Low-Rank Fourier Ptychography
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Subwavelength Resolution Fourier Ptychography with Hemispherical Digital Condensers
Subwavelength resolution Fourier ptychography with hemispherical digital condensers AN PAN,1,2 YAN ZHANG,1,2 KAI WEN,1,3 MAOSEN LI,4 MEILING ZHOU,1,2 JUNWEI MIN,1 MING LEI,1 AND BAOLI YAO1,* 1State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China 2University of Chinese Academy of Sciences, Beijing 100049, China 3College of Physics and Information Technology, Shaanxi Normal University, Xi’an 710071, China 4Xidian University, Xi’an 710071, China *[email protected] Abstract: Fourier ptychography (FP) is a promising computational imaging technique that overcomes the physical space-bandwidth product (SBP) limit of a conventional microscope by applying angular diversity illuminations. However, to date, the effective imaging numerical aperture (NA) achievable with a commercial LED board is still limited to the range of 0.3−0.7 with a 4×/0.1NA objective due to the constraint of planar geometry with weak illumination brightness and attenuated signal-to-noise ratio (SNR). Thus the highest achievable half-pitch resolution is usually constrained between 500−1000 nm, which cannot fulfill some needs of high-resolution biomedical imaging applications. Although it is possible to improve the resolution by using a higher magnification objective with larger NA instead of enlarging the illumination NA, the SBP is suppressed to some extent, making the FP technique less appealing, since the reduction of field-of-view (FOV) is much larger than the improvement of resolution in this FP platform. Herein, in this paper, we initially present a subwavelength resolution Fourier ptychography (SRFP) platform with a hemispherical digital condenser to provide high-angle programmable plane-wave illuminations of 0.95NA, attaining a 4×/0.1NA objective with the final effective imaging performance of 1.05NA at a half-pitch resolution of 244 nm with a wavelength of 465 nm across a wide FOV of 14.60 mm2, corresponding to an SBP of 245 megapixels. -
Near-Field Fourier Ptychography: Super- Resolution Phase Retrieval Via Speckle Illumination
Near-field Fourier ptychography: super- resolution phase retrieval via speckle illumination HE ZHANG,1,4,6 SHAOWEI JIANG,1,6 JUN LIAO,1 JUNJING DENG,3 JIAN LIU,4 YONGBING ZHANG,5 AND GUOAN ZHENG1,2,* 1Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA 2Electrical and Computer Engineering, University of Connecticut, Storrs, CT, 06269, USA 3Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA. 4Ultra-Precision Optoelectronic Instrument Engineering Center, Harbin Institute of Technology, Harbin 150001, China 5Shenzhen Key Lab of Broadband Network and Multimedia, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China 6These authors contributed equally to this work *[email protected] Abstract: Achieving high spatial resolution is the goal of many imaging systems. Designing a high-resolution lens with diffraction-limited performance over a large field of view remains a difficult task in imaging system design. On the other hand, creating a complex speckle pattern with wavelength-limited spatial features is effortless and can be implemented via a simple random diffuser. With this observation and inspired by the concept of near-field ptychography, we report a new imaging modality, termed near-field Fourier ptychography, for tackling high- resolution imaging challenges in both microscopic and macroscopic imaging settings. The meaning of ‘near-field’ is referred to placing the object at a short defocus distance with a large Fresnel number. In our implementations, we project a speckle pattern with fine spatial features on the object instead of directly resolving the spatial features via a high-resolution lens. We then translate the object (or speckle) to different positions and acquire the corresponding images using a low-resolution lens. -
The Geometry of the Phase Retrieval Problem Charles L
The Geometry of the Phase Retrieval Problem Charles L. Epstein The Geometry of the Phase Retrieval Problem Introduction Operator Splitting Methods in Data Analysis Workshop Discrete Problem Torus Geometry Reconstruction Charles L. Epstein Algorithms Numerical Examples CCM at the Flatiron Institute University of Pennsylvania Other Conditions History of CDI March 20, 2019 Bibliography Acknowledgment The Geometry of the Phase Retrieval Problem Charles L. Epstein I want to thank Christian and Patrick for inviting me to speak. Introduction What I will discuss today is somewhat unconventional, ongoing Discrete Problem work, at the intersection of pure mathematics, numerical analysis Torus Geometry and mathematical physics. Reconstruction Algorithms This work was done jointly with Alex Barnett, Leslie Greengard, Numerical and Jeremy Magland and supported by the Centers for Examples Computational Biology and Mathematics at the Flatiron Institute Other Conditions of the Simons Foundation, New York, NY. History of CDI Bibliography Outline The Geometry of the Phase Retrieval Problem 1 Introduction Charles L. Epstein 2 The Discrete Phase Retrieval Problem Introduction 3 Geometry of the Torus Discrete Problem Torus Geometry 4 Reconstruction Algorithms Reconstruction Algorithms 5 Numerical Examples in Phase Retrieval Numerical Examples 6 Other Auxiliary Conditions Other Conditions History of CDI 7 Short History of CDI Bibliography 8 Bibliography High Resolution Imaging The Geometry of the Phase Retrieval Problem Charles L. Epstein Introduction Today I will speak about inverse problems that arise in Coherent Discrete Problem Diffraction Imaging. This is a technique that uses very high Torus Geometry energy, monochromatic light, either electrons or x-rays, to form Reconstruction high resolution images of animate and inanimate materials. -
