconstructions for practical mask-based lensless imaging},

author = { Kristina Monakhova and Joshua Yurtsever and Grace Kuo and Nick Antipa and Kyrollos Yanny and Laura Waller},

url = {https://doi.org/10.1364/OE.27.028075},

doi = {10.1364/OE.27.028075},

year  = {2019},

date = {2019-09-30},

journal = {Optics express},

volume = {27},

number = {20},

pages = {28075--28090},

publisher = {Optical Society of America},

keywords = {diffuser, learning-based, lensless imaging, physics-based},

pubstate = {published},

tppubtype = {article}

}

@article{chowdhury2019high,

title = {High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images},

author = { Shwetadwip Chowdhury and Michael Chen and Regina Eckert and David Ren and Fan Wu and Nicole A Repina and Laura Waller},

url = {https://doi.org/10.1364/OPTICA.6.001211},

doi = {10.1364/OPTICA.6.001211},

year  = {2019},

date = {2019-09-16},

journal = {Optica},

volume = {6},

number = {9},

pages = {1211--1219},

publisher = {Optical Society of America},

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

pubstate = {published},

tppubtype = {article}

}

@article{monakhova2019unrolled,

title = {Unrolled, model-based networks for lensless imaging},

author = { Kristina Monakhova and Joshua Yurtsever and Grace Kuo and Nick Antipa and Kyrollos Yanny and Laura Waller},

url = {https://pdfs.semanticscholar.org/6a49/3ac2a0c8a3be888ece00b52bc1ec013df2bd.pdf},

year  = {2019},

date = {2019-09-14},

keywords = {diffuser, learning-based, lensless imaging, physics-based},

pubstate = {published},

tppubtype = {article}

}

@article{kellman2019physics,

title = {Physics-based learned design: Optimized coded-illumination for quantitative phase imaging},

author = { Michael Kellman and Emrah Bostan and Nicole A Repina and Laura Waller},

url = {https://ieeexplore.ieee.org/document/8667888},

year  = {2019},

date = {2019-09-01},

journal = {IEEE Transactions on Computational Imaging},

volume = {5},

number = {3},

pages = {344--353},

publisher = {IEEE},

keywords = {algorithm, experimental design, learning-based, phase imaging, physics-based},

pubstate = {published},

tppubtype = {article}

}

@article{ophus20193d,

title = {3D Imaging Using HAADF-STEM and HRTEM Atomic Electron Tomography},

author = { Colin Ophus and David Ren and Jihan Zhou and Hannah Devyldere and Michael Chen and Philipp M Pelz and Peter Ercius and Jianwei Miao and Mary C Scott and Laura Waller},

url = {https://doi.org/10.1017/S1431927619002708},

doi = {10.1017/S1431927619002708},

year  = {2019},

date = {2019-08-05},

journal = {Microscopy and Microanalysis},

volume = {25},

number = {S2},

pages = {394--395},

publisher = {Cambridge University Press},

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

pubstate = {published},

tppubtype = {article}

}

@article{yeh2019speckle,

title = {Speckle-structured illumination for 3D phase and fluorescence computational microscopy},

author = { Li-Hao Yeh and Shwetadwip Chowdhury and Nicole A Repina and Laura Waller},

url = {https://doi.org/10.1364/BOE.10.003635},

doi = {10.1364/BOE.10.003635},

year  = {2019},

date = {2019-07-01},

journal = {Biomedical optics express},

volume = {10},

number = {7},

pages = {3635--3653},

publisher = {Optical Society of America},

keywords = {3D imaging, high-throughput, multiple-scattering, speckle},

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{aidukas2019low,

title = {Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware},

author = { Tomas Aidukas and Regina Eckert and Andrew R Harvey and Laura Waller and Pavan C Konda},

url = {https://doi.org/10.1038/s41598-019-43845-9},

year  = {2019},

date = {2019-05-15},

journal = {Scientific reports},

volume = {9},

number = {1},

pages = {1--12},

publisher = {Nature Publishing Group},

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

pubstate = {published},

tppubtype = {article}

}

@article{yeh2019computational,

title = {Computational structured illumination for high-content fluorescence and phase microscopy},

author = { Li-Hao Yeh and Shwetadwip Chowdhury and Laura Waller},

url = {https://www.osapublishing.org/boe/abstract.cfm?uri=boe-10-4-1978

https://doi.org/10.1364/BOE.10.001978},

doi = {10.1364/BOE.10.001978},

year  = {2019},

date = {2019-04-01},

journal = {Biomedical optics express},

volume = {10},

number = {4},

pages = {1978--1998},

publisher = {Optical Society of America},

abstract = {High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample’s super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4× the objective’s diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 μm QP resolution, across a FOV of 2×2.7 mm 2, giving a space-bandwidth product (SBP) of 60 megapixels.},

keywords = {diffuser, fluorescence imaging, high-throughput, phase imaging, structured illumination, super-resolution},

