Publications by David Ren
2022
Yi Xue; David Ren; Laura Waller
Three-dimensional bi-functional refractive index and fluorescence microscopy (BRIEF) Journal Article
In: Biomed. Opt. Express, vol. 13, no. 11, pp. 5900–5908, 2022.
@article{Xue:22,
title = {Three-dimensional bi-functional refractive index and fluorescence microscopy (BRIEF)},
author = {Yi Xue and David Ren and Laura Waller},
url = {https://opg.optica.org/boe/abstract.cfm?URI=boe-13-11-5900},
doi = {10.1364/BOE.456621},
year = {2022},
date = {2022-11-01},
journal = {Biomed. Opt. Express},
volume = {13},
number = {11},
pages = {5900--5908},
publisher = {Optica Publishing Group},
abstract = {Fluorescence microscopy is a powerful tool for imaging biological samples with molecular specificity. In contrast, phase microscopy provides label-free measurement of the sample’s refractive index (RI), which is an intrinsic optical property that quantitatively relates to cell morphology, mass, and stiffness. Conventional imaging techniques measure either the labeled fluorescence (functional) information or the label-free RI (structural) information, though it may be valuable to have both. For example, biological tissues have heterogeneous RI distributions, causing sample-induced scattering that degrades the fluorescence image quality. When both fluorescence and 3D RI are measured, one can use the RI information to digitally correct multiple-scattering effects in the fluorescence image. Here, we develop a new computational multi-modal imaging method based on epi-mode microscopy that reconstructs both 3D fluorescence and 3D RI from a single dataset. We acquire dozens of fluorescence images, each ‘illuminated’ by a single fluorophore, then solve an inverse problem with a multiple-scattering forward model. We experimentally demonstrate our method for epi-mode 3D RI imaging and digital correction of multiple-scattering effects in fluorescence images.},
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Fluorescence microscopy is a powerful tool for imaging biological samples with molecular specificity. In contrast, phase microscopy provides label-free measurement of the sample’s refractive index (RI), which is an intrinsic optical property that quantitatively relates to cell morphology, mass, and stiffness. Conventional imaging techniques measure either the labeled fluorescence (functional) information or the label-free RI (structural) information, though it may be valuable to have both. For example, biological tissues have heterogeneous RI distributions, causing sample-induced scattering that degrades the fluorescence image quality. When both fluorescence and 3D RI are measured, one can use the RI information to digitally correct multiple-scattering effects in the fluorescence image. Here, we develop a new computational multi-modal imaging method based on epi-mode microscopy that reconstructs both 3D fluorescence and 3D RI from a single dataset. We acquire dozens of fluorescence images, each ‘illuminated’ by a single fluorophore, then solve an inverse problem with a multiple-scattering forward model. We experimentally demonstrate our method for epi-mode 3D RI imaging and digital correction of multiple-scattering effects in fluorescence images.
Michael L. Whittaker; David Ren; Colin Ophus; Yugang Zhang; Laura Waller; Benjamin Gilbert; Jillian F. Banfield
Ion complexation waves emerge at the curved interfaces of layered minerals Journal Article
In: Nature Communications volume , vol. 13, iss. 1, 2022.
@article{Ion2022,
title = {Ion complexation waves emerge at the curved interfaces of layered minerals},
author = {Michael L. Whittaker and David Ren and Colin Ophus and Yugang Zhang and Laura Waller and Benjamin Gilbert and Jillian F. Banfield },
doi = {https://doi.org/10.1038/s41467-022-31004-0},
year = {2022},
date = {2022-06-13},
urldate = {2022-06-13},
journal = {Nature Communications volume },
volume = {13},
issue = {1},
abstract = {Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation.},
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Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation.
Ruiming Cao; Michael Kellman; David Ren; Regina Eckert; Laura Waller
Self-calibrated 3D differential phase contrast microscopy with optimized illumination Journal Article
In: Biomed. Opt. Express, vol. 13, no. 3, pp. 1671–1684, 2022.