Aspects of Phase Retrieval in X-Ray Crystallography
Aspects of Phase Retrieval in X-ray Crystallography Romain Arnal A thesis presented for the degree of Doctor of Philosophy in Electrical and Computer Engineering at the University of Canterbury, Christchurch, New Zealand. June 2019 Deputy Vice-Chancellor’s Office Postgraduate Office Co-Authorship Form This form is to accompany the submission of any thesis that contains research reported in co- authored work that has been published, accepted for publication, or submitted for publication. A copy of this form should be included for each co-authored work that is included in the thesis. Completed forms should be included at the front (after the thesis abstract) of each copy of the thesis submitted for examination and library deposit. Please indicate the chapter/section/pages of this thesis that are extracted from co-authored work and provide details of the publication or submission from the extract comes: Chapter 2 describes work by the candidate that is reported in “Millane and Arnal, Uniqueness of the macromolecular crystallographic phase problem, Acta Cryst., A71, 592-598, 2015.” Please detail the nature and extent (%) of contribution by the candidate: This publication describes joint work by the candidate and Millane. The theory was derived jointly by the candidate and Millane. The simulations, the required software development, and presentation of the results were conducted by the candidate. Writing was a joint effort. Certification by Co-authors: If there is more than one co-author then a single co-author can sign on behalf of all The -
Arxiv:2007.14139V2 [Physics.Optics] 1 Apr 2021 Plane and the Detector Plane
Accelerating ptychographic reconstructions using spectral initializations Lorenzo Valzania,1, 2, ∗ Jonathan Dong,1, 3, ∗ and Sylvain Gigan1 1Laboratoire Kastler Brossel, Ecole´ Normale Sup´erieure - Paris Sciences et Lettres (PSL) Research University, Sorbonne Universit´e,Centre National de la Recherche Scientifique (CNRS) UMR 8552, Coll`egede France, 24 rue Lhomond, 75005 Paris, France 2Laboratory for Transport at Nanoscale Interfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, 129 Uberlandstrasse, Dubendorf 8600, Switzerland 3Laboratoire de Physique de l'Ecole´ Normale Sup´erieure - Paris Sciences et Lettres (PSL) Research University, Sorbonne Universit´e,CNRS, Universit´ede Paris, 24 rue Lhomond, 75005 Paris, France (Dated: April 2, 2021) Ptychography is a promising phase retrieval technique for label-free quantitative phase imaging. Recent advances in phase retrieval algorithms witnessed the development of spectral methods, in order to accelerate gradient descent algorithms. Using spectral initializations on experimental data, for the first time we report three times faster ptychographic reconstructions than with a standard gradient descent algorithm and improved resilience to noise. Coming at no additional computational cost compared to gradient-descent-based algorithms, spectral methods have the potential to be implemented in large-scale iterative ptychographic algorithms. I. INTRODUCTION and the acquisition parameters. The quest for improved reconstruction performance culminated in the derivation Ptychography is a computational imaging technique of optimal spectral methods for the random measure- that enables label-free, quantitative phase imaging [1]. ments setting [9, 10]. Due to these breakthroughs, spec- It is based on a simple principle: scan a probe across tral methods for phase retrieval are rather well under- a sample, collect the corresponding intensity diffraction stood theoretically. -
Sub-Diffraction Imaging Using Fourier Ptychography and Structured Sparsity
SUB-DIFFRACTION IMAGING USING FOURIER PTYCHOGRAPHY AND STRUCTURED SPARSITY Gauri Jagatap, Zhengyu Chen, Chinmay Hegde, Namrata Vaswani Electrical and Computer Engineering, Iowa State University, Ames, IA 50011 ABSTRACT fewer samples suffice. The assumption of sparsity is natural in sev- eral applications in imaging systems, such as sub-diffraction imag- We consider the problem of super-resolution for sub-diffraction ing, X-ray crystallography, bio-imaging and astronomical imaging imaging. We adapt conventional Fourier ptychographic approaches, [12, 13, 14]; in these applications, the object to be imaged is often for the case where the images to be acquired have an underlying modeled as sparse in the canonical (or wavelet) basis. structured sparsity. We propose some subsampling strategies which Moving beyond sparsity, several algorithms that leverage more can be easily adapted to existing ptychographic setups. We then refined structured sparsity modeling assumptions (such as block use a novel technique called CoPRAM with