pubstate = {published},

tppubtype = {article}

}

@article{chen2018quantitative,

title = {Quantitative differential phase contrast (DPC) microscopy with computational aberration correction},

author = { Michael Chen and Zachary F Phillips and Laura Waller},

url = {https://doi.org/10.1364/OE.26.032888},

doi = {10.1364/OE.26.032888},

year  = {2018},

date = {2018-11-30},

journal = {Optics express},

volume = {26},

number = {25},

pages = {32888--32899},

publisher = {Optical Society of America},

keywords = {aberrations, DPC, LED array, phase imaging, self-calibration},

pubstate = {published},

tppubtype = {article}

}

@article{kellman2018motionb,

title = {Motion-resolved quantitative phase imaging},

author = { Michael Kellman and Michael Chen and Zachary F Phillips and Michael Lustig and Laura Waller},

url = {https://doi.org/10.1364/BOE.9.005456},

doi = {10.1364/BOE.9.005456},

year  = {2018},

date = {2018-10-15},

journal = {Biomedical optics express},

volume = {9},

number = {11},

pages = {5456--5466},

publisher = {Optical Society of America},

keywords = {algorithm, high throughput, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{deng2018all,

title = {All-Silicon Broadband Ultraviolet Metasurfaces},

author = { Yang Deng and Xi Wang and Zilun Gong and Kaichen Dong and Shuai Lou and Nicolas C Pégard and Kyle B Tom and Fuyi Yang and Zheng You and Laura Waller and Jie Yao},

url = {https://doi.org/10.1002/adma.201802632},

doi = {10.1002/adma.201802632},

year  = {2018},

date = {2018-08-10},

journal = {Advanced Materials},

volume = {30},

number = {38},

pages = {1802632},

keywords = {metasurfaces},

pubstate = {published},

tppubtype = {article}

}

@article{gunjala2018aberration,

title = {Aberration recovery by imaging a weak diffuser},

author = { Gautam Gunjala and Stuart Sherwin and Aamod Shanker and Laura Waller},

url = {https://doi.org/10.1364/OE.26.021054},

doi = {10.1364/OE.26.021054},

year  = {2018},

date = {2018-08-06},

journal = {Optics express},

volume = {26},

number = {16},

pages = {21054--21068},

publisher = {Optical Society of America},

keywords = {aberrations, speckle, statistical optics},

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{mardinly2018precise,

title = {Precise multimodal optical control of neural ensemble activity},

author = { Alan R Mardinly and Ian Antón Oldenburg and Nicolas C Pégard and Savitha Sridharan and Evan H Lyall and Kirill Chesnov and Stephen G Brohawn and Laura Waller and Hillel Adesnik},

url = {https://doi.org/10.1038/s41593-018-0139-8},

doi = {10.1038/s41593-018-0139-8},

year  = {2018},

date = {2018-04-30},

journal = {Nature neuroscience},

volume = {21},

number = {6},

pages = {881--893},

publisher = {Nature Publishing Group},

keywords = {3D imaging, digital holography, multiphoton, neural imaging},

pubstate = {published},

tppubtype = {article}

}

@article{antipa2018diffusercam,

title = {DiffuserCam: Lensless single-exposure 3D imaging},

author = { Nick Antipa and Grace Kuo and Reinhard Heckel and Ben Mildenhall and Emrah Bostan and Ren Ng and Laura Waller},

url = {https://doi.org/10.1364/OPTICA.5.000001},

doi = {10.1364/OPTICA.5.000001},

year  = {2018},

date = {2018-01-20},

journal = {Optica},

volume = {5},

number = {1},

pages = {1--9},

publisher = {Optical Society of America},

keywords = {compressed sensing, diffuser, lensless imaging},

pubstate = {published},

tppubtype = {article}

}

@article{10.1117/1.JMM.16.4.041012,

title = {Modeling high-efficiency extreme ultraviolet etched multilayer phase-shift masks},

author = {Stuart Sherwin and Andrew Neureuther and Patrick Naulleau},

url = {https://doi.org/10.1117/1.JMM.16.4.041012},

doi = {10.1117/1.JMM.16.4.041012},

year  = {2017},

date = {2017-12-09},

journal = {Journal of Micro/Nanolithography, MEMS, and MOEMS},

volume = {16},

number = {4},

pages = {1 -- 15},

publisher = {SPIE},

keywords = {EUV, experimental design, lithography, optical models},

pubstate = {published},

tppubtype = {article}

}

@article{pegard2017three,

title = {Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT)},

author = { Nicolas C Pégard and Alan R Mardinly and Ian Antón Oldenburg and Savitha Sridharan and Laura Waller and Hillel Adesnik},

url = {https://doi.org/10.1038/s41467-017-01031-3},

doi = {10.1038/s41467-017-01031-3},

year  = {2017},

date = {2017-10-31},

journal = {Nature communications},

volume = {8},

number = {1},

pages = {1--14},

publisher = {Nature Publishing Group},

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

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}

}