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Amitonova LV. Multimode fiber endoscopes for computational brain imaging. NEUROPHOTONICS 2024; 11:S11509. [PMID: 38450327 PMCID: PMC10917391 DOI: 10.1117/1.nph.11.s1.s11509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/08/2024] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Advances in imaging tools have always been a pivotal driver for new discoveries in neuroscience. An ability to visualize neurons and subcellular structures deep within the brain of a freely behaving animal is integral to our understanding of the relationship between neural activity and higher cognitive functions. However, fast high-resolution imaging is limited to sub-surface brain regions and generally requires head fixation of the animal under the microscope. Developing new approaches to address these challenges is critical. The last decades have seen rapid progress in minimally invasive endo-microscopy techniques based on bare optical fibers. A single multimode fiber can be used to penetrate deep into the brain without causing significant damage to the overlying structures and provide high-resolution imaging. Here, we discuss how the full potential of high-speed super-resolution fiber endoscopy can be realized by a holistic approach that combines fiber optics, light shaping, and advanced computational algorithms. The recent progress opens up new avenues for minimally invasive deep brain studies in freely behaving mice.
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Affiliation(s)
- Lyubov V. Amitonova
- Vrije Universiteit Amsterdam, Department of Physics and Astronomy, Amsterdam, The Netherlands
- Advanced Research Center for Nanolithography, Amsterdam, The Netherlands
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2
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Lorca-Cámara A, Blot FGC, Accanto N. Recent advances in light patterned optogenetic photostimulation in freely moving mice. NEUROPHOTONICS 2024; 11:S11508. [PMID: 38404422 PMCID: PMC10885521 DOI: 10.1117/1.nph.11.s1.s11508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Optogenetics opened the door to a new era of neuroscience. New optical developments are under way to enable high-resolution neuronal activity imaging and selective photostimulation of neuronal ensembles in freely moving animals. These advancements could allow researchers to interrogate, with cellular precision, functionally relevant neuronal circuits in the framework of naturalistic brain activity. We provide an overview of the current state-of-the-art of imaging and photostimulation in freely moving rodents and present a road map for future optical and engineering developments toward miniaturized microscopes that could reach beyond the currently existing systems.
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Affiliation(s)
| | - François G C Blot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Nicolò Accanto
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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3
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Karpova A, Aly AAA, Marosi EL, Mikulovic S. Fiber-based in vivo imaging: unveiling avenues for exploring mechanisms of synaptic plasticity and neuronal adaptations underlying behavior. NEUROPHOTONICS 2024; 11:S11507. [PMID: 38390518 PMCID: PMC10883581 DOI: 10.1117/1.nph.11.s1.s11507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
In recent decades, various subfields within neuroscience, spanning molecular, cellular, and systemic dimensions, have significantly advanced our understanding of the elaborate molecular and cellular mechanisms that underpin learning, memory, and adaptive behaviors. There have been notable advancements in imaging techniques, particularly in reaching superficial brain structures. This progress has led to their widespread adoption in numerous laboratories. However, essential physiological and cognitive processes, including sensory integration, emotional modulation of motivated behavior, motor regulation, learning, and memory consolidation, are intricately encoded within deeper brain structures. Hence, visualization techniques such as calcium imaging using miniscopes have gained popularity for studying brain activity in unrestrained animals. Despite its utility, miniscope technology is associated with substantial brain tissue damage caused by gradient refractive index lens implantation. Furthermore, its imaging capabilities are primarily confined to the neuronal somata level, thus constraining a comprehensive exploration of subcellular processes underlying adaptive behaviors. Consequently, the trajectory of neuroscience's future hinges on the development of minimally invasive optical fiber-based endo-microscopes optimized for cellular, subcellular, and molecular imaging within the intricate depths of the brain. In pursuit of this goal, select research groups have invested significant efforts in advancing this technology. In this review, we present a perspective on the potential impact of this innovation on various aspects of neuroscience, enabling the functional exploration of in vivo cellular and subcellular processes that underlie synaptic plasticity and the neuronal adaptations that govern behavior.
