1
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Zhou X, Li Z, Qiao Z, Wang Y, Huang G, Chi D, Li X, Liu S, Liu Z. Fast autofocusing of recorded planes by salient feature region for coherent diffraction imaging. J Biophotonics 2024; 17:e202300278. [PMID: 37717259 DOI: 10.1002/jbio.202300278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
In multi-distance coherent diffraction imaging, the task of distance calculation for multi-diffraction images is cumbersome. The information features are hard-to-extract and the region of interest extraction algorithms are difficult to be adopted. A universal salient feature region selection algorithm by using the area with the highest density of corners is proposed to extract the most representative feature region. In addition, equally spaced recording modes and mismatched diffraction distances will result in system noise and destroy image quality. The polydirectional maximum gradient is offered as a sharpness criterion to weigh a quantitative feature for the final pattern. A fast, sensitive, and high-accuracy autofocusing and sample reconstruction can be achieved using only a small number of images while ensuring that morphological properties and quantification of the reconstructions are not compromised. The proposed method is promising for biological and medical dynamic observations for computational imaging systems.
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Affiliation(s)
- Xuyang Zhou
- School of Physics, Harbin Institute of Technology, Harbin, China
| | - Ziyang Li
- School of Physics, Harbin Institute of Technology, Harbin, China
| | - Ziling Qiao
- School of Physics, Harbin Institute of Technology, Harbin, China
| | - Yiran Wang
- School of Physics, Harbin Institute of Technology, Harbin, China
| | - Guancheng Huang
- School of Physics, Harbin Institute of Technology, Harbin, China
| | - Dazhao Chi
- State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Harbin, China
| | - Xiaomei Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shutian Liu
- School of Physics, Harbin Institute of Technology, Harbin, China
| | - Zhengjun Liu
- School of Physics, Harbin Institute of Technology, Harbin, China
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2
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Yu F, Du K, Ju X, Wang F, Li K, Chen C, Du G, Deng B, Xie H, Xiao T. Dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval based on deep learning. IUCrJ 2024; 11:73-81. [PMID: 38096037 PMCID: PMC10833393 DOI: 10.1107/s2052252523010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 11/22/2023] [Indexed: 01/10/2024]
Abstract
Speckle-tracking X-ray imaging is an attractive candidate for dynamic X-ray imaging owing to its flexible setup and simultaneous yields of phase, transmission and scattering images. However, traditional speckle-tracking imaging methods suffer from phase distortion at locations with abrupt changes in density, which is always the case for real samples, limiting the applications of the speckle-tracking X-ray imaging method. In this paper, we report a deep-learning based method which can achieve dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval. The calibration results of a phantom show that the profile of the retrieved phase is highly consistent with the theoretical one. Experiments of polyurethane foaming demonstrated that the proposed method revealed the evolution of the complicated microstructure of the bubbles accurately. The proposed method is a promising solution for dynamic X-ray imaging with high-accuracy phase retrieval, and has extensive applications in metrology and quantitative analysis of dynamics in material science, physics, chemistry and biomedicine.
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Affiliation(s)
- Fucheng Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Kang Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Xiaolu Ju
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Feixiang Wang
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Ke Li
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Can Chen
- Zhejiang Institute of Metrology, Hangzhou 310063, People’s Republic of China
| | - Guohao Du
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Biao Deng
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Honglan Xie
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Tiqiao Xiao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
- Shanghai Synchrotron Radiation Facility/Zhang Jiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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3
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Chen Z, Cheng J, Wu H. Phase Retrieval Based on Shaped Incoherent Sources. Sensors (Basel) 2023; 23:9405. [PMID: 38067776 PMCID: PMC10708693 DOI: 10.3390/s23239405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 04/13/2024]
Abstract
Current ghost imaging phase reconstruction schemes require either complex optical systems, iterative algorithms, Fourier transform steps, or entangled photon pairs. These factors may increase the difficulty of system design, lead to phase retrieval errors, or result in excessive time consumption. To tackle this challenge, we propose a five-step phase-shifting method that eliminates the need for complex optical systems, Fourier transform steps, entangled photon pairs, or iterative algorithms. Using five specifically designed incoherent sources, we can generate five distinct ghost imaging patterns. Subsequently, the phase information of the object can be calculated from these five speckle patterns. Additionally, we offer a detailed theoretical explanation for choosing the five-step phase-shifting method over the more commonly used three-step or four-step phase-shifting methods. We demonstrate the applicability of this theoretical proposal through numerical simulations involving two types of complicated objects. The results illustrate that the phase information of the complex object can be successfully and quantitatively reconstructed.
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Affiliation(s)
- Ziyan Chen
- Guangdong Provincial Key Laboratory of Cyber-Physical System, School of Automation, Guangdong University of Technology, Guangzhou 510006, China;
- School of Computer, Guangdong University of Technology, Guangzhou 510006, China
| | - Jing Cheng
- School of Physics, South China University of Technology, Guangzhou 510641, China;
| | - Heng Wu
- Guangdong Provincial Key Laboratory of Cyber-Physical System, School of Automation, Guangdong University of Technology, Guangzhou 510006, China;
- School of Computer, Guangdong University of Technology, Guangzhou 510006, China
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4
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Luo Z, Wu R, Chen H, Zhen J, Liu M, Zhang H, Luo J, Han D, Yan L, Wu Y. Fast and robust Fourier ptychographic microscopy with position misalignment correction. J Biomed Opt 2023; 28:116503. [PMID: 38078152 PMCID: PMC10704086 DOI: 10.1117/1.jbo.28.11.116503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Significance Fourier ptychographic microscopy (FPM) is a new, developing computational imaging technology. It can realize the quantitative phase imaging of a wide field of view and high-resolution (HR) simultaneously by means of multi-angle illumination via a light emitting diode (LED) array, combined with a phase recovery algorithm and the synthetic aperture principle. However, in the FPM reconstruction process, LED position misalignment affects the quality of the reconstructed image, and the reconstruction efficiency of the existing LED position correction algorithms needs to be improved. Aim This study aims to improve the FPM correction method based on simulated annealing (SA) and proposes a position misalignment correction method (AA-C algorithm) using an improved phase recovery strategy. Approach The spectrum function update strategy was optimized by adding an adaptive control factor, and the reconstruction efficiency of the algorithm was improved. Results The experimental results show that the proposed method is effective and robust for position misalignment correction of LED arrays in FPM, and the convergence speed can be improved by 21.2% and 54.9% compared with SC-FPM and PC-FPM, respectively. Conclusions These results can reduce the requirement of the FPM system for LED array accuracy and improve robustness.
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Affiliation(s)
- Zicong Luo
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Ruofei Wu
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Hanbao Chen
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Junrui Zhen
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Mingdi Liu
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Haiqi Zhang
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Jiaxiong Luo
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Dingan Han
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
| | - Lisong Yan
- Huazhong University of Science and Technology, School of Optical and Electronic Information, Wuhan, China
| | - Yanxiong Wu
- Foshan University, School of Physics and Optoelectronic Engineering, Foshan, China
- Ji Hua Laboratory, Foshan, China
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Zhang Y, Sun J. A Phase Retrieval Method for 3D Shape Measurement of High-Reflectivity Surface Based on π Phase-Shifting Fringes. Sensors (Basel) 2023; 23:8848. [PMID: 37960546 PMCID: PMC10648934 DOI: 10.3390/s23218848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
Fringe projection profilometry (FPP) has been widely used for 3D reconstruction, surface measurement, and reverse engineering. However, if the surface of an object has a high reflectivity, overexposure can easily occur. Image saturation caused by overexposure can lead to an incorrect intensity of the captured pattern images, resulting in phase and measurement errors of FPP. To address this issue, we propose a phase retrieval method for the 3D shape measurement of high-reflectivity surfaces based on π phase-shifting fringes. Our method only requires eight images to be projected, including three single-frequency three-step phase-shifting patterns and one pattern used to provide phase unwrapping constraints, called conventional patterns, as well as the π phase-shifting patterns corresponding to the four conventional patterns, called supplemental patterns. Saturated pixels of conventional fringes are replaced by unsaturated pixels in supplemental fringes to suppress phase retrieval errors. We analyzed all 16 replacement cases of fringe patterns and provided calculation methods for unwrapped phases. The main advantages of our method are as follows: (1) By combining the advantages of the stereo phase unwrapping (SPU) algorithm, the number of projected fringes is reduced. (2) By utilizing the phase unwrapping constraint provided by the fourth fringe pattern, the accuracy of SPU is improved. For highly reflective surfaces, the experimental results demonstrate the performance of the proposed method.
