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Principles Of Optics Electromagnetic Theory Of Propagation Interference And Diffraction Of Light

In the last few years, the deep learning (DL) computing paradigm has been deemed the Gold Standard in the machine learning (ML) community. Moreover, it has gradually become the most widely used computational approach in the field of ML, thus achieving outstanding results on several complex cognitive tasks, matching or even beating those provided by human performance. One of the benefits of DL is the ability to learn massive amounts of data. The DL field has grown fast in the last few years and it has been extensively used to successfully address a wide range of traditional applications. More importantly, DL has outperformed well-known ML techniques in many domains, e.g., cybersecurity, natural language processing, bioinformatics, robotics and control, and medical information processing, among many others. Despite it has been contributed several works reviewing the State-of-the-Art on DL, all of them only tackled one aspect of the DL, which leads to an overall lack of knowledge about it. Therefore, in this contribution, we propose using a more holistic approach in order to provide a more suitable starting point from which to develop a full understanding of DL. Specifically, this review attempts to provide a more comprehensive survey of the most important aspects of DL and including those enhancements recently added to the field. In particular, this paper outlines the importance of DL, presents the types of DL techniques and networks. It then presents convolutional neural networks (CNNs) which the most utilized DL network type and describes the development of CNNs architectures together with their main features, e.g., starting with the AlexNet network and closing with the High-Resolution network (HR.Net). Finally, we further present the challenges and suggested solutions to help researchers understand the existing research gaps. It is followed by a list of the major DL applications. Computational tools including FPGA, GPU, and CPU are summarized along with a description of their influence on DL. The paper ends with the evolution matrix, benchmark datasets, and summary and conclusion.

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Review of deep learning: concepts, CNN architectures, challenges, applications, future directions

Artificial intelligence tasks across numerous applications require accelerators for fast and low-power execution. Optical computing systems may be able to meet these domain-specific needs but, despite half a century of research, general-purpose optical computing systems have yet to mature into a practical technology. Artificial intelligence inference, however, especially for visual computing applications, may offer opportunities for inference based on optical and photonic systems. In this Perspective, we review recent work on optical computing for artificial intelligence applications and discuss its promise and challenges.

Inference in artificial intelligence with deep optics and photonics.

Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM. This Primer explains the central concepts of single-molecule localization microscopy (SMLM) before discussing experimental considerations regarding fluorophores, optics and data acquisition, processing and analysis. The Primer further describes recent high-impact discoveries made by SMLM techniques and concludes by discussing emerging methodologies.

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Single-molecule localization microscopy

Deep learning in the context of nano-photonics is mostly discussed in terms of its potential for inverse design of photonic devices or nano-structures. Many of the recent works on machine-learning inverse design are highly specific, and the drawbacks of the respective approaches are often not immediately clear. In this review we want therefore to provide a critical review on the capabilities of deep learning for inverse design and the progress which has been made so far. We classify the different deep-learning-based inverse design approaches at a higher level as well as by the context of their respective applications and critically discuss their strengths and weaknesses. While a significant part of the community’s attention lies on nano-photonic inverse design, deep learning has evolved as a tool for a large variety of applications. The second part of the review will focus therefore on machine learning research in nano-photonics “beyond inverse design.” This spans from physics-informed neural networks for tremendous acceleration of photonics simulations, over sparse data reconstruction, imaging and “knowledge discovery” to experimental applications.

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Deep learning in nano-photonics: inverse design and beyond

An outstanding challenge in single-molecule localization microscopy is the accurate and precise localization of individual point emitters in three dimensions in densely labeled samples. One established approach for three-dimensional single-molecule localization is point-spread-function (PSF) engineering, in which the PSF is engineered to vary distinctively with emitter depth using additional optical elements. However, images of dense emitters, which are desirable for improving temporal resolution, pose a challenge for algorithmic localization of engineered PSFs, due to lateral overlap of the emitter PSFs. Here we train a neural network to localize multiple emitters with densely overlapping Tetrapod PSFs over a large axial range. We then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach experimentally with super-resolution reconstructions of mitochondria and volumetric imaging of fluorescently labeled telomeres in cells. Our approach, DeepSTORM3D, enables the study of biological processes in whole cells at timescales that are rarely explored in localization microscopy.

DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning

Localization microscopy is an imaging technique in which the positions of individual nanoscale point emitters (e.g. fluorescent molecules) are determined at high precision from their images. This is the key ingredient in single/multiple-particle-tracking and several super-resolution microscopy approaches. Localization in three-dimensions (3D) can be performed by modifying the image that a point-source creates on the camera, namely, the point-spread function (PSF). The PSF is engineered using additional optical elements to vary distinctively with the depth of the point-source. However, localizing multiple adjacent emitters in 3D poses a significant algorithmic challenge, due to the lateral overlap of their PSFs. Here, we train a neural network to receive an image containing densely overlapping PSFs of multiple emitters over a large axial range and output a list of their 3D positions. Furthermore, we then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach numerically as well as experimentally by 3D STORM imaging of mitochondria, and volumetric imaging of dozens of fluorescently-labeled telomeres occupying a mammalian nucleus in a single snapshot.

DeepSTORM3D: dense three dimensional localization microscopy and point spread function design by deep learning

Dense three dimensional localization microscopy by deep learning

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Racheli Gordon

Papers

DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning

DeepSTORM3D: dense three dimensional localization microscopy and point spread function design by deep learning

Dense three dimensional localization microscopy by deep learning

Publisher Correction: DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning.