Adaptive Optical Microscopy Systems: Unifying theory, practice and applications

Project Information

AdOMiS

Grant agreement ID: 695140

DOI

10.3030/695140

Project closed

EC signature date 8 June 2016

Start date 1 September 2016

End date 31 August 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 3 234 789,00

EU contribution

€ 3 234 789,00

Coordinated by

THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
United Kingdom

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Other (11)

Alignment of an SLM-based STED depletion beam

Author(s): Barbotin, A.
Published in: Issue 3, 2020
Publisher: -
DOI: 10.5281/zenodo.3567748

Microscope Resolution Estimation and Normalised Coordinates

Author(s): Booth, M. J.
Published in: Issue 1, 2020
Publisher: -
DOI: 10.5281/zenodo.4302488

A basic introduction to adaptive optics for microscopy

Author(s): Booth, M. J.
Published in: Issue 1, 2019
Publisher: -
DOI: 10.5281/zenodo.3471042

Practical Implementation of Adaptive Optical Microscopes

Author(s): Hampson, Karen Mary; Žurauskas, Mantas; Barbotin, Aurélien; Booth, Martin J.
Published in: Issue 3, 2020
Publisher: -
DOI: 10.5281/zenodo.4080674

Shack-Hartmann sensing with arbitrarily shaped pupil

Author(s): Cui, J.; Dong, B.; Booth, M. J.
Published in: Issue 3, 2020
Publisher: -
DOI: 10.5281/zenodo.3885507

Protocol for imaging through a multimode optical fibre

Author(s): Turcotte, Raphaël; Emptage, Nigel J.; Booth, Martin J.
Published in: Issue 1, 2020
Publisher: -
DOI: 10.5281/zenodo.3839326

Interferometric calibration of a deformable mirror

Author(s): Antonello, Jacopo; Wang, Jingyu; He, Chao; Phillips, Mick; Booth, Martin
Published in: Issue 1, 2020
Publisher: https://aomicroscopy.org/
DOI: 10.5281/zenodo.3714950

svmPSF quickstart manual

Author(s): Turcotte, Raphaël; Schmidt, Carla C.; Emptage, Nigel J.; Booth, Martin J.
Published in: Issue 1, 2020
Publisher: -
DOI: 10.5281/zenodo.3901391

Sensorless Adaptive Optics

Author(s): Hampson, Karen Mary; Antonello, Jacopo; Lane, Richard; Booth, Martin
Published in: Issue 3, 2020
Publisher: -
DOI: 10.5281/zenodo.4065553

Designing and aligning optical systems incorporating Liquid crystal spatial light modulators (SLMs)

Author(s): Salter, P. S.; Booth, M. J.
Published in: Issue 3, 2020
Publisher: -
DOI: 10.5281/zenodo.4518992

Pinhole alignment in a confocal microscope

Author(s): Rahman, S. A.; Cui, J.; Booth, M. J.
Published in: Issue 1, 2020
Publisher: -
DOI: 10.5281/zenodo.3894896

Peer reviewed articles (36)

Asymptotic behaviour of the Strehl ratio in the presence of Zernike polynomial aberrations

Author(s): M Booth, Q Hu
Published in: Asian Journal of Physics, Issue 30, 2022, Page(s) 1377, ISSN 0971-3093
Publisher: AJP

Extended range and aberration-free autofocusing via remote focusing and sequence-dependent learning.