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Affiliation(s)
| | - Junhua Sun
- School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China;
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Shichi A, Ishizuka H, Saitoh K. Phase Retrieval of Electron Rocking Curves using Total Variation and Total Squared Variation Regularizations. Microscopy (Oxf) 2023:dfad048. [PMID: 37793048 DOI: 10.1093/jmicro/dfad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/15/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
In this study, a new method for the phase retrieval of electron rocking curves observed using convergent-beam electron diffraction, which is applicable to the determination of three-dimensional lattice displacement fields along the beam direction, is proposed. Total variation and total squared variation regularizations are introduced for phase retrieval to suppress overfitting to noise or background signals in the rocking curves and to reproduce the sparse characteristics of displacement fields, which exist only near lattice defects. The results show that the proposed algorithm is effective for rocking curves modulated by the dynamical effect of electron diffraction. The accuracy of phase reconstruction using the proposed method is also discussed. Phase retrieval of the experimental rocking curves obtained from a stacking fault in stainless steel is demonstrated.
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Affiliation(s)
- Akihiro Shichi
- Department of Applied Physics, Graduate School of Engineering, Nagoya University
| | - Hiroyuki Ishizuka
- Department of Applied Physics, Graduate School of Engineering, Nagoya University
| | - Koh Saitoh
- Institute of Materials and Systems for Sustainability, Nagoya University
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7
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Tao S, Tian Z, Bai L, Wang W, Xu Y, Kuang C, Liu X. Tri-directional x-ray phase contrast multimodal imaging using one hexagonal mesh modulator. Phys Med Biol 2023; 68:195017. [PMID: 37652041 DOI: 10.1088/1361-6560/acf5c3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/31/2023] [Indexed: 09/02/2023]
Abstract
Objective. X-ray phase contrast imaging is a promising technique for future clinical diagnostic as it can provide enhanced contrast in soft tissues compared to traditional x-ray attenuation-contrast imaging. However, the strict requirements on the x-ray coherence and the precise alignment of optical elements limit its applications towards clinical use. To solve this problem, mesh-based x-ray phase contrast imaging method with one hexagonal mesh is proposed for easy alignment and better image visualization.Approach. The mesh produces structured illuminations and the detector captures its distortions to reconstruct the absorption, differential phase contrast (DPC) and dark-field (DF) images of the sample. In this work, we fabricated a hexagonal mesh to simultaneously retrieve DPC and DF signals in three different directions with single shot. A phase retrieval algorithm to obtain artifacts-free phase from DPC images with three different directions is put forward and false color dark-field image is also reconstructed with tri-directional images. Mesh-shifting method based on this hexagonal mesh modulator is also proposed to reconstruct images with better image quality at the expense of increased dose.Main results. In numerical simulations, the proposed hexagonal mesh outperforms the traditional square mesh in image evaluation metrics performance and false color visualization with the same radiation dose. The experimental results demonstrate its feasiblity in real imaging systems and its advantages in quantitive imaging and better visualization. The proposed hexagonal mesh is easy to fabricate and can be successfully applied to x-ray source with it spot size up to 300μm.Significance. This work opens new possibilities for quantitative x-ray non-destructive imaging and may also be instructive for research fields such as x-ray structured illumination microscopy (SIM), x-ray spectral imaging and x-ray phase contrast and dark-field computed tomography (CT).
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Affiliation(s)
- Siwei Tao
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Zonghan Tian
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Ling Bai
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Yueshu Xu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
- State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 315100, People's Republic of China
| | - Cuifang Kuang
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
- State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 315100, People's Republic of China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Xu Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
- State Key Laboratory of Extreme Photonics and Instrumentation, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 315100, People's Republic of China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, People's Republic of China
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Sadri A, Findlay SD. Determining the Projected Crystal Structure from Four-dimensional Scanning Transmission Electron Microscopy via the Scattering Matrix. Microsc Microanal 2023; 29:967-982. [PMID: 37749695 DOI: 10.1093/micmic/ozad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/15/2023] [Accepted: 02/05/2023] [Indexed: 09/27/2023]
Abstract
We present a gradient-descent-based approach to determining the projected electrostatic potential from four-dimensional scanning transmission electron microscopy measurements of a periodic, crystalline material even when dynamical scattering occurs. The method solves for the scattering matrix as an intermediate step, but overcomes the so-called truncation problem that limited previous scattering-matrix-based projected structure determination methods. Gradient descent is made efficient by using analytic expressions for the gradients. Through simulated case studies, we show that iteratively improving the scattering matrix determination can significantly improve the accuracy of the projected structure determination.
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Affiliation(s)
- Alireza Sadri
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
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Østergaard M, Naver EB, Kaestner A, Willendrup PK, Brüel A, Sørensen HO, Thomsen JS, Schmidt S, Poulsen HF, Theil Kuhn L, Birkedal H. Polychromatic neutron phase-contrast imaging of weakly absorbing samples enabled by phase retrieval. J Appl Crystallogr 2023; 56:673-682. [PMID: 37284268 PMCID: PMC10241042 DOI: 10.1107/s1600576723003011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/01/2023] [Indexed: 06/08/2023] Open
Abstract
The use of a phase-retrieval technique for propagation-based phase-contrast neutron imaging with a polychromatic beam is demonstrated. This enables imaging of samples with low absorption contrast and/or improving the signal-to-noise ratio to facilitate e.g. time-resolved measurements. A metal sample, designed to be close to a phase pure object, and a bone sample with canals partially filled with D2O were used for demonstrating the technique. These samples were imaged with a polychromatic neutron beam followed by phase retrieval. For both samples the signal-to-noise ratios were significantly improved and, in the case of the bone sample, the phase retrieval allowed for separation of bone and D2O, which is important for example for in situ flow experiments. The use of deuteration contrast avoids the use of chemical contrast enhancement and makes neutron imaging an interesting complementary method to X-ray imaging of bone.
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Affiliation(s)
- Maja Østergaard
- Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, Aarhus, Denmark
| | - Estrid Buhl Naver
- Department of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, Kongens Lyngby, Denmark
| | - Anders Kaestner
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, Villigen, Switzerland
| | - Peter K. Willendrup
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
- European Spallation Source ERIC, PO Box 176, Lund, Sweden
| | - Annemarie Brüel
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus, Denmark
| | - Henning Osholm Sørensen
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
- Xnovo Technology ApS, Galoche Alle 15, 1, Køge, Denmark
| | | | - Søren Schmidt
- European Spallation Source ERIC, PO Box 176, Lund, Sweden
| | - Henning Friis Poulsen
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
| | - Luise Theil Kuhn
- Department of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, Kongens Lyngby, Denmark
| | - Henrik Birkedal
- Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, Aarhus, Denmark
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10
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Tang R, Chen Y, Yan F, Chen KM. Phase Retrieval-Based Phase-Contrast Imaging and CT of Living Zebrafish. Zebrafish 2023. [PMID: 37023400 DOI: 10.1089/zeb.2022.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Zebrafish are widely used as experimental animal models. They are small and move fast in the water. Real-time imaging of fast-moving zebrafish is a challenge, and it requires that the imaging technique has higher spatiotemporal resolution and penetration ability. The purpose of this study was to evaluate the feasibility of dynamic phase retrieval (PR)-based phase-contrast imaging (PCI) for real-time displaying of the breathing and swimming process in unanesthetized free-moving zebrafish, and to evaluate the feasibility of PR-based phase-contrast CT (PCCT) for visualizing the soft tissues in anesthetized living zebrafish. PR was performed using the phase-attenuation duality (PAD) method with the δ/β values (PAD property) of 100 and 1000 for dynamic PR-based PCI and PR-based PCCT, respectively. The contrast-to-noise ratio (CNR) was used for quantitatively assessing the visibility of the adipose tissue and muscle tissue. The skeleton and swim bladder chambers in fast-moving zebrafish were clearly shown. The dynamic processes of breathing and swimming were visibly recorded. The respiratory intensity and frequency and the movement flexibility of the zebrafish could be dynamically evaluated. By producing more obvious image contrast, PR-based PCCT clearly showed the adipose tissue and muscle tissue. The CNRs from PR-based PCCT were significantly higher than those from PR-free PCCT for both adipose tissue (9.256 ± 2.037 vs. 0.429 ± 0.426, p < 0.0001) and muscle tissue (7.095 ± 1.443 vs. 0.324 ± 0.267, p < 0.0001). Dynamic PR-based PCI holds the potential for investigating both morphological abnormalities and motor disorders. PR-based PCCT offers clear visualization and the potential for quantification of soft tissues in living zebrafish.