some modifications, sparsity) achieve considerably improved sample-complexity for re- to recover sparse (and block sparse) images from subsampled pty- constructing images from compressive measurements [15, 16, 17]. chographic measurements. We demonstrate experimentally that this However, analogous algorithms in the context of phase retrieval are algorithm performs better than existing phase retrieval techniques, in not well-studied. In recent previous work [18], we have developed terms of quality of reconstruction, using fewer number of samples. a theoretically-sound algorithmic approach for phase retrieval that Index Terms— Phase retrieval, ptychography, sparsity, non- integrate sparsity (as well as structured sparsity) modeling assump- convex algorithms tions within the reconstruction process. However, that work also assumes certain stringent probabilistic assumptions on the measure- 1. -
This Is a Repository Copy of Ptychography. White Rose
This is a repository copy of Ptychography. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/127795/ Version: Accepted Version Book Section: Rodenburg, J.M. orcid.org/0000-0002-1059-8179 and Maiden, A.M. (2019) Ptychography. In: Hawkes, P.W. and Spence, J.C.H., (eds.) Springer Handbook of Microscopy. Springer Handbooks . Springer . ISBN 9783030000684 https://doi.org/10.1007/978-3-030-00069-1_17 This is a post-peer-review, pre-copyedit version of a chapter published in Hawkes P.W., Spence J.C.H. (eds) Springer Handbook of Microscopy. The final authenticated version is available online at: https://doi.org/10.1007/978-3-030-00069-1_17. Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Ptychography John Rodenburg and Andy Maiden Abstract: Ptychography is a computational imaging technique. A detector records an extensive data set consisting of many inference patterns obtained as an object is displaced to various positions relative to an illumination field. -
Iterative Phase Retrieval in Coherent Diffractive Imaging: Practical Issues
Iterative phase retrieval in coherent diffractive imaging: practical issues Tatiana Latychevskaia, [email protected] ABSTRACT In this work, issues in phase retrieval in the coherent diffractive imaging (CDI) technique, from discussion on parameters for setting up a CDI experiment to evaluation of the goodness of the final reconstruction, are discussed. The distribution of objects under study by CDI often cannot be cross- validated by another imaging technique. It is therefore important to make sure that the developed CDI procedure delivers an artifact-free object reconstruction. Critical issues that can lead to artifacts are presented and recipes on how to avoid them are provided. Contents Iterative phase retrieval in coherent diffractive imaging: practical issues ............................................. 1 1. Introduction ......................................................................................................................................... 3 2. Basics of CDI experiment ..................................................................................................................... 3 2.1. Diffraction pattern formation ...................................................................................................... 3 2.2 Oversampling ................................................................................................................................. 6 2.3 Iterative phase-retrieval algorithms .............................................................................................. 7 2.3.1 -
Phase Retrieval for Fourier Ptychography Under Varying Amount of Measurements
BOOMINATHAN ET AL.: PHASE RETRIEVAL FOR FOURIER PTYCHOGRAPHY 1 Phase retrieval for Fourier Ptychography under varying amount of measurements Lokesh Boominathan12 1 Computational Imaging Lab, [email protected] Indian Institute of Technology Madras, Mayug Maniparambil1 Chennai, India [email protected] 2 Aindra Systems Honey Gupta1 Bengaluru, India [email protected] Rahul Baburajan1 [email protected] Kaushik Mitra1 [email protected] Abstract Fourier Ptychography is a recently proposed imaging technique that yields high- resolution images by computationally transcending the diffraction blur of an optical system. At the crux of this method is the phase retrieval algorithm, which is used for computationally stitching together low-resolution images taken under varying illumina- tion angles of a coherent light source. However, the traditional iterative phase retrieval technique relies heavily on the initialization and also needs a good amount of overlap in the Fourier domain for the successively captured low-resolution images, thus increas- ing the acquisition time and data. We show that an auto-encoder based architecture can be adaptively trained for phase retrieval under both low overlap, where traditional tech- niques completely fail, and at higher levels of overlap. For the low overlap case we show that a supervised deep learning technique using an autoencoder generator is a good choice for solving the Fourier ptychography problem. And for the high overlap case, we show that optimizing the generator for reducing the forward model error is an appropriate choice. Using simulations for the challenging case of uncorrelated phase and amplitude, we show that our method outperforms many of the previously proposed Fourier ptychog- raphy phase retrieval techniques. -