@article{Cao:22,
title = {Self-calibrated 3D differential phase contrast microscopy with optimized illumination},
author = {Ruiming Cao and Michael Kellman and David Ren and Regina Eckert and Laura Waller},
url = {http://opg.optica.org/boe/abstract.cfm?URI=boe-13-3-1671},
doi = {10.1364/BOE.450838},
year = {2022},
date = {2022-03-01},
urldate = {2022-03-01},
journal = {Biomed. Opt. Express},
volume = {13},
number = {3},
pages = {1671--1684},
publisher = {OSA},
abstract = {3D phase imaging recovers an object’s volumetric refractive index from intensity and/or holographic measurements. Partially coherent methods, such as illumination-based differential phase contrast (DPC), are particularly simple to implement in a commercial brightfield microscope. 3D DPC acquires images at multiple focus positions and with different illumination source patterns in order to reconstruct 3D refractive index. Here, we present a practical extension of the 3D DPC method that does not require a precise motion stage for scanning the focus and uses optimized illumination patterns for improved performance. The user scans the focus by hand, using the microscope’s focus knob, and the algorithm self-calibrates the axial position to solve for the 3D refractive index of the sample through a computational inverse problem. We further show that the illumination patterns can be optimized by an end-to-end learning procedure. Combining these two, we demonstrate improved 3D DPC with a commercial microscope whose only hardware modification is LED array illumination.},
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3D phase imaging recovers an object’s volumetric refractive index from intensity and/or holographic measurements. Partially coherent methods, such as illumination-based differential phase contrast (DPC), are particularly simple to implement in a commercial brightfield microscope. 3D DPC acquires images at multiple focus positions and with different illumination source patterns in order to reconstruct 3D refractive index. Here, we present a practical extension of the 3D DPC method that does not require a precise motion stage for scanning the focus and uses optimized illumination patterns for improved performance. The user scans the focus by hand, using the microscope’s focus knob, and the algorithm self-calibrates the axial position to solve for the 3D refractive index of the sample through a computational inverse problem. We further show that the illumination patterns can be optimized by an end-to-end learning procedure. Combining these two, we demonstrate improved 3D DPC with a commercial microscope whose only hardware modification is LED array illumination.
2020
Michael Chen; David Ren; Hsiou-Yuan Liu; Shwetadwip Chowdhury; Laura Waller
Multi-layer Born multiple-scattering model for 3D phase microscopy Journal Article
In: Optica, vol. 7, no. 5, pp. 394–403, 2020.
@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.},
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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.
David Ren; Colin Ophus; Michael Chen; Laura Waller
A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography Journal Article
In: Ultramicroscopy, vol. 208, pp. 112860, 2020.
@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},
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Ruiming Cao; Michael Kellman; David Ren; Laura Waller
3D Differential Phase Contrast Microscopy with Axial Motion Deblurring Inproceedings
In: Imaging and Applied Optics Congress, pp. CF4C.2, Optical Society of America, 2020.
@inproceedings{Cao:20,
title = {3D Differential Phase Contrast Microscopy with Axial Motion Deblurring},
author = {Ruiming Cao and Michael Kellman and David Ren and Laura Waller},
url = {http://www.osapublishing.org/abstract.cfm?URI=COSI-2020-CF4C.2},
year = {2020},
date = {2020-01-01},
booktitle = {Imaging and Applied Optics Congress},
journal = {Imaging and Applied Optics Congress},
pages = {CF4C.2},
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abstract = {We demonstrate 3D phase imaging using asymmetric illumination patterns and defocused intensity measurements taken with continuous axial motion. The sample's 3D refractive index is reconstructed with a motion-corrected transfer function.},
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We demonstrate 3D phase imaging using asymmetric illumination patterns and defocused intensity measurements taken with continuous axial motion. The sample's 3D refractive index is reconstructed with a motion-corrected transfer function.
Ruiming Cao; Michael Kellman; David Ren; Laura Waller
3D Differential Phase Contrast Microscopy with Axial Motion Deblurring Inproceedings
In: Imaging and Applied Optics Congress, pp. CF4C.2, Optical Society of America, 2020.
@inproceedings{Cao:20b,
title = {3D Differential Phase Contrast Microscopy with Axial Motion Deblurring},
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abstract = {We demonstrate 3D phase imaging using asymmetric illumination patterns and defocused intensity measurements taken with continuous axial motion. The sample's 3D refractive index is reconstructed with a motion-corrected transfer function.},
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We demonstrate 3D phase imaging using asymmetric illumination patterns and defocused intensity measurements taken with continuous axial motion. The sample's 3D refractive index is reconstructed with a motion-corrected transfer function.
2019
Shwetadwip Chowdhury; Michael Chen; Regina Eckert; David Ren; Fan Wu; Nicole A Repina; Laura Waller
High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images Journal Article
In: Optica, vol. 6, no. 9, pp. 1211–1219, 2019.
@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},
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Colin Ophus; David Ren; Jihan Zhou; Hannah Devyldere; Michael Chen; Philipp M Pelz; Peter Ercius; Jianwei Miao; Mary C Scott; Laura Waller
3D Imaging Using HAADF-STEM and HRTEM Atomic Electron Tomography Journal Article
In: Microscopy and Microanalysis, vol. 25, no. S2, pp. 394–395, 2019.