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Affiliation(s)
- Rongbiao Tang
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Yi Chen
- Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Fuhua Yan
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Ke-Min Chen
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
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11
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Park CW, Jeon S, Kwon SH, Jung JH, Seol JE, Park CS, Cho SK, Ko DK. Comparative analysis of dermal collagen and lipids in cereblon ablated mice using a multimodal nonlinear optical system. J Biophotonics 2023; 16:e202200139. [PMID: 36127858 DOI: 10.1002/jbio.202200139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
By utilizing a multimodal nonlinear optical system that combines coherent anti-Stokes Raman scattering and second harmonic generation to investigate biological characteristics of dermal tissues ex vivo, we demonstrate the potential feasibility of using this optical approach as a powerful new investigative tool for future biomedical research. For this study, our optical system was utilized for the first time to analyze lipid and collagen profiles in cereblon knockout (KO) mouse skin, and we were able to discover significant alterations in the number of carbon-carbon double bonds (wild-type vs. cereblon KO; NCC : 0.75 vs. 0.85) of skin fatty acids in triacylglycerides as well as changes in dermal collagen fibers (25% reduction in cereblon KO). By adopting our optical system to biological studies, we provide researchers with another diagnostic approach to validate their experimental results, which will significantly advance the state of biomedical research.
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Affiliation(s)
- Chang Woo Park
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Seungje Jeon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
- Smart Marine Therapeutics Center, Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea
| | - Seong-Hoon Kwon
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk, South Korea
| | - Jun-Hyung Jung
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Jung Eun Seol
- Smart Marine Therapeutics Center, Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea
- Department of Dermatology, Inje University Busan Paik Hospital, Inje University, Busan, South Korea
| | - Chul-Seung Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Steve K Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Do-Kyeong Ko
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju, South Korea
- Research Center for Photon Science Technology, Gwangju Institute of Science and Technology, Gwangju, South Korea
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12
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Xu M, Zhang Y, Wan Y, Luo L, Peng J. Single-Shot Multi-Frequency 3D Shape Measurement for Discontinuous Surface Object Based on Deep Learning. Micromachines (Basel) 2023; 14:328. [PMID: 36838028 PMCID: PMC9964939 DOI: 10.3390/mi14020328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
It is challenging to stably and rapidly achieve accurate absolute phase retrieval for isolated objects with a single-shot pattern in fringe projection profilometry (FPP). In this context, a single-shot multi-frequency absolute phase retrieval (SAPR-DL) method based on deep learning is proposed, which only needs to capture one fringe image to obtain the full-field precise absolute phase. Specifically, a low-frequency deformed fringe image is loaded into the trained one-to-two deep learning framework (DLFT) to predict unit-frequency and high-frequency deformed fringe images. Then, three fringe images with different frequencies are loaded into the trained deep learning phase retrieval framework (DLPR) to calculate the corresponding absolute phase. The experimental results prove that the proposed SAPR-DL method can obtain the three-dimensional (3D) shape measurement of multiple complex objects by collecting a single-shot fringe image, showing great prospects in advancing scientific and engineering applications.
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13
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Hyder R, Cai Z, Asif MS. Learning to Sense for Coded Diffraction Imaging. Sensors (Basel) 2022; 22:9964. [PMID: 36560332 PMCID: PMC9788068 DOI: 10.3390/s22249964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
In this paper, we present a framework to learn illumination patterns to improve the quality of signal recovery for coded diffraction imaging. We use an alternating minimization-based phase retrieval method with a fixed number of iterations as the iterative method. We represent the iterative phase retrieval method as an unrolled network with a fixed number of layers where each layer of the network corresponds to a single step of iteration, and we minimize the recovery error by optimizing over the illumination patterns. Since the number of iterations/layers is fixed, the recovery has a fixed computational cost. Extensive experimental results on a variety of datasets demonstrate that our proposed method significantly improves the quality of image reconstruction at a fixed computational cost with illumination patterns learned only using a small number of training images.
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14
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Han M, Smith D, Ng SH, Katkus T, John Francis Rajeswary AS, Praveen PA, Bambery KR, Tobin MJ, Vongsvivut J, Juodkazis S, Anand V. Single Shot Lensless Interferenceless Phase Imaging of Biochemical Samples Using Synchrotron near Infrared Beam. Biosensors (Basel) 2022; 12:1073. [PMID: 36551040 PMCID: PMC9775640 DOI: 10.3390/bios12121073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Phase imaging of biochemical samples has been demonstrated for the first time at the Infrared Microspectroscopy (IRM) beamline of the Australian Synchrotron using the usually discarded near-IR (NIR) region of the synchrotron-IR beam. The synchrotron-IR beam at the Australian Synchrotron IRM beamline has a unique fork shaped intensity distribution as a result of the gold coated extraction mirror shape, which includes a central slit for rejection of the intense X-ray beam. The resulting beam configuration makes any imaging task challenging. For intensity imaging, the fork shaped beam is usually tightly focused to a point on the sample plane followed by a pixel-by-pixel scanning approach to record the image. In this study, a pinhole was aligned with one of the lobes of the fork shaped beam and the Airy diffraction pattern was used to illuminate biochemical samples. The diffracted light from the samples was captured using a NIR sensitive lensless camera. A rapid phase-retrieval algorithm was applied to the recorded intensity distributions to reconstruct the phase information. The preliminary results are promising to develop multimodal imaging capabilities at the IRM beamline of the Australian Synchrotron.
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Affiliation(s)
- Molong Han
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Daniel Smith
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Soon Hock Ng
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Tomas Katkus
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | | | | | - Keith R. Bambery
- Infrared Microspectroscopy (IRM) Beamline, ANSTO—Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Mark J. Tobin
- Infrared Microspectroscopy (IRM) Beamline, ANSTO—Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Jitraporn Vongsvivut
- Infrared Microspectroscopy (IRM) Beamline, ANSTO—Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Saulius Juodkazis
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Tokyo Tech World Research Hub Initiative, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Vijayakumar Anand
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
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15
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Ochner H, Szilagyi S, Edte M, Malavolti L, Rauschenbach S, Kern K. Phase Reconstruction of Low-Energy Electron Holograms of Individual Proteins. ACS Nano 2022; 16:18568-18578. [PMID: 36367752 PMCID: PMC9706659 DOI: 10.1021/acsnano.2c06897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Low-energy electron holography (LEEH) is one of the few techniques capable of imaging large and complex three-dimensional molecules, such as proteins, on the single-molecule level at subnanometer resolution. During the imaging process, the structural information about the object is recorded both in the amplitude and in the phase of the hologram. In low-energy electron holography imaging of proteins, the object's amplitude distribution, which directly reveals molecular size and shape on the single-molecule level, can be retrieved via a one-step reconstruction process. However, such a one-step reconstruction routine cannot directly recover the phase information encoded in the hologram. In order to extract the full information about the imaged molecules, we thus implemented an iterative phase retrieval algorithm and applied it to experimentally acquired low-energy electron holograms, reconstructing the phase shift induced by the protein along with the amplitude data. We show that phase imaging can map the projected atomic density of the molecule given by the number of atoms in the electron path. This directly implies a correlation between reconstructed phase shift and projected mean inner potential of the molecule, and thus a sensitivity to local changes in potential, an interpretation that is further substantiated by the strong phase signatures induced by localized charges.
