Publications by Nick Antipa
2020
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.
@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.},
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Fanglin Linda Liu; Grace Kuo; Nick Antipa; Kyrollos Yanny; Laura Waller
Fourier DiffuserScope: single-shot 3D Fourier light field microscopy with a diffuser Journal Article
In: Opt. Express, vol. 28, no. 20, pp. 28969–28986, 2020.
@article{LindaLiu:20,
title = {Fourier DiffuserScope: single-shot 3D Fourier light field microscopy with a diffuser},
author = {Fanglin Linda Liu and Grace Kuo and Nick Antipa and Kyrollos Yanny and Laura Waller},
url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-28-20-28969},
doi = {10.1364/OE.400876},
year = {2020},
date = {2020-09-01},
journal = {Opt. Express},
volume = {28},
number = {20},
pages = {28969--28986},
publisher = {OSA},
abstract = {Light field microscopy (LFM) uses a microlens array (MLA) near the sensor plane of a microscope to achieve single-shot 3D imaging of a sample without any moving parts. Unfortunately, the 3D capability of LFM comes with a significant loss of lateral resolution at the focal plane. Placing the MLA near the pupil plane of the microscope, instead of the image plane, can mitigate the artifacts and provide an efficient forward model, at the expense of field-of-view (FOV). Here, we demonstrate improved resolution across a large volume with Fourier DiffuserScope, which uses a diffuser in the pupil plane to encode 3D information, then computationally reconstructs the volume by solving a sparsity-constrained inverse problem. Our diffuser consists of randomly placed microlenses with varying focal lengths; the random positions provide a larger FOV compared to a conventional MLA, and the diverse focal lengths improve the axial depth range. To predict system performance based on diffuser parameters, we, for the first time, establish a theoretical framework and design guidelines, which are verified by numerical simulations, and then build an experimental system that achieves < 3 µm lateral and 4 µm axial resolution over a 1000 × 1000 × 280 µm3 volume. Our diffuser design outperforms the MLA used in LFM, providing more uniform resolution over a larger volume, both laterally and axially.},
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Nathan Tessema Ersumo; Cem Yalcin; Nick Antipa; Nicolas C Pégard; Laura Waller; Daniel Lopez; Rikky Muller
Design framework for high-speed 3D scanning tools and development of an axial focusing micromirror-based array Inproceedings
In: MOEMS and Miniaturized Systems XIX, pp. 1129303, International Society for Optics and Photonics 2020.
@inproceedings{ersumo2020design,
title = {Design framework for high-speed 3D scanning tools and development of an axial focusing micromirror-based array},
author = { Nathan Tessema Ersumo and Cem Yalcin and Nick Antipa and Nicolas C Pégard and Laura Waller and Daniel Lopez and Rikky Muller},
url = {https://doi.org/10.1117/12.2550994},
doi = {10.1117/12.2550994},
year = {2020},
date = {2020-02-28},
booktitle = {MOEMS and Miniaturized Systems XIX},
volume = {11293},
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Kyrollos Yanny; Nick Antipa; William Liberti; Sam Dehaeck; Kristina Monakhova; Fanglin Linda Liu; Konlin Shen; Ren Ng; Laura Waller
Compressed Sensing 3D Fluorescence Microscopy Using Optimized Phase Mask Inproceedings
In: Imaging and Applied Optics Congress, pp. CW4B.5, Optical Society of America, 2020.
@inproceedings{Yanny:20,
title = {Compressed Sensing 3D Fluorescence Microscopy Using Optimized Phase Mask},
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 = {http://www.osapublishing.org/abstract.cfm?URI=COSI-2020-CW4B.5},
year = {2020},
date = {2020-01-01},
booktitle = {Imaging and Applied Optics Congress},
journal = {Imaging and Applied Optics Congress},
pages = {CW4B.5},
publisher = {Optical Society of America},
abstract = {We demonstrate a single-shot miniature 3D computational microscope with an optimized phase encoder. Our method uses sparsity-based reconstruction to achieve a 2.76-m lateral and 15،nm axial resolution across most of the 900 x 700 x 390،nm3 volume.},
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2019
Kristina Monakhova; Joshua Yurtsever; Grace Kuo; Nick Antipa; Kyrollos Yanny; Laura Waller
Learned reconstructions for practical mask-based lensless imaging Journal Article
In: Optics express, vol. 27, no. 20, pp. 28075–28090, 2019.
@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},
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publisher = {Optical Society of America},
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Kristina Monakhova; Joshua Yurtsever; Grace Kuo; Nick Antipa; Kyrollos Yanny; Laura Waller
Unrolled, model-based networks for lensless imaging Journal Article
In: 2019.
@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},
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Kristina Monakhova; Nick Antipa; Laura Waller
Learning for lensless mask-based imaging Inproceedings
In: Computational Optical Sensing and Imaging, pp. CTu3A–2, Optical Society of America 2019.