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Affiliation(s)
- Anna Karpova
- Leibniz Institute for Neurobiology, RG Neuroplasticity, Magdeburg, Germany
- Otto von Guericke University, Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Ahmed A A Aly
- Leibniz Institute for Neurobiology, RG Neuroplasticity, Magdeburg, Germany
| | - Endre Levente Marosi
- Leibniz Institute for Neurobiology, RG Cognition and Emotion, Magdeburg, Germany
| | - Sanja Mikulovic
- Otto von Guericke University, Center for Behavioral Brain Sciences, Magdeburg, Germany
- Leibniz Institute for Neurobiology, RG Cognition and Emotion, Magdeburg, Germany
- German Centre for Mental Health (DZPG), Magdeburg, Germany
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4
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Wang T, Dremel J, Richter S, Polanski W, Uckermann O, Eyüpoglu I, Czarske JW, Kuschmierz R. Resolution-enhanced multi-core fiber imaging learned on a digital twin for cancer diagnosis. NEUROPHOTONICS 2024; 11:S11505. [PMID: 38298866 PMCID: PMC10828892 DOI: 10.1117/1.nph.11.s1.s11505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
Significance Deep learning enables label-free all-optical biopsies and automated tissue classification. Endoscopic systems provide intraoperative diagnostics to deep tissue and speed up treatment without harmful tissue removal. However, conventional multi-core fiber (MCF) endoscopes suffer from low resolution and artifacts, which hinder tumor diagnostics. Aim We introduce a method to enable unpixelated, high-resolution tumor imaging through a given MCF with a diameter of around 0.65 mm and arbitrary core arrangement and inhomogeneous transmissivity. Approach Image reconstruction is based on deep learning and the digital twin concept of the single-reference-based simulation with inhomogeneous optical properties of MCF and transfer learning on a small experimental dataset of biological tissue. The reference provided physical information about the MCF during the training processes. Results For the simulated data, hallucination caused by the MCF inhomogeneity was eliminated, and the averaged peak signal-to-noise ratio and structural similarity were increased from 11.2 dB and 0.20 to 23.4 dB and 0.74, respectively. By transfer learning, the metrics of independent test images experimentally acquired on glioblastoma tissue ex vivo can reach up to 31.6 dB and 0.97 with 14 fps computing speed. Conclusions With the proposed approach, a single reference image was required in the pre-training stage and laborious acquisition of training data was bypassed. Validation on glioblastoma cryosections with transfer learning on only 50 image pairs showed the capability for high-resolution deep tissue retrieval and high clinical feasibility.
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Affiliation(s)
- Tijue Wang
- TU Dresden, Laboratory of Measurement and Sensor System Technique, Dresden, Germany
- TU Dresden, Competence Center BIOLAS, Dresden, Germany
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
| | - Jakob Dremel
- TU Dresden, Laboratory of Measurement and Sensor System Technique, Dresden, Germany
- TU Dresden, Competence Center BIOLAS, Dresden, Germany
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
| | - Sven Richter
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
- University Hospital Carl Gustav Carus, TU Dresden, Department of Neurosurgery, Dresden, Germany
| | - Witold Polanski
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
- University Hospital Carl Gustav Carus, TU Dresden, Department of Neurosurgery, Dresden, Germany
| | - Ortrud Uckermann
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
- University Hospital Carl Gustav Carus, TU Dresden, Department of Neurosurgery, Dresden, Germany
- University Hospital Carl Gustav Carus, TU Dresden, Division of Medical Biology, Department of Psychiatry, Faculty of Medicine, Dresden, Germany
| | - Ilker Eyüpoglu
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
- University Hospital Carl Gustav Carus, TU Dresden, Department of Neurosurgery, Dresden, Germany
| | - Jürgen W. Czarske
- TU Dresden, Laboratory of Measurement and Sensor System Technique, Dresden, Germany
- TU Dresden, Competence Center BIOLAS, Dresden, Germany
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
- TU Dresden, Excellence Cluster Physics of Life, Dresden, Germany
- TU Dresden, School of Science, Faculty of Physics, Dresden, Germany
| | - Robert Kuschmierz
- TU Dresden, Laboratory of Measurement and Sensor System Technique, Dresden, Germany
- TU Dresden, Competence Center BIOLAS, Dresden, Germany
- TU Dresden, Else Kröner Fresenius Center for Digital Health, Germany