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Affiliation(s)
- Hannah Ochner
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
| | - Sven Szilagyi
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
| | - Moritz Edte
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
| | - Luigi Malavolti
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
| | - Stephan Rauschenbach
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Klaus Kern
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
- Institut
de Physique, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
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16
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Wang J, Li Y, Ji Y, Qian J, Che Y, Zuo C, Chen Q, Feng S. Deep Learning-Based 3D Measurements with Near-Infrared Fringe Projection. Sensors (Basel) 2022; 22:s22176469. [PMID: 36080928 PMCID: PMC9460471 DOI: 10.3390/s22176469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 05/27/2023]
Abstract
Fringe projection profilometry (FPP) is widely applied to 3D measurements, owing to its advantages of high accuracy, non-contact, and full-field scanning. Compared with most FPP systems that project visible patterns, invisible fringe patterns in the spectra of near-infrared demonstrate fewer impacts on human eyes or on scenes where bright illumination may be avoided. However, the invisible patterns, which are generated by a near-infrared laser, are usually captured with severe speckle noise, resulting in 3D reconstructions of limited quality. To cope with this issue, we propose a deep learning-based framework that can remove the effect of the speckle noise and improve the precision of the 3D reconstruction. The framework consists of two deep neural networks where one learns to produce a clean fringe pattern and the other to obtain an accurate phase from the pattern. Compared with traditional denoising methods that depend on complex physical models, the proposed learning-based method is much faster. The experimental results show that the measurement accuracy can be increased effectively by the presented method.
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Affiliation(s)
- Jinglei Wang
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Yixuan Li
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Yifan Ji
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Jiaming Qian
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Yuxuan Che
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Chao Zuo
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Qian Chen
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
| | - Shijie Feng
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Smart Computational Imaging Research Institute (SCIRI), Nanjing University of Science and Technology, Nanjing 210019, China
- Jiangsu Key Laboratory of Spectral Imaging and Intelligent Sense, Nanjing 210094, China
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17
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Nguyen TL, Pradeep S, Judson-Torres RL, Reed J, Teitell MA, Zangle TA. Quantitative Phase Imaging: Recent Advances and Expanding Potential in Biomedicine. ACS Nano 2022; 16:11516-11544. [PMID: 35916417 PMCID: PMC10112851 DOI: 10.1021/acsnano.1c11507] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Quantitative phase imaging (QPI) is a label-free, wide-field microscopy approach with significant opportunities for biomedical applications. QPI uses the natural phase shift of light as it passes through a transparent object, such as a mammalian cell, to quantify biomass distribution and spatial and temporal changes in biomass. Reported in cell studies more than 60 years ago, ongoing advances in QPI hardware and software are leading to numerous applications in biology, with a dramatic expansion in utility over the past two decades. Today, investigations of cell size, morphology, behavior, cellular viscoelasticity, drug efficacy, biomass accumulation and turnover, and transport mechanics are supporting studies of development, physiology, neural activity, cancer, and additional physiological processes and diseases. Here, we review the field of QPI in biology starting with underlying principles, followed by a discussion of technical approaches currently available or being developed, and end with an examination of the breadth of applications in use or under development. We comment on strengths and shortcomings for the deployment of QPI in key biomedical contexts and conclude with emerging challenges and opportunities based on combining QPI with other methodologies that expand the scope and utility of QPI even further.
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18
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Biran I, Houben L, Weissman H, Hildebrand M, Kronik L, Rybtchinski B. Real-Space Crystal Structure Analysis by Low-Dose Focal-Series TEM Imaging of Organic Materials with Near-Atomic Resolution. Adv Mater 2022; 34:e2202088. [PMID: 35451121 DOI: 10.1002/adma.202202088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Structural analysis of beam-sensitive materials by transmission electron microscopy (TEM) represents a significant challenge, as high-resolution TEM (HRTEM) requires high electron doses that limit its applicability to stable inorganic materials. Beam-sensitive materials, e.g., organic crystals, must be imaged under low dose conditions, leading to problematic contrast interpretation and loss of fine structural details. Here, HRTEM imaging of organic crystalline materials with near-atomic resolution of up to 1.6 Å is described, which enables real-space studies of crystal structures, as well as observation of co-existing polymorphs, crystal defects, and atoms. This is made possible by a low-dose focal-series reconstruction methodology, which provides HRTEM images where contrast reflects true object structure and can be performed on contemporary cryo-EM instruments available to many research institutions. Copper phthalocyanine (CuPc), a perchlorinated analogue of CuPc, and indigo crystalline films are imaged. In the case of indigo crystals, co-existing polymorphs and individual atoms (carbonyl oxygen) can be observed. In the case of CuPc, several polymorphs are observed, including a new one, for which the crystal structure is found based on direct in-focus imaging, accomplishing real-space crystal structure elucidation. Such direct analysis can be transformative for structure studies of organic materials.
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Affiliation(s)
- Idan Biran
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lothar Houben
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Weissman
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Mariana Hildebrand
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Leeor Kronik
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Boris Rybtchinski
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
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19
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Sun W, Pyakurel U, MacDonald C, Petruccelli J. Grating-free quantitative phase retrieval for x-ray phase-contrast imaging with conventional sources. Biomed Phys Eng Express 2022; 8. [PMID: 35623335 DOI: 10.1088/2057-1976/ac741d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/27/2022] [Indexed: 11/11/2022]
Abstract
X-ray phase-contrast imaging can display subtle differences in low-density materials (e.g., soft tissues) more readily than conventional x-ray imaging. However, producing x-ray phase images requires significant spatial coherence of the beam which requires highly specialized sources such as synchrotrons, small and low power microfocus sources, or complex procedures, such as multiple exposures with several carefully stepped precision gratings. To find appropriate approaches for producing x-ray phase-contrast imaging in a clinically meaningful way, we employed a grating-free method that utilized a low-cost, coarse wire mesh and simple processing. This method relaxes the spatial coherence constraint and allows quantitative phase retrieval for not only monochromatic but also polychromatic beams. We also combined the mesh-based system with polycapillary optics to significantly improve the accuracy of quantitative phase retrieval.
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Affiliation(s)
- Weiyuan Sun
- Department of Physics, University at Albany, 1400 Washington Ave, Albany, New York, 12222, UNITED STATES
| | - Uttam Pyakurel
- Department of Physics, University at Albany, 1400 Washington Ave, Albany, New York, 12222, UNITED STATES
| | - Carolyn MacDonald
- Department of Physics, University at Albany, 1400 Washington Ave, Albany, New York, 12222, UNITED STATES
| | - Jonathan Petruccelli
- Department of Physics, University at Albany, 1400 Washington Ave, Albany, Albany, New York, 12222-1000, UNITED STATES
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20
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Xing C, Qi F, Guo S. Enhanced Terahertz Phase Retrieval Imaging by Unequal Spaced Measurement. Sensors (Basel) 2022; 22:3816. [PMID: 35632225 PMCID: PMC9148081 DOI: 10.3390/s22103816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Terahertz lensless phase retrieval imaging is a promising technique for non-destructive inspection applications. In the conventional multiple-plane phase retrieval method, the convergence speed due to wave propagations and measures with equal interval distance is slow and leads to stagnation. To address this drawback, we propose a nonlinear unequal spaced measurement scheme in which the interval space between adjacent measurement planes is gradually increasing, it can significantly increase the diversity of the intensity with a smaller number of required images. Both the simulation and experimental results demonstrate that our method enables quantitative phase and amplitude imaging with a faster speed and better image quality, while also being computationally efficient and robust to noise.