@inproceedings{monakhova2019learning,
title = {Learning for lensless mask-based imaging},
author = { Kristina Monakhova and Nick Antipa and Laura Waller},
url = {https://www.osapublishing.org/abstract.cfm?uri=COSI-2019-CTu3A.2},
year = {2019},
date = {2019-06-24},
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Nick Antipa; Patrick Oare; Emrah Bostan; Ren Ng; Laura Waller
Video from stills: Lensless imaging with rolling shutter Inproceedings
In: 2019 IEEE International Conference on Computational Photography (ICCP), pp. 1–8, IEEE 2019.
@inproceedings{antipa2019video,
title = {Video from stills: Lensless imaging with rolling shutter},
author = { Nick Antipa and Patrick Oare and Emrah Bostan and Ren Ng and Laura Waller},
url = {https://doi.org/10.1109/ICCPHOT.2019.8747341},
doi = {10.1109/ICCPHOT.2019.8747341},
year = {2019},
date = {2019-05-15},
booktitle = {2019 IEEE International Conference on Computational Photography (ICCP)},
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Kyrollos Yanny; Nick Antipa; Ren Ng; Laura Waller
Miniature 3D fluorescence microscope using random microlenses Inproceedings
In: Optics and the Brain, pp. BT3A–4, Optical Society of America 2019.
@inproceedings{yanny2019miniature,
title = {Miniature 3D fluorescence microscope using random microlenses},
author = { Kyrollos Yanny and Nick Antipa and Ren Ng and Laura Waller},
url = {https://www.osapublishing.org/abstract.cfm?uri=BRAIN-2019-BT3A.4},
year = {2019},
date = {2019-04-14},
booktitle = {Optics and the Brain},
pages = {BT3A--4},
organization = {Optical Society of America},
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Fanglin Linda Liu; Vaishnavi Madhavan; Nick Antipa; Grace Kuo; Saul Kato; Laura Waller
Single-shot 3D fluorescence microscopy with Fourier DiffuserCam Inproceedings
In: Novel Techniques in Microscopy, pp. NS2B–3, Optical Society of America 2019.
@inproceedings{liu2019single,
title = {Single-shot 3D fluorescence microscopy with Fourier DiffuserCam},
author = { Fanglin Linda Liu and Vaishnavi Madhavan and Nick Antipa and Grace Kuo and Saul Kato and Laura Waller},
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year = {2019},
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Thomas Zimmerman; Nick Antipa; Daniel Elnatan; Alessio Murru; Sujoy Biswas; Vito Pastore; Mayara Bonani; Laura Waller; Jennifer Fung; Gianni Fenu; others
Stereo in-line holographic digital microscope Inproceedings
In: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI, pp. 1088315, International Society for Optics and Photonics 2019.
@inproceedings{zimmerman2019stereo,
title = {Stereo in-line holographic digital microscope},
author = { Thomas Zimmerman and Nick Antipa and Daniel Elnatan and Alessio Murru and Sujoy Biswas and Vito Pastore and Mayara Bonani and Laura Waller and Jennifer Fung and Gianni Fenu and others},
url = {https://doi.org/10.1117/12.2509033},
doi = {10.1117/12.2509033},
year = {2019},
date = {2019-02-21},
booktitle = {Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI},
volume = {10883},
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2018
Nick Antipa; Grace Kuo; Laura Waller
Lensless Cameras May Offer Detailed Imaging of Neural Circuitry Online
Photonics Media 2018, visited: 17.04.2020.
@online{antipalensless,
title = {Lensless Cameras May Offer Detailed Imaging of Neural Circuitry},
author = { Nick Antipa and Grace Kuo and Laura Waller},
url = {https://www.photonics.com/Articles/Lensless_Cameras_May_Offer_Detailed_Imaging_of/a63680},
year = {2018},
date = {2018-07-01},
urldate = {2020-04-17},
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Grace Kuo; Nick Antipa; Ren Ng; Laura Waller
3D fluorescence microscopy with DiffuserCam Inproceedings
In: Computational Optical Sensing and Imaging, pp. CM3E–3, Optical Society of America 2018.
@inproceedings{kuo20183d,
title = {3D fluorescence microscopy with DiffuserCam},
author = { Grace Kuo and Nick Antipa and Ren Ng and Laura Waller},
url = {https://doi.org/10.1364/COSI.2018.CM3E.3},
doi = {10.1364/COSI.2018.CM3E.3},
year = {2018},
date = {2018-06-25},
booktitle = {Computational Optical Sensing and Imaging},
pages = {CM3E--3},
organization = {Optical Society of America},
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Nick Antipa; Grace Kuo; Reinhard Heckel; Ben Mildenhall; Emrah Bostan; Ren Ng; Laura Waller
DiffuserCam: Lensless single-exposure 3D imaging Journal Article
In: Optica, vol. 5, no. 1, pp. 1–9, 2018.