The Numerics of Phase Retrieval
THE NUMERICS OF PHASE RETRIEVAL ALBERT FANNJIANG AND THOMAS STROHMER Abstract. Phase retrieval, i.e., the problem of recovering a function from the squared magnitude of its Fourier transform, arises in many applications such as X-ray crystallog- raphy, diffraction imaging, optics, quantum mechanics, and astronomy. This problem has confounded engineers, physicists, and mathematicians for many decades. Recently, phase re- trieval has seen a resurgence in research activity, ignited by new imaging modalities and novel mathematical concepts. As our scientific experiments produce larger and larger datasets and we aim for faster and faster throughput, it becomes increasingly important to study the involved numerical algorithms in a systematic and principled manner. Indeed, the last decade has witnessed a surge in the systematic study of computational algorithms for phase retrieval. In this paper we will review these recent advances from a numerical viewpoint. Contents 1. Introduction 2 1.1. Overview 4 2. Phase retrieval and ptychography: basic setup 5 2.1. Mathematical formulation 5 2.2. Prior information 6 2.3. Measurement techniques 7 2.4. Measurement of coded diffraction patterns 8 2.5. Ptychography 10 2.6. Ptychography and time-frequency analysis 11 2.7. 2D Ptychography 12 3. Uniqueness, ambiguities, noise 13 3.1. Uniqueness and ambiguities with coded diffraction patterns 14 3.2. Ambiguities with one diffraction pattern 15 3.3. Phase retrieval as feasibility 17 3.4. Noise models and log-likelihood functions 18 3.5. Spectral gap and local convexity 20 4. Nonconvex optimization 20 4.1. Alternating Projections (AP) 20 4.2. Averaged Alternating Reflections (AAR) 21 4.3. -
Sample Efficient Fourier Ptychography for Structured Data
1 Sample Efficient Fourier Ptychography for Structured Data Gauri Jagatap, Zhengyu Chen, Seyedehsara Nayer, Chinmay Hegde, Senior Member, IEEE and Namrata Vaswani, Fellow, IEEE Abstract—We study the problem of recovering structured data shifts induced by the optical lens setup. However, the sensing from Fourier ptychography measurements. Fourier ptychogra- apparatus is incapable of estimating the phase of the complex phy is an image acquisition scheme that uses an array of images values, and only the magnitudes can be measured. to produce high-resolution images in microscopy as well as long- distance imaging, to mitigate the effects of diffraction blurring. This setup can be molded to that of the classical problem The number of measurements is typically much larger than the of phase retrieval [7], [8], [9], which is a non-linear, ill- size of the signal (image or video) to be reconstructed, which posed inverse problem. In phase retrieval, the goal is to recon- translates to high storage and computational requirements. struct a discretized image (or video) of size n (or nq) from The issue of high sample complexity can be alleviated by utiliz- noisy, magnitude-only observations of the image’s discrete ing structural properties of the image (or video). In this paper, we first discuss a range of sub-sampling schemes which can reduce Fourier transform (DFT) coefficients. A generalized version the amount of measurements in Fourier ptychography setups; of this problem replaces the DFT coefficients with a generic however, this makes the problem ill-posed. Correspondingly, we linear operator constructed by sampling certain families of impose structural constraints on the signals to be recovered, probability distributions. -
Algorithms for Coherent Diffractive Imaging with X-Ray Lasers
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1589 Algorithms for Coherent Diffractive Imaging with X-ray Lasers BENEDIKT J. DAURER ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-0129-7 UPPSALA urn:nbn:se:uu:diva-329012 2017 Dissertation presented at Uppsala University to be publicly examined in Room B7:101a, Biomedicinska Centrum (BMC), Husargatan 3, Uppsala, Friday, 15 December 2017 at 13:00 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Richard Neutze (University of Gothenburg). Abstract Daurer, B. J. 2017. Algorithms for Coherent Diffractive Imaging with X-ray Lasers. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1589. 64 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0129-7. Coherent diffractive imaging (CDI) has become a very popular technique over the past two decades. CDI is a "lensless" imaging method which replaces the objective lens of a conventional microscope by a computational image reconstruction procedure. Its increase in popularity came together with the development of X-ray free-electron lasers (XFELs) which produce extremely bright and coherent X-rays. By facilitating these unique properties, CDI enables structure determination of non-crystalline samples at nanometre resolution and has many applications in structural biology, material science and X-ray optics among others. This work focuses on two specific CDI techniques, flash X-ray diffractive imaging (FXI) on biological samples and X- ray ptychography. While the first FXI demonstrations using soft X-rays have been quite promising, they also revealed remaining technical challenges.