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Affiliation(s)
- Chungui Xing
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, China;
| | - Feng Qi
- Key Laboratory of Opto-Electronic Information Processing, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110169, China;
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- Key Laboratory of Liaoning Province in Terahertz Imaging and Sensing, Shenyang 110169, China
| | - Shuxu Guo
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, China;
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21
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Schaff F, Pollock JA, Morgan KS, Kitchen MJ. Spectral propagation-based x-ray phase-contrast computed tomography. J Med Imaging (Bellingham) 2022; 9:031506. [PMID: 35310451 PMCID: PMC8923692 DOI: 10.1117/1.jmi.9.3.031506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/23/2022] [Indexed: 11/14/2022] Open
Abstract
Purpose: Propagation-based x-ray imaging (PBI) is a phase-contrast technique that is employed in high-resolution imaging by introducing some distance between sample and detector. PBI causes characteristic intensity fringes that have to be processed with appropriate phase-retrieval algorithms, which has historically been a difficult task for objects composed of several different materials. Spectral x-ray imaging has been introduced to PBI to overcome this issue and to potentially utilize the spectral nature of the data for material-specific imaging. We aim to explore the potential of spectral PBI in three-dimensional computed tomography (CT) imaging in this work. Approach: We demonstrate phase-retrieval for experimental high-resolution spectral propagation-based CT data of a simple two-component sample, as well as a multimaterial capacitor test sample. Phase-retrieval was performed using an algorithm based on the Alvarez-Macovski model. Virtual monochromatic (VMI) and effective atomic number images were calculated after phase-retrieval. Results: Phase-retrieval results from the spectral data set show a distinct gray-level for each material with no residual phase-contrast fringes. Several representations of the phase-retrieved data are provided. The VMI is used to display an attenuation-equivalent image at a chosen display energy of 80 keV, to provide good separation of materials with minimal noise. The effective atomic number image shows the material composition of the sample. Conclusions: Spectral photon-counting detector technology has already been shown to be compatible with spectral PBI, and there is a foreseeable need for robust phase-retrieval in high-resolution, spectral x-ray CT in the future. Our results demonstrate the feasibility of phase-retrieval for spectral PBI CT.
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Affiliation(s)
- Florian Schaff
- Monash University, School of Physics and Astronomy, Clayton, Victoria, Australia
| | - James A Pollock
- Monash University, School of Physics and Astronomy, Clayton, Victoria, Australia
| | - Kaye S Morgan
- Monash University, School of Physics and Astronomy, Clayton, Victoria, Australia
| | - Marcus J Kitchen
- Monash University, School of Physics and Astronomy, Clayton, Victoria, Australia.,Monash University, The Ritchie Centre, Clayton, Victoria, Australia
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22
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Wolf A, Akstaller B, Cipiccia S, Flenner S, Hagemann J, Ludwig V, Meyer P, Schropp A, Schuster M, Seifert M, Weule M, Michel T, Anton G, Funk S. Single-exposure X-ray phase imaging microscopy with a grating interferometer. J Synchrotron Radiat 2022; 29:794-806. [PMID: 35511012 PMCID: PMC9070728 DOI: 10.1107/s160057752200193x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
The advent of hard X-ray free-electron lasers enables nanoscopic X-ray imaging with sub-picosecond temporal resolution. X-ray grating interferometry offers a phase-sensitive full-field imaging technique where the phase retrieval can be carried out from a single exposure alone. Thus, the method is attractive for imaging applications at X-ray free-electron lasers where intrinsic pulse-to-pulse fluctuations pose a major challenge. In this work, the single-exposure phase imaging capabilities of grating interferometry are characterized by an implementation at the I13-1 beamline of Diamond Light Source (Oxfordshire, UK). For comparison purposes, propagation-based phase contrast imaging was also performed at the same instrument. The characterization is carried out in terms of the quantitativeness and the contrast-to-noise ratio of the phase reconstructions as well as via the achievable spatial resolution. By using a statistical image reconstruction scheme, previous limitations of grating interferometry regarding the spatial resolution can be mitigated as well as the experimental applicability of the technique.
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Affiliation(s)
- Andreas Wolf
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Bernhard Akstaller
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Silvia Cipiccia
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 ODE, United Kingdom
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Silja Flenner
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, D-21502 Geesthacht, Germany
| | - Johannes Hagemann
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
- Helmholtz Imaging Platform, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Veronika Ludwig
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Pascal Meyer
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Andreas Schropp
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
- Helmholtz Imaging Platform, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Max Schuster
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Maria Seifert
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Mareike Weule
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Thilo Michel
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Gisela Anton
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
| | - Stefan Funk
- Erlangen Centre for Astroparticle Physics (ECAP), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erwin-Rommel-Strasse 1, D-91058 Erlangen, Germany
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Migga A, Schulz G, Rodgers G, Osterwalder M, Tanner C, Blank H, Jerjen I, Salmon P, Twengström W, Scheel M, Weitkamp T, Schlepütz CM, Bolten JS, Huwyler J, Hotz G, Madduri S, Müller B. Comparative hard x-ray tomography for virtual histology of zebrafish larva, human tooth cementum, and porcine nerve. J Med Imaging (Bellingham) 2022; 9:031507. [PMID: 35372637 PMCID: PMC8968075 DOI: 10.1117/1.jmi.9.3.031507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/08/2022] [Indexed: 07/26/2023] Open
Abstract
Purpose: Synchrotron radiation-based tomography yields microanatomical features in human and animal tissues without physical slicing. Recent advances in instrumentation have made laboratory-based phase tomography feasible. We compared the performance of three cutting-edge laboratory systems benchmarked by synchrotron radiation-based tomography for three specimens. As an additional criterion, the user-friendliness of the three microtomography systems was considered. Approach: The three tomography systems-SkyScan 2214 (Bruker-microCT, Kontich, Belgium), Exciscope prototype (Stockholm, Sweden), and Xradia 620 Versa (Zeiss, Oberkochen, Germany)-were given 36 h to measure three medically relevant specimens, namely, zebrafish larva, archaeological human tooth, and porcine nerve. The obtained datasets were registered to the benchmark synchrotron radiation-based tomography from the same specimens and selected ones to the SkyScan 1275 and phoenix nanotom m® laboratory systems to characterize development over the last decade. Results: Next-generation laboratory-based microtomography almost reached the quality achieved by synchrotron-radiation facilities with respect to spatial and density resolution, as indicated by the visualization of the medically relevant microanatomical features. The SkyScan 2214 system and the Exciscope prototype demonstrated the complementarity of phase information by imaging the eyes of the zebrafish larva. The 3 - μ m thin annual layers in the tooth cementum were identified using Xradia 620 Versa. Conclusions: SkyScan 2214 was the simplest system and was well-suited to visualizing the wealth of anatomical features in the zebrafish larva. Data from the Exciscope prototype with the high photon flux from the liquid metal source showed the spiral nature of the myelin sheaths in the porcine nerve. Xradia 620 Versa, with detector optics as typically installed for synchrotron tomography beamlines, enabled the three-dimensional visualization of the zebrafish larva with comparable quality to the synchrotron data and the annual layers in the tooth cementum.
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Affiliation(s)
- Alexandra Migga
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Georg Schulz
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, Allschwil, Switzerland
| | - Griffin Rodgers
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Melissa Osterwalder
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Christine Tanner
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | | | | | | | | | | | | | | | - Jan S. Bolten
- University of Basel, Pharmaceutical Technology, Department of Pharmaceutical Sciences, Basel, Switzerland
| | - Jörg Huwyler
- University of Basel, Pharmaceutical Technology, Department of Pharmaceutical Sciences, Basel, Switzerland
| | - Gerhard Hotz
- Natural History Museum of Basel, Anthropological Collection, Basel, Switzerland
- University of Basel, Integrative Prehistory and Archaeological Science, Basel, Switzerland
| | - Srinivas Madduri
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Geneva, Department of Surgery, Geneva, Switzerland
- University Hospital Basel, Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, Basel, Switzerland
| | - Bert Müller
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
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Faragó T, Gasilov S, Emslie I, Zuber M, Helfen L, Vogelgesang M, Baumbach T. Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography. J Synchrotron Radiat 2022; 29:916-927. [PMID: 35511025 PMCID: PMC9070706 DOI: 10.1107/s160057752200282x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/14/2022] [Indexed: 06/01/2023]
Abstract
Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.