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Du Y, Dylda E, Stibůrek M, Gomes AD, Turtaev S, Pakan JMP, Čižmár T. Advancing the path to in-vivo imaging in freely moving mice via multimode-multicore fiber based holographic endoscopy. NEUROPHOTONICS 2024; 11:S11506. [PMID: 38352728 PMCID: PMC10863504 DOI: 10.1117/1.nph.11.s1.s11506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Significance Hair-thin multimode optical fiber-based holographic endoscopes have gained considerable interest in modern neuroscience for their ability to achieve cellular and even subcellular resolution during in-vivo deep brain imaging. However, the application of multimode fibers in freely moving animals presents a persistent challenge as it is difficult to maintain optimal imaging performance while the fiber undergoes deformations. Aim We propose a fiber solution for challenging in-vivo applications with the capability of deep brain high spatial resolution imaging and neuronal activity monitoring in anesthetized as well as awake behaving mice. Approach We used our previously developed M 3 CF multimode-multicore fiber to record fluorescently labeled neurons in anesthetized mice. Our M 3 CF exhibits a cascaded refractive index structure, enabling two distinct regimes of light transport that imitate either a multimode or a multicore fiber. The M 3 CF has been specifically designed for use in the initial phase of an in-vivo experiment, allowing for the navigation of the endoscope's distal end toward the targeted brain structure. The multicore regime enables the transfer of light to and from each individual neuron within the field of view. For chronic experiments in awake behaving mice, it is crucial to allow for disconnecting the fiber and the animal between experiments. Therefore, we provide here an effective solution and establish a protocol for reconnection of two segments of M 3 CF with hexagonally arranged corelets. Results We successfully utilized the M 3 CF to image neurons in anaesthetized transgenic mice expressing enhanced green fluorescent protein. Additionally, we compared imaging results obtained with the M 3 CF with larger numerical aperture (NA) fibers in fixed whole-brain tissue. Conclusions This study focuses on addressing challenges and providing insights into the use of multimode-multicore fibers as imaging solutions for in-vivo applications. We suggest that the upcoming version of the M 3 CF increases the overall NA between the two cladding layers to allow for access to high resolution spatial imaging. As the NA increases in the multimode regime, the fiber diameter and ring structure must be reduced to minimize the computational burden and invasiveness.
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Affiliation(s)
- Yang Du
- University of Chinese Academy of Sciences, Hangzhou Institute for Advanced Study, Hangzhou, China
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Evelyn Dylda
- Otto-von-Guericke-University Magdeburg, Institute of Cognitive Neurology and Dementia Research, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | | | - André D Gomes
- Leibniz Institute of Photonic Technology, Jena, Germany
| | | | - Janelle M. P. Pakan
- Otto-von-Guericke-University Magdeburg, Institute of Cognitive Neurology and Dementia Research, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
- German Centre for Neurodegenerative Diseases, Magdeburg, Germany
- Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Tomáš Čižmár
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute of Scientific Instruments of CAS, Brno, Czechia
- Friedrich Schiller University Jena, Institute of Applied Optics, Jena, Germany
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Uhlířová H, Stibůrek M, Pikálek T, Gomes A, Turtaev S, Kolbábková P, Čižmár T. "There's plenty of room at the bottom": deep brain imaging with holographic endo-microscopy. NEUROPHOTONICS 2024; 11:S11504. [PMID: 38250297 PMCID: PMC10798506 DOI: 10.1117/1.nph.11.s1.s11504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Significance Over more than 300 years, microscopic imaging keeps providing fundamental insights into the mechanisms of living organisms. Seeing microscopic structures beyond the reach of free-space light-based microscopy, however, requires dissection of the tissue-an intervention seriously disturbing its physiological functions. The hunt for low-invasiveness tools has led a growing community of physicists and engineers into the realm of complex media photonics. One of its activities represents exploiting multimode optical fibers (MMFs) as ultra-thin endoscopic probes. Employing wavefront shaping, these tools only recently facilitated the first peeks at cells and their sub-cellular compartments at the bottom of the mouse brain with the impact of micro-scale tissue damage. Aim Here, we aim to highlight advances in MMF-based holographic endo-microscopy facilitating microscopic imaging throughout the whole depth of the mouse brain. Approach We summarize the important technical and methodological prerequisites for stabile high-resolution imaging in vivo. Results We showcase images of the microscopic building blocks of brain tissue, including neurons, neuronal processes, vessels, intracellular calcium signaling, and red blood cell velocity in individual vessels. Conclusions This perspective article helps to understand the complexity behind the technology of holographic endo-microscopy, summarizes its recent advances and challenges, and stimulates the mind of the reader for further exploitation of this tool in the neuroscience research.