Author(s): Jiahe Cui; Raphaël Turcotte; Nigel J. Emptage; Martin J. Booth
Published in: Optics Express, Issue 2, 2021, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.442025

Full Poincaré polarimetry enabled through physical inference

Author(s): Jianyu Lin; Jintao Chang; Jacopo Antonello; Ben Dai; Jingyu Wang; Jiahe Cui; Ji Qi; Min Wu; Daniel S. Elson; Peng Xi; Andrew Forbes; Martin J. Booth
Published in: Optica, Issue 1, 2022, ISSN 2334-2536
Publisher: Optica
DOI: 10.1364/optica.452646

Adaptive optics for high-resolution imaging

Author(s): Karen M. Hampson, Raphaël Turcotte, Donald T. Miller, Kazuhiro Kurokawa, Jared R. Males, Na Ji & Martin J. Booth
Published in: Nature Reviews Methods Primers, Issue 1, 2021, ISSN 2662-8449
Publisher: Springer Nature
DOI: 10.1038/s43586-021-00066-7

Multi-scale sensorless adaptive optics: application to stimulated emission depletion microscopy

Author(s): Jacopo Antonello, Aurélien Barbotin, Ee Zhuan Chong, Jens Rittscher, Martin J. Booth
Published in: Optics Express, Issue 28/11, 2020, Page(s) 16749, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.393363

Compressed imaging with focused light

Author(s): Biswajit Pathak; Martin J Booth; Raphaël Turcotte
Published in: Journal of Optics, Issue 1, 2022, ISSN 2040-8978
Publisher: Institute of Physics Publishing
DOI: 10.1088/2040-8986/ac6880

Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution

Author(s): Xiang Hao, Edward S. Allgeyer, Dong-Ryoung Lee, Jacopo Antonello, Katherine Watters, Julianne A. Gerdes, Lena K. Schroeder, Francesca Bottanelli, Jiaxi Zhao, Phylicia Kidd, Mark D. Lessard, James E. Rothman, Lynn Cooley, Thomas Biederer, Martin J. Booth & Joerg Bewersdorf
Published in: Nature Methods, Issue 18, 2021, Page(s) 688, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01149-9

Volumetric two-photon fluorescence imaging of live neurons using a multimode optical fiber

Author(s): Raphaël Turcotte, Carla C. Schmidt, Martin J. Booth, Nigel J. Emptage
Published in: Optics Letters, Issue 45/24, 2020, Page(s) 6599, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.409464

Practical sensorless aberration estimation for 3D microscopy with deep learning

Author(s): Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurelien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert, Eugene W. Myers
Published in: Optics Express, Issue 28/20, 2020, Page(s) 29044, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.401933

The Lattice Geometry of Walsh-Function-Based Adaptive Optics

Author(s): Hu, Q; Xiao, Y; Cui, J; Turcotte, R; Booth, MJ
Published in: Photonics; Volume 9; Issue 8; Pages: 547, Issue 2, 2022, ISSN 2304-6732
Publisher: MDPI
DOI: 10.3390/photonics9080547

3D super-resolution deep-tissue imaging in living mice

Author(s): Martin J. Booth; Peng Yuan; Jaime Grutzendler; Mary Grace M. Velasco; Edward S. Allgeyer; Ons M’Saad; Valentina Greco; Dennis May; Joerg Bewersdorf; Phylicia Kidd; Andrew E.S. Barentine; Jacopo Antonello; Mengyang Zhang
Published in: Optica, Issue 14, 2021, ISSN 2334-2536
Publisher: OSA
DOI: 10.1101/790212

On-chip beam rotators, adiabatic mode converters, and waveplates through low-loss waveguides with variable cross-sections

Author(s): Bangshan Sun, Fyodor Morozko, Patrick S. Salter, Simon Moser, Zhikai Pong, Raj B. Patel, Ian A. Walmsley, Mohan Wang, Adir Hazan, Nicolas Barré, Alexander Jesacher, Julian Fells, Chao He, Aviad Katiyi, Zhen-Nan Tian, Alina Karabchevsky & Martin J. Booth
Published in: Light:Science and Applications, Issue 11, 2022, Page(s) 214, ISSN 2095-5545
Publisher: Springer Nature
DOI: 10.1038/s41377-022-00907-4

Anisoplanatic adaptive optics in parallelized laser scanning microscopy

Author(s): Paolo Pozzi, Carlas Smith, Elizabeth Carroll, Dean Wilding, Oleg Soloviev, Martin Booth, Gleb Vdovin, Michel Verhaegen
Published in: Optics Express, Issue 28/10, 2020, Page(s) 14222, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.389974