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Affiliation(s)
- Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sergey Gasilov
- Canadian Light Source, 44 Innovation Blvd, Saskatoon, Canada S7N 2V3
| | - Iain Emslie
- Canadian Light Source, 44 Innovation Blvd, Saskatoon, Canada S7N 2V3
| | - Marcus Zuber
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Lukas Helfen
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Matthias Vogelgesang
- Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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Ma X, Wang J, Wang B, Liu X. Measurement of Small-Slope Free-Form Optical Surfaces with the Modified Phase Retrieval. Micromachines (Basel) 2022; 13:mi13010082. [PMID: 35056247 PMCID: PMC8779078 DOI: 10.3390/mi13010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022]
Abstract
In this paper, we demonstrate the use of the modified phase retrieval as a method for application in the measurement of small-slope free-form optical surfaces. This technique is a solution for the measurement of small-slope free-form optical surfaces, based on the modified phase retrieval algorithm, whose essence is that only two defocused images are needed to estimate the wave front with an accuracy similar to that of the traditional phase retrieval but with less image capturing and computation time. An experimental arrangement used to measure the small-slope free-form optical surfaces using the modified phase retrieval is described. The results of these experiments demonstrate that the modified phase retrieval method can achieve measurements comparable to those of the standard interferometer.
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26
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Yu C, Wang S, Chen R, Hao J, Zheng Q, Wang J, Qiu X, Wang K, Lin D, Yang Y, Li H, Lin X, Tan X. Improved phase retrieval in holographic data storage based on a designed iterative embedded data. Front Optoelectron 2021; 14:529-539. [PMID: 36637766 PMCID: PMC9743944 DOI: 10.1007/s12200-021-1218-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/17/2021] [Indexed: 06/17/2023]
Abstract
Embedded data are used to retrieve phases quicker with high accuracy in phase-modulated holographic data storage (HDS). We propose a method to design an embedded data distribution using iterations to enhance the intensity of the high-frequency signal in the Fourier spectrum. The proposed method increases the antinoise performance and signal-to-noise ratio (SNR) of the Fourier spectrum distribution, realizing a more efficient phase retrieval. Experiments indicate that the bit error rate (BER) of this method can be reduced by a factor of one after 10 iterations.
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Affiliation(s)
- Changyu Yu
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Suping Wang
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Ruixian Chen
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Jianying Hao
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Qijing Zheng
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Jinyu Wang
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Xianying Qiu
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Kun Wang
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
- Fujian Provincial Key Laboratory of Photonics Technology, Fuzhou, 350117, China
| | - Dakui Lin
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Yi Yang
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Hui Li
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fuzhou, 350117, China
| | - Xiao Lin
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China.
- Wuhan National Laboratory for Optoelectronics, Wuhan, 430074, China.
| | - Xiaodi Tan
- Information Photonics Research Center, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China.
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27
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Ghani MU, Fajardo LL, Omoumi F, Yan A, Jenkins P, Wong M, Li Y, Peterson ME, Callahan EJ, Hillis SL, Zheng B, Wu X, Liu H. A phase sensitive x-ray breast tomosynthesis system: Preliminary patient images with cancer lesions. Phys Med Biol 2021; 66. [PMID: 34633295 DOI: 10.1088/1361-6560/ac2ea6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/11/2021] [Indexed: 11/11/2022]
Abstract
Phase-sensitive x-ray imaging continues to attract research for its ability to visualize weakly absorbing details like those often encountered in biology and medicine. We have developed and assembled the first inline-based high-energy phase sensitive breast tomosynthesis (PBT) system, which is currently undergoing patient imaging testing at a clinical site. The PBT system consists of a microfocus polychromatic x-ray source and a direct conversion-based flat panel detector coated with a 1 mm thick amorphous selenium layer allowing a high detective quantum efficiency at high energies. The PBT system scans a compressed breast over 15° with 9 angular projection views. The high-energy scan parameters are carefully selected to ensure similar or lower mean glandular dose levels to the clinical standard of care systems. Phase retrieval and data binning are applied to the phase contrast angular projection views and a filtered back-projection algorithm is used to reconstruct the final images. This article reports the distributions of radiation dose versus thickness of the compressed breasts at 59 and 89 kV and sample PBT images acquired from 3 patients. Preliminary PBT images demonstrate the feasibility of this new imaging modality to acquire breast images at lower radiation dose as compared to the clinical digital breast tomosynthesis system with enhanced lesion characteristics (i.e. lesion spiculation and margins).
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Affiliation(s)
- Muhammad U Ghani
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
| | - Laurie L Fajardo
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT 84132, United States of America
| | - Farid Omoumi
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
| | - Aimin Yan
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
| | - Peter Jenkins
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT 84132, United States of America
| | - Molly Wong
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
| | - Yuhua Li
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
| | - Michael E Peterson
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT 84132, United States of America
| | - Edward J Callahan
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT 84132, United States of America
| | - Stephen L Hillis
- Departments of Radiology and Biostatistics, University of Iowa, Iowa City, IA 52242, United States of America
| | - Bin Zheng
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
| | - Xizeng Wu
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35249, United States of America
| | - Hong Liu
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, United States of America
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28
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Findlay SD, Brown HG, Pelz PM, Ophus C, Ciston J, Allen LJ. Scattering Matrix Determination in Crystalline Materials from 4D Scanning Transmission Electron Microscopy at a Single Defocus Value. Microsc Microanal 2021; 27:744-757. [PMID: 34311809 DOI: 10.1017/s1431927621000490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent work has revived interest in the scattering matrix formulation of electron scattering in transmission electron microscopy as a stepping stone toward atomic-resolution structure determination in the presence of multiple scattering. We discuss ways of visualizing the scattering matrix that make its properties clear. Through a simulation-based case study incorporating shot noise, we shown how regularizing on this continuity enables the scattering matrix to be reconstructed from 4D scanning transmission electron microscopy (STEM) measurements from a single defocus value. Intriguingly, for crystalline samples, this process also yields the sample thickness to nanometer accuracy with no a priori knowledge about the sample structure. The reconstruction quality is gauged by using the reconstructed scattering matrix to simulate STEM images at defocus values different from that of the data from which it was reconstructed.
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Affiliation(s)
- Scott D Findlay
- School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
| | - Hamish G Brown
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
- Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC3052, Australia
| | - Philipp M Pelz
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA94720, USA
| | - Colin Ophus
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
| | - Jim Ciston
- National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
| | - Leslie J Allen
- School of Physics, University of Melbourne, Parkville, VIC3010, Australia
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29
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Langer M, Zhang Y, Figueirinhas D, Forien JB, Mom K, Mouton C, Mokso R, Villanueva-Perez P. PyPhase - a Python package for X-ray phase imaging. J Synchrotron Radiat 2021; 28:1261-1266. [PMID: 34212892 PMCID: PMC8284402 DOI: 10.1107/s1600577521004951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 06/01/2023]
Abstract
X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).
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Affiliation(s)
- Max Langer
- Univ Lyon, INSA Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1206, F-69621 Villeurbanne, France
| | - Yuhe Zhang
- Division of Synchrotron Radiation Research and NanoLund, Department of Physics, Lund University, SE-221 00 Lund, Sweden
| | - Diogo Figueirinhas
- Division of Packaging Logistics, Faculty of Engineering, Lund University, SE-22100 Lund, Sweden
- MAX IV Laboratory, Lund University, SE-22100 Lund, Sweden
| | | | - Kannara Mom
- Univ Lyon, INSA Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1206, F-69621 Villeurbanne, France
| | - Claire Mouton
- Univ Lyon, INSA Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1206, F-69621 Villeurbanne, France
| | - Rajmund Mokso
- Division of Solid Mechanics, Faculty of Engineering, Lund University, SE-22100 Lund, Sweden
| | - Pablo Villanueva-Perez
- Division of Synchrotron Radiation Research and NanoLund, Department of Physics, Lund University, SE-221 00 Lund, Sweden
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Tang R, Li Y, Qin L, Yan F, Yang GY, Chen KM. Phase retrieval-based phase-contrast CT for vascular imaging with microbubble contrast agent. Med Phys 2021; 48:3459-3469. [PMID: 33657645 DOI: 10.1002/mp.14819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 11/11/2022] Open
Abstract
PURPOSE The introduction of microbubble contrast agent into tissues can create significant phase shifts. Phase retrieval (PR)-based phase-contrast computed tomography (PCCT) is an imaging method for retrieving and reconstructing the phase shifts within an object. This study aimed to evaluate the feasibility of PR-based PCCT with microbubble contrast agent for vascular imaging. METHODS Projection phase-contrast images of individual microbubbles and a cluster of microbubbles were captured and compared. Contrast enhancement from microbubbles was evaluated by comparing to the gold standard iodine-based contrast agent in vitro. The arterial systems of 14 Sprague-Dawley rats were perfused with microbubbles or saline. The rat hearts and the arterial systems were excised and imaged ex vivo. CT imaging was performed at the energy of 22 keV. PR was performed using the phase-attenuation duality (PAD) method with different δ/β values (PAD property). The contrast-to-noise ratio (CNR) was used for quantitatively assessing the contrast enhancement. RESULTS Individual microbubbles functioned as a lens to focus the x rays, whereas, a cluster of microbubbles scattered the x rays. In the in vitro experiment, the contrast enhancement from iodine was significantly greater than that from microbubbles (P < 0.05). In the heart samples, the CNRs for microbubbles on PR-based PCCT were significantly greater than those on absorption-contrast CT (ACCT) and PR-free PCCT (both P < 0.001). The CNRs for microbubbles were also significantly greater than those for saline on PR-based PCCT in the samples (P < 0.001). Although they provided weaker contrast enhancement than that from iodine, microbubbles could still provide sufficient contrast enhancement to clearly show the 3D architecture of rat aortas and their main branches. CONCLUSION The imaging modality can currently be used as a complement or alternative to absorption-based microCT for imaging vessels in biological samples.