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Affiliation(s)
- Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Stibůrek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Tomáš Pikálek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - André Gomes
- Leibniz Institute of Photonic Technology, Jena, Germany
| | | | - Petra Kolbábková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
- Leibniz Institute of Photonic Technology, Jena, Germany
- Friedrich Schiller University Jena, Institute of Applied Optics, Jena, Germany
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Xia F, Rimoli CV, Akemann W, Ventalon C, Bourdieu L, Gigan S, de Aguiar HB. Neurophotonics beyond the surface: unmasking the brain's complexity exploiting optical scattering. NEUROPHOTONICS 2024; 11:S11510. [PMID: 38617592 PMCID: PMC11014413 DOI: 10.1117/1.nph.11.s1.s11510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
The intricate nature of the brain necessitates the application of advanced probing techniques to comprehensively study and understand its working mechanisms. Neurophotonics offers minimally invasive methods to probe the brain using optics at cellular and even molecular levels. However, multiple challenges persist, especially concerning imaging depth, field of view, speed, and biocompatibility. A major hindrance to solving these challenges in optics is the scattering nature of the brain. This perspective highlights the potential of complex media optics, a specialized area of study focused on light propagation in materials with intricate heterogeneous optical properties, in advancing and improving neuronal readouts for structural imaging and optical recordings of neuronal activity. Key strategies include wavefront shaping techniques and computational imaging and sensing techniques that exploit scattering properties for enhanced performance. We discuss the potential merger of the two fields as well as potential challenges and perspectives toward longer term in vivo applications.
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Affiliation(s)
- Fei Xia
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
| | - Caio Vaz Rimoli
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Walther Akemann
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Cathie Ventalon
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Laurent Bourdieu
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Sylvain Gigan
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
| | - Hilton B. de Aguiar
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
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Xia F, Rimoli CV, Akemann W, Ventalon C, Bourdieu L, Gigan S, de Aguiar HB. Neurophotonics beyond the Surface: Unmasking the Brain's Complexity Exploiting Optical Scattering. ARXIV 2024:arXiv:2403.14809v1. [PMID: 38562443 PMCID: PMC10984001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The intricate nature of the brain necessitates the application of advanced probing techniques to comprehensively study and understand its working mechanisms. Neurophotonics offers minimally invasive methods to probe the brain using optics at cellular and even molecular levels. However, multiple challenges persist, especially concerning imaging depth, field of view, speed, and biocompatibility. A major hindrance to solving these challenges in optics is the scattering nature of the brain. This perspective highlights the potential of complex media optics, a specialized area of study focused on light propagation in materials with intricate heterogeneous optical properties, in advancing and improving neuronal readouts for structural imaging and optical recordings of neuronal activity. Key strategies include wavefront shaping techniques and computational imaging and sensing techniques that exploit scattering properties for enhanced performance. We discuss the potential merger of the two fields as well as potential challenges and perspectives toward longer term in vivo applications.
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Affiliation(s)
- Fei Xia
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Caio Vaz Rimoli
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Walther Akemann
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cathie Ventalon
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Laurent Bourdieu
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sylvain Gigan
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Hilton B de Aguiar
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
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Michálková I, Colombel S, Gomes AD, Čižmár T. Generating Airy beams through multimode fibres. OPTICS EXPRESS 2024; 32:6838-6847. [PMID: 38439380 DOI: 10.1364/oe.506926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/17/2023] [Indexed: 03/06/2024]
Abstract
Focussing light through a multimode fibre (MMF) is the basis of holographic endoscopes, which currently enable detailed imaging of deep tissue. Achieving high fidelity and purity diffraction-limited foci has been shown to be possible, when fully controlling the amplitude, phase, and two orthogonal polarisation states of the input field. Yet, generating more complex field distributions with similar performance remains to be assessed. Here, we demonstrate the generation of Airy beams through an MMF containing in excess of 90 % of the optical power delivered by the fibre. We discuss two distinct methods for generating optical landscapes: the direct field and the Fourier domain synthesis. Moreover, we showcase the flexibility of the Fourier domain synthesis to modify the generated beam.
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