@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},
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2017
Nick Antipa; Grace Kuo; Ren Ng; Laura Waller
3D DiffuserCam: Single-shot compressive lensless imaging Inproceedings
In: Computational Optical Sensing and Imaging, pp. CM2B–2, Optical Society of America 2017.
@inproceedings{antipa20173d,
title = {3D DiffuserCam: Single-shot compressive lensless imaging},
author = { Nick Antipa and Grace Kuo and Ren Ng and Laura Waller},
url = {https://doi.org/10.1364/COSI.2017.CM2B.2},
doi = {10.1364/COSI.2017.CM2B.2},
year = {2017},
date = {2017-06-27},
booktitle = {Computational Optical Sensing and Imaging},
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Grace Kuo; Nick Antipa; Ren Ng; Laura Waller
DiffuserCam: Diffuser-based lensless cameras Inproceedings
In: Computational Optical Sensing and Imaging, pp. CTu3B–2, Optical Society of America 2017.
@inproceedings{kuo2017diffusercam,
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year = {2017},
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2016
Nicolas C Pégard; Hsiou-Yuan Liu; Nick Antipa; Maximillian Gerlock; Hillel Adesnik; Laura Waller
Recording 3-D Neural Activity Online
Optics & Photonics News 2016, visited: 17.04.2020.
@online{pegardrecording,
title = {Recording 3-D Neural Activity},
author = { Nicolas C Pégard and Hsiou-Yuan Liu and Nick Antipa and Maximillian Gerlock and Hillel Adesnik and Laura Waller},
url = {https://www.osa-opn.org/home/articles/volume_27/december_2016/extras/recording_3-d_neural_activity/},
year = {2016},
date = {2016-12-01},
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Nick Antipa; Sylvia Necula; Ren Ng; Laura Waller
Single-shot diffuser-encoded light field imaging Inproceedings
In: 2016 IEEE International Conference on Computational Photography (ICCP), pp. 1–11, IEEE 2016.
@inproceedings{antipa2016single,
title = {Single-shot diffuser-encoded light field imaging},
author = { Nick Antipa and Sylvia Necula and Ren Ng and Laura Waller},
url = {https://doi.org/10.1109/ICCPHOT.2016.7492880},
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booktitle = {2016 IEEE International Conference on Computational Photography (ICCP)},
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Nicolas C Pégard; Hsiou-Yuan Liu; Nick Antipa; Maximillian Gerlock; Hillel Adesnik; Laura Waller
Compressive light-field microscopy for 3D neural activity recording Journal Article
In: Optica, vol. 3, no. 5, pp. 517–524, 2016.
@article{pegard2016compressive,
title = {Compressive light-field microscopy for 3D neural activity recording},
author = { Nicolas C Pégard and Hsiou-Yuan Liu and Nick Antipa and Maximillian Gerlock and Hillel Adesnik and Laura Waller},
url = {https://doi.org/10.1364/OPTICA.3.000517},
doi = {10.1364/OPTICA.3.000517},
year = {2016},
date = {2016-05-12},
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Gautam Gunjala; Aamod Shanker; Volker Jaedicke; Nick Antipa; Laura Waller
Optical transfer function characterization using a weak diffuser Inproceedings
In: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIII, pp. 971315, International Society for Optics and Photonics 2016.
@inproceedings{gunjala2016optical,
title = {Optical transfer function characterization using a weak diffuser},
author = { Gautam Gunjala and Aamod Shanker and Volker Jaedicke and Nick Antipa and Laura Waller},
url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/9713/1/Optical-transfer-function-characterization-using-a-weak-diffuser/10.1117/12.2213271.short?SSO=1},
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2015
Nicolas C Pégard; Hsiou-Yuan Liu; Nick Antipa; Laura Waller; Hillel Adesnik
Functional brain imaging at cellular resolution with Compressive Light-Field Microscopy Inproceedings
In: Imaging Systems and Applications, pp. JTh4A–3, Optical Society of America 2015.
@inproceedings{pegard2015functional,
title = {Functional brain imaging at cellular resolution with Compressive Light-Field Microscopy},
author = { Nicolas C Pégard and Hsiou-Yuan Liu and Nick Antipa and Laura Waller and Hillel Adesnik},
url = {https://doi.org/10.1364/ISA.2015.JTh4A.3},
doi = {10.1364/ISA.2015.JTh4A.3},
year = {2015},
date = {2015-06-07},
booktitle = {Imaging Systems and Applications},
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Nicolas C Pégard; Evan H Lyall; Alan R Mardinly; Nick Antipa; Laura Waller; Hillel Adesnik
High-speed 3D brain activity quantification with Compressive Light-Field Microscopy Inproceedings
In: Novel Techniques in Microscopy, pp. NW2C–3, Optical Society of America 2015.
@inproceedings{pegard2015high,
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