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Affiliation(s)
- Rongbiao Tang
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Yongfang Li
- Department of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Le Qin
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Fuhua Yan
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
| | - Guo-Yuan Yang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ke-Min Chen
- Department of Radiology, Rui Jin Hospital, Shanghai Jiao Tong University, and School of Medicine, Shanghai, China
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Wu Z, Gao K, Wang Z, Wang S, Zhu P, Ren Y, Tian Y. Generalized reverse projection method for grating-based phase tomography. J Synchrotron Radiat 2021; 28:854-863. [PMID: 33949993 DOI: 10.1107/s1600577521001806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
The reverse projection protocol results in fast phase-contrast imaging thanks to its compatibility with conventional computed-tomography scanning. Many researchers have proposed variants. However, all these reverse projection methods in grating-based phase-contrast imaging are built on the hypothesis of the synchronous phase of reference shifting curves in the whole field of view. The hypothesis imposes uniformity and alignment requirements on the gratings, thus the field of view is generally limited. In this paper, a generalized reverse projection method is presented analytically for the case of non-uniform reference in grating-based phase tomography. The method is demonstrated by theoretical derivation, numerical simulations and synchrotron radiation experiments. The influence of imaging position to sensitivity, and the phase-wrapping phenomenon are also discussed. The proposed method combines the advantages of the high efficiency of the reverse projection method and the universal applicability of the phase-stepping method. The authors believe that the method would be used widely in fast and dose-constrained imaging.
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Affiliation(s)
- Zhao Wu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People's Republic of China
| | - Kun Gao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People's Republic of China
| | - Zhili Wang
- School of Electronic Science and Applied Physics, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Shengxiang Wang
- Institute of High-Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Peiping Zhu
- Institute of High-Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuqi Ren
- Shanghai Synchrotron Radiation Facility, Chinese Academy of Sciences, Shanghai 201204, People's Republic of China
| | - Yangchao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People's Republic of China
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Ghani MU, Wu X, Fajardo LL, Jing Z, Wong MD, Zheng B, Omoumi F, Li Y, Yan A, Jenkins P, Hillis SL, Linstroth L, Liu H. Development and preclinical evaluation of a patient-specific high energy x-ray phase sensitive breast tomosynthesis system. Med Phys 2021; 48:2511-2520. [PMID: 33523479 DOI: 10.1002/mp.14743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND This article reports the first x-ray phase sensitive breast tomosynthesis (PBT) system that is aimed for direct translation to clinical practice for the diagnosis of breast cancer. PURPOSE To report the preclinical evaluation and comparison of the newly built PBT system with a conventional digital breast tomosynthesis (DBT) system. METHODS AND MATERIALS The PBT system is developed based on a comprehensive inline phase contrast theoretical model. The system consists of a polyenergetic microfocus x-ray source and a flat panel detector mounted on an arm that is attached to a rotating gantry. It acquires nine projections over a 15° angular span in a stop-and-shoot manner. A dedicated phase retrieval algorithm is integrated with a filtered back-projection method that reconstructs tomographic slices. The American College of Radiology (ACR) accreditation phantom, a contrast detail (CD) phantom and mastectomy tissue samples were imaged at the same glandular dose levels by both the PBT and a standard of care DBT system for image quality characterizations and comparisons. RESULTS The PBT imaging scores with the ACR phantom are in good to excellent range and meet the quality assurance criteria set by the Mammography Quality Standard Act. The CD phantom image comparison and associated statistical analyses from two-alternative forced-choice reader studies confirm the improvement offered by the PBT system in terms of contrast resolution, spatial resolution, and conspicuity. The artifact spread function (ASF) analyses revealed a sizable lateral spread of metal artifacts in PBT slices as compared to DBT slices. Signal-to-noise ratio values for various inserts of the ACR and CD phantoms further validated the superiority of the PBT system. Mastectomy sample images acquired by the PBT system showed a superior depiction of microcalcifications vs the DBT system. CONCLUSION The PBT imaging technology can be clinically employed for improving the accuracy of breast cancer screening and diagnosis.
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Affiliation(s)
- Muhammad U Ghani
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA
| | - Xizeng Wu
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Laurie L Fajardo
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, 84132, USA
| | | | - Molly D Wong
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA
| | - Bin Zheng
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA
| | - Farid Omoumi
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA
| | - Yuhua Li
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA
| | - Aimin Yan
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Peter Jenkins
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, 84132, USA
| | - Stephen L Hillis
- Department of Radiology and Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Laura Linstroth
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, 84132, USA
| | - Hong Liu
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, 73019, USA
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33
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Mitome M. Transport of intensity equation method and its applications. Microscopy (Oxf) 2021; 70:69-74. [PMID: 33524150 DOI: 10.1093/jmicro/dfaa053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
A phase retrieval technique based on a transport of intensity equation (TIE) is one of the defocus series reconstruction techniques in microscopy. Since it does not require any dedicated devices like a biprism, and only three defocus images are enough to retrieve phase information, it has been applied to observe magnetic fields, magnetic domains, electrostatic potentials and strains. It is also used to improve image resolution by correcting spherical aberration. This technique is simple and easy to use, but some artifacts often appear in the retrieved phase map. One should pay careful attention to the experimental conditions and the algorithms and boundary conditions used to solve the TIE. This paper reviews the principle of the TIE method, the algorithms used to solve it and application results in materials science.
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Affiliation(s)
- Masanori Mitome
- Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki Tsukuba Ibaraki, 305-0044, Japan
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Chalmers MC, Kitchen MJ, Uesugi K, Falzon G, Quin P, Pavlov KM. Tomographic reconstruction using tilted Laue analyser-based X-ray phase-contrast imaging. J Synchrotron Radiat 2021; 28:283-291. [PMID: 33399579 DOI: 10.1107/s1600577520013995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Analyser-based phase-contrast imaging (ABPCI) is a highly sensitive phase-contrast imaging method that produces high-contrast images of weakly absorbing materials. However, it is only sensitive to phase gradient components lying in the diffraction plane of the analyser crystal [i.e. in one dimension (1-D)]. In order to accurately account for and measure phase effects produced by the wavefield-sample interaction, ABPCI and other 1-D phase-sensitive methods must achieve 2-D phase gradient sensitivity. An inclined geometry method was applied to a Laue geometry setup for X-ray ABPCI through rotation of the detector and object about the optical axis. This allowed this traditionally 1-D phase-sensitive phase-contrast method to possess 2-D phase gradient sensitivity. Tomographic datasets were acquired over 360° of a multi-material phantom with the detector and sample tilted by 8°. The real and imaginary parts of the refractive index were reconstructed for the phantom.
