Publications

@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{Chen:20,

title = {Multi-layer Born multiple-scattering model for 3D phase microscopy},

author = {Michael Chen and David Ren and Hsiou-Yuan Liu and Shwetadwip Chowdhury and Laura Waller},

url = {http://www.osapublishing.org/optica/abstract.cfm?URI=optica-7-5-394},

doi = {10.1364/OPTICA.383030},

year  = {2020},

date = {2020-05-01},

journal = {Optica},

volume = {7},

number = {5},

pages = {394--403},

publisher = {OSA},

abstract = {We propose an accurate and computationally efficient 3D scattering model, multi-layer Born (MLB), and use it to recover the 3D refractive index (RI) of thick biological samples. For inverse problems recovering the complex field of thick samples, weak scattering models (e.g., first Born) may fail or underestimate the RI, especially with a large index contrast. Multi-slice (MS) beam propagation methods model multiple scattering to provide more realistic reconstructions; however, MS does not properly account for highly oblique scattering, nor does it model backward scattering. Our proposed MLB model uses a first Born model at each of many slices, accurately capturing the oblique scattering effects and estimating the backward scattering process. When used in conjunction with an inverse solver, the model provides more accurate RI reconstructions for high-resolution phase tomography. Importantly, MLB retains a reasonable computation time that is critical for practical implementation with iterative inverse algorithms.},

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

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{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{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{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{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{chen20163d,

title = {3D differential phase contrast microscopy},

author = { Michael Chen and Lei Tian and Laura Waller},

url = {https://doi.org/10.1364/BOE.7.003940},

year  = {2016},

date = {2016-10-01},

journal = {Biomedical Optics Express},

volume = {7},

number = {10},

pages = {3940--3950},

publisher = {Optical Society of America},

keywords = {3D imaging, DPC, phase imaging},

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{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{tian2015computational,

title = {Computational illumination for high-speed in vitro Fourier ptychographic microscopy},

author = { Lei Tian and Ziji Liu and Li-Hao Yeh and Michael Chen and Jingshan Zhong and Laura Waller},

url = {https://doi.org/10.1364/OPTICA.2.000904},

doi = {10.1364/OPTICA.2.000904},

year  = {2015},

date = {2015-10-14},

journal = {Optica},

volume = {2},

number = {10},

pages = {904--911},

publisher = {Optical Society of America},

keywords = {FPM, high-resolution, high-throughput, in vitro imaging, 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{phillips2015multi,

title = {Multi-contrast imaging and digital refocusing on a mobile microscope with a domed LED array},

author = { Zachary F Phillips and Michael V D'Ambrosio and Lei Tian and Jared J Rulison and Hurshal S Patel and Nitin Sadras and Aditya V Gande and Neil A Switz and Daniel A Fletcher and Laura Waller},

url = {https://doi.org/10.1371/journal.pone.0124938

},

doi = {10.1371/journal.pone.0124938},

year  = {2015},

date = {2015-05-13},

journal = {PloS one},

volume = {10},

number = {5},

publisher = {Public Library of Science},

keywords = {3D imaging, CellScope, LED array, multi-contrast, phase imaging},

pubstate = {published},

tppubtype = {article}

}

@article{tian2015quantitativeb,

title = {Quantitative differential phase contrast imaging in an LED array microscope},

author = { Lei Tian and Laura Waller},

url = {https://doi.org/10.1364/OE.23.011394},

doi = {10.1364/OE.23.011394},

year  = {2015},

date = {2015-04-22},

journal = {Optics express},

volume = {23},

number = {9},

pages = {11394--11403},

publisher = {Optical Society of America},

keywords = {DPC, LED array, partial coherence, phase imaging, real-time},

pubstate = {published},

tppubtype = {article}

}