Publications
Michael Kellman; Kevin Zhang; Eric Markley; Jon Tamir; Emrah Bostan; Michael Lustig; Laura Waller
Memory-efficient Learning for Large-Scale Computational Imaging Journal Article
In: IEEE Transactions on Computational Imaging, vol. 6, pp. 1403-1414, 2020.
Links | BibTeX | Tags: algorithms, computational imaging, experimental design, learning-based, LED array, memory efficient, memory-efficient, physics-based
@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}
}
Michael Kellman
Physics-based Learning for Large-scale Computational Imaging PhD Thesis
EECS Department, University of California, Berkeley, 2020.
Abstract | Links | BibTeX | Tags: algorithms, computational imaging, experimental design, learning-based, LED array, memory efficient, memory-efficient, physics-based
@phdthesis{Kellman:EECS-2020-167,
title = {Physics-based Learning for Large-scale Computational Imaging},
author = {Michael Kellman},
url = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2020/EECS-2020-167.html},
year = {2020},
date = {2020-08-01},
number = {UCB/EECS-2020-167},
school = {EECS Department, University of California, Berkeley},
abstract = {In computational imaging systems (e.g. tomographic systems, computational optics, magnetic resonance imaging) the acquisition of data and reconstruction of images are co-designed to retrieve information which is not traditionally accessible. The performance of such systems is characterized by how information is encoded to (forward process) and decoded from (inverse problem) the measurements. Recently, critical aspects of these systems, such as their signal prior, have been optimized using deep neural networks formed from unrolling the iterations of a physics-based image reconstruction.
In this dissertation, I will detail my work, physics-based learned design, to optimize the performance of the entire computational imaging system by jointly learning aspects of its experimental design and computational reconstruction. As an application, I introduce how the LED-array microscope performs super-resolved quantitative phase imaging and demonstrate how physics-based learning can optimize a reduced set of measurements without sacrificing performance to enable the imaging of live fast moving biology.
In this dissertation's latter half, I will discuss how to overcome some of the computational challenges encountered in applying physics-based learning concepts to large-scale computational imaging systems. I will describe my work, memory-efficient learning, that makes physics-based learning for large-scale systems feasible on commercially-available graphics processing units. I demonstrate this method on two large-scale real-world systems: 3D multi-channel compressed sensing MRI and super-resolution optical microscopy.},
keywords = {algorithms, computational imaging, experimental design, learning-based, LED array, memory efficient, memory-efficient, physics-based},
pubstate = {published},
tppubtype = {phdthesis}
}
In this dissertation, I will detail my work, physics-based learned design, to optimize the performance of the entire computational imaging system by jointly learning aspects of its experimental design and computational reconstruction. As an application, I introduce how the LED-array microscope performs super-resolved quantitative phase imaging and demonstrate how physics-based learning can optimize a reduced set of measurements without sacrificing performance to enable the imaging of live fast moving biology.
In this dissertation's latter half, I will discuss how to overcome some of the computational challenges encountered in applying physics-based learning concepts to large-scale computational imaging systems. I will describe my work, memory-efficient learning, that makes physics-based learning for large-scale systems feasible on commercially-available graphics processing units. I demonstrate this method on two large-scale real-world systems: 3D multi-channel compressed sensing MRI and super-resolution optical microscopy.
Emrah Bostan; Reinhard Heckel; Michael Chen; Michael Kellman; Laura Waller
Deep Phase Decoder: Self-calibrating phase microscopy with an untrained deep neural network Journal Article
In: Optica, vol. 7, no. 6, pp. 559-562, 2020.
Links | BibTeX | Tags: algorithms, learning-based, LED array, measurement diversity, phase imaging, physics-based, self-calibration
@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}
}
Henry Pinkard; Zachary F Phillips; Arman Babakhani; Daniel A Fletcher; Laura Waller
Deep learning for single-shot autofocus microscopy Journal Article
In: Optica, vol. 6, no. 6, pp. 794–797, 2019.
Links | BibTeX | Tags: algorithms, high-throughput, LED array
@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}
}
Tomas Aidukas; Regina Eckert; Andrew R Harvey; Laura Waller; Pavan C Konda
Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware Journal Article
In: Scientific reports, vol. 9, no. 1, pp. 1–12, 2019.
Links | BibTeX | Tags: FPM, LED array, phase imaging, self-calibration
@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}
}
Zachary F Phillips
Quantitative Microscopy using Coded Illumination PhD Thesis
University of California, Berkeley, 2019.
Links | BibTeX | Tags: algorithms, DPC, LED array, motion deblur, self-calibration
@phdthesis{phillips2019quant,
title = {Quantitative Microscopy using Coded Illumination},
author = {Zachary F Phillips},
url = {https://escholarship.org/uc/item/70d9j190
https://search.proquest.com/openview/ac36264c1a5b90ee3c8e4085759b0cc4/1?pq-origsite=gscholar&cbl=18750&diss=y},
year = {2019},
date = {2019-05-01},
school = {University of California, Berkeley},
keywords = {algorithms, DPC, LED array, motion deblur, self-calibration},
pubstate = {published},
tppubtype = {phdthesis}
}
Michael Chen; Zachary F Phillips; Laura Waller
Quantitative differential phase contrast (DPC) microscopy with computational aberration correction Journal Article
In: Optics express, vol. 26, no. 25, pp. 32888–32899, 2018.