Aberrations in 4Pi Microscopy

Author(s): Xiang Hao, Jacopo Antonello, Edward S. Allgeyer, Joerg Bewersdorf, Martin J. Booth
Published in: Optics Express, Issue 25/13, 2017, Page(s) 14049, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.25.014049

z-STED imaging and spectroscopy to investigate nanoscale membrane structure and dynamics

Author(s): Silvia Galiani; Martin J. Booth; Iztok Urbančič; Aurélien Barbotin; Christian Eggeling; Erdinc Sezgin
Published in: Biophysical Journal, Issue 15, 2020, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1101/2019.12.28.889923

Adaptive optics allows STED-FCS measurements in the cytoplasm of living cells

Author(s): Aurélien Barbotin, Silvia Galiani, Iztok Urbančič, Christian Eggeling, Martin J. Booth
Published in: Optics Express, Issue 27/16, 2019, Page(s) 23378, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.27.023378

Arbitrary complex retarders using a sequence of spatial light modulators as the basis for adaptive polarisation compensation

Author(s): Qi Hu; Chao He; Martin J. Booth
Published in: 1, Issue 1, 2021, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1088/2040-8986/abed33

Background Reduction in STED-FCS Using a Bivortex Phase Mask

Author(s): Aurélien Barbotin, Iztok Urbančič, Silvia Galiani, Christian Eggeling, Martin Booth
Published in: ACS Photonics, Issue 7/7, 2020, Page(s) 1742-1753, ISSN 2330-4022
Publisher: American Chemical Society
DOI: 10.1021/acsphotonics.0c00388

Wavefront control in adaptive microscopy using Shack-Hartmann sensors with arbitrarily shaped pupils

Author(s): Bing Dong, Martin J. Booth
Published in: Optics Express, Issue 26/2, 2018, Page(s) 1655, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.26.001655

Polarisation optics for biomedical and clinical applications: a review.

Author(s): Chao He; Honghui He; Jintao Chang; Binguo Chen; Hui Ma; Martin J. Booth
Published in: Light: Science & Applications, Vol 10, Iss 1, Pp 1-20 (2021), Issue 1, 2021, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1038/s41377-021-00639-x

Four-dimensional light shaping: manipulating ultrafast spatiotemporal foci in space and time

Author(s): Bangshan Sun, Patrick S Salter, Clemens Roider, Alexander Jesacher, Johannes Strauss, Johannes Heberle, Michael Schmidt, Martin J Booth
Published in: Light: Science & Applications, Issue 7/1, 2017, Page(s) 17117, ISSN 2047-7538
Publisher: Nature Publishing Group
DOI: 10.1038/lsa.2017.117

Rapid adaptive remote focusing microscope for sensing of volumetric neural activity

Author(s): Mantas Žurauskas, Oliver Barnstedt, Maria Frade-Rodriguez, Scott Waddell, Martin J. Booth
Published in: Biomedical Optics Express, Issue 8/10, 2017, Page(s) 4369, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/BOE.8.004369

Calibration of a phase-only spatial light modulator for both phase and retardance modulation

Author(s): Yuanyuan Dai, Jacopo Antonello, Martin J. Booth
Published in: Optics Express, Issue 27/13, 2019, Page(s) 17912, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.27.017912

IsoSense: frequency enhanced sensorless adaptive optics through structured illumination

Author(s): Mantas Žurauskas, Ian M. Dobbie, Richard M. Parton, Mick A. Phillips, Antonia Göhler, Ilan Davis, Martin J. Booth
Published in: Optica, Issue 6/3, 2019, Page(s) 370, ISSN 2334-2536
Publisher: OSA
DOI: 10.1364/optica.6.000370

Focusing light in biological tissue through a multimode optical fiber: refractive index matching

Author(s): Raphaël Turcotte, Carla C. Schmidt, Nigel J. Emptage, Martin J. Booth
Published in: Optics Letters, Issue 44/10, 2019, Page(s) 2386, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.44.002386