@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},
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pubstate = {published},
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Regina Eckert; David Ren; Michael Chen; Emrah Bostan; Laura Waller
Pupil coding for increased measurement diversity in 3D Fourier ptychography Inproceedings
In: Computational Optical Sensing and Imaging, pp. CW3A–1, Optical Society of America 2019.
@inproceedings{eckert2019pupil,
title = {Pupil coding for increased measurement diversity in 3D Fourier ptychography},
author = { Regina Eckert and David Ren and Michael Chen and Emrah Bostan and Laura Waller},
url = {https://doi.org/10.1364/COSI.2019.CW3A.1},
year = {2019},
date = {2019-06-24},
booktitle = {Computational Optical Sensing and Imaging},
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organization = {Optical Society of America},
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Michael Chen; Hsiou-Yuan Liu; David Ren; Laura Waller
Multi-layer Born scattering: an efficient model for 3D phase tomography with multiple scattering objects (Conference Presentation) Inproceedings
In: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI, pp. 108830I, International Society for Optics and Photonics 2019.
@inproceedings{chen2019multi,
title = {Multi-layer Born scattering: an efficient model for 3D phase tomography with multiple scattering objects (Conference Presentation)},
author = { Michael Chen and Hsiou-Yuan Liu and David Ren and Laura Waller},
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booktitle = {Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI},
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2018
Emrah Bostan; Mahdi Soltanolkotabi; David Ren; Laura Waller
Accelerated Wirtinger flow for multiplexed Fourier ptychographic microscopy Inproceedings
In: 2018 25th IEEE International Conference on Image Processing (ICIP), pp. 3823–3827, IEEE 2018.
@inproceedings{bostan2018accelerated,
title = {Accelerated Wirtinger flow for multiplexed Fourier ptychographic microscopy},
author = { Emrah Bostan and Mahdi Soltanolkotabi and David Ren and Laura Waller},
url = {https://doi.org/10.1109/ICIP.2018.8451437},
doi = {10.1109/ICIP.2018.8451437},
year = {2018},
date = {2018-10-07},
booktitle = {2018 25th IEEE International Conference on Image Processing (ICIP)},
pages = {3823--3827},
organization = {IEEE},
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Colin Ophus; David Ren; Michael Chen; Catherine Groschner; Mary C Scott; Laura Waller
Linear and Nonlinear Reconstruction Algorithms for Atomic-Resolution Tomography Using Phase Contrast Electron Microscopy Journal Article
In: Microscopy and Microanalysis, vol. 24, no. S1, pp. 110–111, 2018.
@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},
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year = {2018},
date = {2018-08-01},
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pages = {110--111},
publisher = {Cambridge University Press},
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Michael Kellman; Zachary F Phillips; David Ren; Michael Lustig; Laura Waller
Motion resolved quantitative phase imaging Inproceedings
In: Computational Imaging III, pp. 106690D, International Society for Optics and Photonics 2018.
@inproceedings{kellman2018motion,
title = {Motion resolved quantitative phase imaging},
author = { Michael Kellman and Zachary F Phillips and David Ren and Michael Lustig and Laura Waller},
url = {https://doi.org/10.1117/12.2300100},
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year = {2018},
date = {2018-05-15},
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David Ren; Michael Chen; Colin Ophus; Laura Waller
Tomographic reconstruction of 3D atomic potentials from intensity-only TEM measurements Inproceedings
In: Mathematics in Imaging, pp. MM2D–3, Optical Society of America 2018.
@inproceedings{ren2018tomographic,
title = {Tomographic reconstruction of 3D atomic potentials from intensity-only TEM measurements},
author = { David Ren and Michael Chen and Colin Ophus and Laura Waller},
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Michael Chen; Hsiou-Yuan Liu; David Ren; Laura Waller
Multi-layered born scattering model for 3D phase imaging with multiple scattering objects Inproceedings
In: Computational Optical Sensing and Imaging, pp. CM3E–1, Optical Society of America 2018.
@inproceedings{chen2018multi,
title = {Multi-layered born scattering model for 3D phase imaging with multiple scattering objects},
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2017
David Ren; Emrah Bostan; Li-Hao Yeh; Laura Waller
Total-variation regularized Fourier ptychographic microscopy with multiplexed coded illumination Inproceedings
In: Mathematics in Imaging, pp. MM3C–5, Optical Society of America 2017.
@inproceedings{ren2017total,
title = {Total-variation regularized Fourier ptychographic microscopy with multiplexed coded illumination},
author = { David Ren and Emrah Bostan and Li-Hao Yeh and Laura Waller},
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