Links | BibTeX | Tags: aberrations, DPC, LED array, phase imaging, self-calibration
@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}
}
Regina Eckert; Zachary F Phillips; Laura Waller
Efficient illumination angle self-calibration in Fourier ptychography Journal Article
In: Applied Optics, vol. 57, no. 19, pp. 5434–5442, 2018.
Links | BibTeX | Tags: algorithms, FPM, LED array, phase imaging, self-calibration
@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}
}
Jingshan Zhong; Lei Tian; Paroma Varma; Laura Waller
Nonlinear optimization algorithm for partially coherent phase retrieval and source recovery Journal Article
In: IEEE Transactions on Computational Imaging, vol. 2, no. 3, pp. 310–322, 2016.
Links | BibTeX | Tags: algorithms, LED array, nonlinear optimization, partial coherence, phase from defocus, phase imaging
@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}
}
Li-Hao Yeh; Jonathan Dong; Jingshan Zhong; Lei Tian; Michael Chen; Gongguo Tang; Mahdi Soltanolkotabi; Laura Waller
Experimental robustness of Fourier ptychography phase retrieval algorithms Journal Article
In: Optics express, vol. 23, no. 26, pp. 33214–33240, 2015.
Links | BibTeX | Tags: algorithms, FPM, high-resolution, high-throughput, LED array, phase imaging
@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}
}
Lei Tian; Ziji Liu; Li-Hao Yeh; Michael Chen; Jingshan Zhong; Laura Waller
Computational illumination for high-speed in vitro Fourier ptychographic microscopy Journal Article
In: Optica, vol. 2, no. 10, pp. 904–911, 2015.
Links | BibTeX | Tags: FPM, high-resolution, high-throughput, in vitro imaging, LED array, phase imaging
@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}
}
Zachary F Phillips; Michael V D'Ambrosio; Lei Tian; Jared J Rulison; Hurshal S Patel; Nitin Sadras; Aditya V Gande; Neil A Switz; Daniel A Fletcher; Laura Waller
Multi-contrast imaging and digital refocusing on a mobile microscope with a domed LED array Journal Article
In: PloS one, vol. 10, no. 5, 2015.
Links | BibTeX | Tags: 3D imaging, CellScope, LED array, multi-contrast, phase imaging
@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}
}
Chenguang Ma; Ziji Liu; Lei Tian; Qionghai Dai; Laura Waller
Motion deblurring with temporally coded illumination in an LED array microscope Journal Article
In: Optics letters, vol. 40, no. 10, pp. 2281–2284, 2015.
Links | BibTeX | Tags: algorithms, coded illumination, LED array, motion deblur
@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}
}
Lei Tian; Laura Waller
Quantitative differential phase contrast imaging in an LED array microscope Journal Article
In: Optics express, vol. 23, no. 9, pp. 11394–11403, 2015.
Links | BibTeX | Tags: DPC, LED array, partial coherence, phase imaging, real-time
@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}
}
Lei Tian; Laura Waller
3D intensity and phase imaging from light field measurements in an LED array microscope Journal Article
In: optica, vol. 2, no. 2, pp. 104–111, 2015.
Links | BibTeX | Tags: 3D imaging, algorithms, FPM, LED array, light field
@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}
}
Ziji Liu; Lei Tian; Sijia Liu; Laura Waller
Real-time brightfield, darkfield, and phase contrast imaging in a light-emitting diode array microscope Journal Article
In: Journal of biomedical optics, vol. 19, no. 10, pp. 106002, 2014.
Links | BibTeX | Tags: LED array, multi-contrast, real-time
@article{liu2014real,
title = {Real-time brightfield, darkfield, and phase contrast imaging in a light-emitting diode array microscope},
author = { Ziji Liu and Lei Tian and Sijia Liu and Laura Waller},
url = {https://doi.org/10.1117/1.JBO.19.10.106002},
doi = {10.1117/1.JBO.19.10.106002},
year = {2014},
date = {2014-10-01},
journal = {Journal of biomedical optics},
volume = {19},
number = {10},
pages = {106002},
publisher = {International Society for Optics and Photonics},
keywords = {LED array, multi-contrast, real-time},
pubstate = {published},
tppubtype = {article}
}
Lei Tian; Xiao Li; Kannan Ramchandran; Laura Waller
Multiplexed coded illumination for Fourier Ptychography with an LED array microscope Journal Article
In: Biomedical optics express, vol. 5, no. 7, pp. 2376–2389, 2014.
Links | BibTeX | Tags: algorithms, experimental design, FPM, high-resolution, high-throughput, LED array, multiplexed illumination
@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}
}
Lei Tian; Jingyan Wang; Laura Waller
3D differential phase-contrast microscopy with computational illumination using an LED array Journal Article
In: Optics letters, vol. 39, no. 5, pp. 1326–1329, 2014.
Links | BibTeX | Tags: 3D imaging, DPC, LED array, phase imaging
@article{tian20143d,
title = {3D differential phase-contrast microscopy with computational illumination using an LED array},
author = { Lei Tian and Jingyan Wang and Laura Waller},
url = {https://doi.org/10.1364/OL.39.001326},
doi = {10.1364/OL.39.001326},
year = {2014},
date = {2014-02-28},
journal = {Optics letters},
volume = {39},
number = {5},
pages = {1326--1329},
publisher = {Optical Society of America},
keywords = {3D imaging, DPC, LED array, phase imaging},
pubstate = {published},
tppubtype = {article}
}