Journal papers
Kyrollos Yanny; Nick Antipa; William Liberti; Sam Dehaeck; Kristina Monakhova; Fanglin Linda Liu; Konlin Shen; Ren Ng; Laura Waller
Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy Journal Article
In: Light: Science & Applications, vol. 9, no. 171, 2020.
Abstract | Links | BibTeX | Tags: 3D imaging, algorithms, diffuser, fluorescence imaging
@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}
}
Grace Kuo; Fanglin Linda Liu; Irene Grossrubatscher; Ren Ng; Laura Waller
On-chip fluorescence microscopy with a random microlens diffuser Journal Article
In: Optics Express, vol. 28, no. 6, pp. 8384–8399, 2020.
Links | BibTeX | Tags: 3D imaging, diffuser, fluorescence imaging, lensless imaging, on-chip
@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}
}
Zachary F Phillips; Sarah Dean; Benjamin Recht; Laura Waller
High-throughput fluorescence microscopy using multi-frame motion deblurring Journal Article
In: Biomedical Optics Express, vol. 11, no. 1, pp. 281–300, 2019.
Links | BibTeX | Tags: deconvolution, fluorescence imaging, high-throughput, motion deblur
@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}
}
Li-Hao Yeh; Shwetadwip Chowdhury; Laura Waller
Computational structured illumination for high-content fluorescence and phase microscopy Journal Article
In: Biomedical optics express, vol. 10, no. 4, pp. 1978–1998, 2019.
Abstract | Links | BibTeX | Tags: diffuser, fluorescence imaging, high-throughput, phase imaging, structured illumination, super-resolution
@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}
}
Emrah Bostan; Ulugbek S Kamilov; Laura Waller
Learning-based image reconstruction via parallel proximal algorithm Journal Article
In: IEEE Signal Processing Letters, vol. 25, no. 7, pp. 989–993, 2018.
Links | BibTeX | Tags: algorithms, fluorescence imaging, learning-based, regularization
@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}
}
Nicolas C Pégard; Alan R Mardinly; Ian Antón Oldenburg; Savitha Sridharan; Laura Waller; Hillel Adesnik
Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT) Journal Article
In: Nature communications, vol. 8, no. 1, pp. 1–14, 2017.
Links | BibTeX | Tags: 3D imaging, digital holography, fluorescence imaging, neural imaging
@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}
}
Jingzhao Zhang; Nicolas C Pégard; Jingshan Zhong; Hillel Adesnik; Laura Waller
3D computer-generated holography by non-convex optimization Journal Article
In: Optica, vol. 4, no. 10, pp. 1306–1313, 2017.
Links | BibTeX | Tags: 3D imaging, algorithms, digital holography, fluorescence imaging, neural imaging
@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}
}
Hsiou-Yuan Liu; Jingshan Zhong; Laura Waller
Multiplexed phase-space imaging for 3D fluorescence microscopy Journal Article
In: Optics express, vol. 25, no. 13, pp. 14986–14995, 2017.
Links | BibTeX | Tags: 3D imaging, fluorescence imaging, phase space
@article{liu2017multiplexed,
title = {Multiplexed phase-space imaging for 3D fluorescence microscopy},
author = { Hsiou-Yuan Liu and Jingshan Zhong and Laura Waller},
url = {https://doi.org/10.1364/OE.25.014986},
doi = {10.1364/OE.25.014986},
year = {2017},
date = {2017-06-21},
journal = {Optics express},
volume = {25},
number = {13},
pages = {14986--14995},
publisher = {Optical Society of America},
keywords = {3D imaging, fluorescence imaging, phase space},
pubstate = {published},
tppubtype = {article}
}
Hillel Adesnik; Alan R Mardinly; Nicolas C Pegard; Ian Anton Oldenburg; Laura Waller
New Approaches and Insights into Cortical Microcircuits Journal Article
In: The FASEB Journal, vol. 30, no. 1_supplement, pp. 371–1, 2016.
Links | BibTeX | Tags: fluorescence imaging, multiphoton, neural imaging
@article{adesnik2016new,
title = {New Approaches and Insights into Cortical Microcircuits},
author = { Hillel Adesnik and Alan R Mardinly and Nicolas C Pegard and Ian Anton Oldenburg and Laura Waller},
url = {https://www.fasebj.org/doi/abs/10.1096/fasebj.30.1_supplement.371.1},
doi = {10.1096/fasebj.30.1_supplement.371.1},
year = {2016},
date = {2016-04-01},
journal = {The FASEB Journal},
volume = {30},
number = {1_supplement},
pages = {371--1},
publisher = {The Federation of American Societies for Experimental Biology},
keywords = {fluorescence imaging, multiphoton, neural imaging},
pubstate = {published},
tppubtype = {article}
}