Active compensation of extrinsic polarization errors using adaptive optics

Author(s): Yuanyuan Dai, Chao He, Jingyu Wang, Raphaël Turcotte, Lewis Fish, Matthew Wincott, Qi Hu, Martin J. Booth
Published in: Optics Express, Issue 27/24, 2019, Page(s) 35797, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.27.035797

Implementation of a 4Pi-SMS super-resolution microscope

Author(s): Jingyu Wang, Edward S. Allgeyer, George Sirinakis, Yongdeng Zhang, Kevin Hu, Mark D. Lessard, Yiming Li, Robin Diekmann, Michael A. Phillips, Ian M. Dobbie, Jonas Ries, Martin J. Booth, Joerg Bewersdorf
Published in: Nature Protocols, Issue 16/2, 2021, Page(s) 677-727, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-020-00428-7

Microscope-AOtools: a generalised adaptive optics implementation

Author(s): Nicholas Hall, Josh Titlow, Martin J. Booth, Ian M. Dobbie
Published in: Optics Express, Issue 28/20, 2020, Page(s) 28987, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.401117

Wavefront‐sensorless adaptive optics with a laser‐free spinning disk confocal microscope

Author(s): Syed Asad Hussain, Toshiki Kubo, Nicholas Hall, Dalia Gala, Karen Hampson, Richard Parton, Mick A. Phillips, Matthew Wincott, Katsumasa Fujita, Ilan Davis, Ian Dobbie, Martin J. Booth
Published in: Journal of Microscopy, 2020, ISSN 0022-2720
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/jmi.12976

A universal framework for microscope sensorless adaptive optics: Generalized aberration representations

Author(s): Q. Hu, J. Wang, J. Antonello, M. Hailstone, M. Wincott, R. Turcotte, D. Gala, M. J. Booth
Published in: APL Photonics, Issue 5/10, 2020, Page(s) 100801, ISSN 2378-0967
Publisher: SCI
DOI: 10.1063/5.0022523

Compact and contactless reflectance confocal microscope for neurosurgery

Author(s): Karen M. Hampson; Nigel J. Emptage; Matthew Wincott; Jiahe Cui; Patra Charalampaki; Raphaël Turcotte; Carla Schmidt; Martin J. Booth
Published in: Biomed Opt Express, Issue 16, 2020, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1101/2020.05.13.093435

Generalised adaptive optics method for high-NA aberration-free refocusing in refractive-index-mismatched media

Author(s): Jiahe Cui; Jacopo Antonello; Andrew R. Kirkpatrick; Patrick S. Salter; Martin J. Booth
Published in: Optics Express, Issue 2, 2022, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.454912

Deconvolution for multimode fiber imaging: modeling of spatially variant PSF

Author(s): Raphaël Turcotte, Eusebiu Sutu, Carla C. Schmidt, Nigel J. Emptage, Martin J. Booth
Published in: Biomedical Optics Express, Issue 11/8, 2020, Page(s) 4759, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.399983

Complex vectorial optics through gradient index lens cascades

Author(s): Chao He, Jintao Chang, Qi Hu, Jingyu Wang, Jacopo Antonello, Honghui He, Shaoxiong Liu, Jianyu Lin, Ben Dai, Daniel S. Elson, Peng Xi, Hui Ma, Martin J. Booth
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-12286-3

Repeated imaging through a multimode optical fiber using adaptive optics

Author(s): Carla C. Schmidt; Raphaël Turcotte; Martin J. Booth; Nigel J. Emptage
Published in: Biomedical optics express, Issue 1, 2021, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.448277

Arbitrary vectorial state conversion using liquid crystal spatial light modulators

Author(s): Qi Hu, Yuanyuan Dai, Chao He, Martin J. Booth
Published in: Optics Communications, Issue 459, 2020, Page(s) 125028, ISSN 0030-4018
Publisher: Elsevier BV
DOI: 10.1016/j.optcom.2019.125028