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Affiliation(s)
- M C Chalmers
- University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, Christchurch 8041, New Zealand
| | - M J Kitchen
- Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - K Uesugi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - G Falzon
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5001, Australia
| | - P Quin
- University of New England, Armidale, NSW 2351, Australia
| | - K M Pavlov
- University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, Christchurch 8041, New Zealand
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35
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Lu X, Wang Z, Zhang S, Konijnenberg AP, Ouyang Y, Zhao C, Cai Y. Microscopic phase reconstruction of cervical exfoliated cell under partially coherent illumination. J Biophotonics 2021; 14:e202000401. [PMID: 33128849 DOI: 10.1002/jbio.202000401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Basic coherent diffraction imaging methods strongly rely on having a highly coherent illumination in order to reconstruct the phase accurately. However, regardless of considering the turbulent transport medium, the instability of the system or the generation mechanism of the light source, partially coherent illumination is more common in real case. In this paper, we proposed an efficient microscopic phase imaging method to study normal and abnormal cervical exfoliated cells. By applying three phase modulations in a single point of the sample's transmitted field, the phase can be retrieved with correspoding three intensities under partially coherent illumination. Compared with intensity map, we can efficiently and clearly judge the proportion of high density shrinking abnormal cells from the phase distributions, which provides a confident analysis and evaluation basis for early medical diagnosis of cervical cancer. This study also has potential applications in noninvasive optical imaging of dynamic biological tissues.
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Affiliation(s)
- Xingyuan Lu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Zhuoyi Wang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Suxia Zhang
- Tongji Hospital of Tongji University, Shanghai, China
| | | | - Yiqin Ouyang
- Tongji Hospital of Tongji University, Shanghai, China
| | - Chengliang Zhao
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yangjian Cai
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong, China
- Shandong Provincial Engineering and Technical Center of Light Manipulations, Shandong Provincial Key Laboratory of Optics and Photonic Device, Jinan, Shandong, China
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36
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Abstract
The reconstruction of a single-particle image from the modulus of its Fourier transform, by phase-retrieval methods, has been extensively applied in X-ray structural science. Particularly for strong-phase objects, such as the phase domains found inside crystals by Bragg coherent diffraction imaging (BCDI), conventional iteration methods are time consuming and sensitive to their initial guess because of their iterative nature. Here, a deep-neural-network model is presented which gives a fast and accurate estimate of the complex single-particle image in the form of a universal approximator learned from synthetic data. A way to combine the deep-neural-network model with conventional iterative methods is then presented to refine the accuracy of the reconstructed results from the proposed deep-neural-network model. Improved convergence is also demonstrated with experimental BCDI data.
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Affiliation(s)
- Longlong Wu
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Pavol Juhas
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Shinjae Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ian Robinson
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- London Centre for Nanotechnology, University College London, London, WC1E 6BT, United Kingdom
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37
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Abstract
The potential for convolutional neural networks to provide real-time imaging capabilities for coherent diffraction imaging experiments at XFELs is discussed.
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Affiliation(s)
- Ross Harder
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
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Zboray R. Optimizing and applying high-resolution, in-line laboratory phase-contrast X-ray imaging for low-density material samples. J Microsc 2020; 282:123-135. [PMID: 33219697 DOI: 10.1111/jmi.12986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/24/2020] [Accepted: 11/18/2020] [Indexed: 11/29/2022]
Abstract
In-line, or propagation-based phase-contrast X-ray imaging (PBI) is an attractive alternative to the attenuation-based modality for low-density, soft samples showing low attenuation contrast. With the growing availability of micro- and nano-focus X-ray tubes, the method is increasingly applied in the laboratory. Here, we discuss the technique and demonstrate its advantages for selected low-density, low attenuation material samples using a lab-based micro- and nano-computed tomography systems Easytom XL Ultra, providing micron and sub-micron range resolution PBI images. We demonstrate a multi-step optimization of the lab-based PBI technique on our scanner that includes choosing the optimal detector-source hardware combination available in the setup, then optimizing the imaging geometry and finally the phase retrieval process through a parametric study. We point out and elaborate on the effect of noise correlation and texturing due to phase retrieval. We demonstrate the overall benefits of using the phase image and the phase retrieval for the selected samples such as improved image quality, increased contrast-to-noise ratio while only marginally influencing the spatial resolution. The improvement in image quality also enables further image processing steps for detailed structural analysis of the samples, which would be much more complicated if not impossible based on the transmission image.
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Affiliation(s)
- Robert Zboray
- Center for X-ray Analytics, Department Materials Meet Life, Swiss Federal Laboratories for Material Science and Technology, Empa, Überlandstrasse 129, Dübendorf, Switzerland
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Frohn J, Pinkert-Leetsch D, Missbach-Güntner J, Reichardt M, Osterhoff M, Alves F, Salditt T. 3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography. J Synchrotron Radiat 2020; 27:1707-1719. [PMID: 33147198 PMCID: PMC7642968 DOI: 10.1107/s1600577520011327] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 05/05/2023]
Abstract
A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick-Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s-1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.
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Affiliation(s)
- Jasper Frohn
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Diana Pinkert-Leetsch
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Jeannine Missbach-Güntner
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Marius Reichardt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Frauke Alves
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
- Clinic of Hematology and Medical Oncology, University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells (MBExC), University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
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40
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Geng Q, Fu Z, Chen SC. High-resolution 3D light-field imaging. J Biomed Opt 2020; 25:JBO-200169R. [PMID: 33047519 PMCID: PMC7548856 DOI: 10.1117/1.jbo.25.10.106502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
SIGNIFICANCE High-speed 3D imaging methods have been playing crucial roles in many biological discoveries. AIM We present a hybrid light-field imaging system and image processing algorithm that can visualize high-speed biological events. APPROACH The hybrid light-field imaging system uses the selective plane optical illumination, which simultaneously records a high-resolution 2D image and a low-resolution 4D light-field image. The high-resolution 4D light-field image is obtained by applying the hybrid algorithm derived from the deconvolution and phase retrieval methods. RESULTS High-resolution 3D imaging at a speed of 100-s volumes per second over an imaging field of 250 × 250 × 80 μm3 in the x, y, and z axis, respectively, is achieved with a 2.5 times enhancement in lateral resolution over the entire imaging field compared with standard light-field systems. In comparison to the deconvolution algorithm, the hybrid algorithm addresses the artifact issue at the focal plane and reduces the computation time by a factor of 4. CONCLUSIONS The new hybrid light-field imaging method realizes high-resolution and ultrafast 3D imaging with a compact setup and simple algorithm, which may help discover important applications in biophotonics to visualize high-speed biological events.
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Affiliation(s)
- Qiang Geng
- The Chinese University of Hong Kong, Department of Mechanical and Automation Engineering, Shatin, Hong Kong, China
| | - Zhiqiang Fu
- The Chinese University of Hong Kong, Department of Mechanical and Automation Engineering, Shatin, Hong Kong, China
| | - Shih-Chi Chen
- The Chinese University of Hong Kong, Department of Mechanical and Automation Engineering, Shatin, Hong Kong, China
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41
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Anand V, Katkus T, Linklater DP, Ivanova EP, Juodkazis S. Lensless Three-Dimensional Quantitative Phase Imaging Using Phase Retrieval Algorithm. J Imaging 2020; 6:99. [PMID: 34460756 DOI: 10.3390/jimaging6090099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022] Open
Abstract
Quantitative phase imaging (QPI) techniques are widely used for the label-free examining of transparent biological samples. QPI techniques can be broadly classified into interference-based and interferenceless methods. The interferometric methods which record the complex amplitude are usually bulky with many optical components and use coherent illumination. The interferenceless approaches which need only the intensity distribution and works using phase retrieval algorithms have gained attention as they require lesser resources, cost, space and can work with incoherent illumination. With rapid developments in computational optical techniques and deep learning, QPI has reached new levels of applications. In this tutorial, we discuss one of the basic optical configurations of a lensless QPI technique based on the phase-retrieval algorithm. Simulative studies on QPI of thin, thick, and greyscale phase objects with assistive pseudo-codes and computational codes in Octave is provided. Binary phase samples with positive and negative resist profiles were fabricated using lithography, and a single plane and two plane phase objects were constructed. Light diffracted from a point object is modulated by phase samples and the corresponding intensity patterns are recorded. The phase retrieval approach is applied for 2D and 3D phase reconstructions. Commented codes in Octave for image acquisition and automation using a web camera in an open source operating system are provided.
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42
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Heacock B, Sarenac D, Cory DG, Huber MG, MacLean JPW, Miao H, Wen H, Pushin DA. Neutron sub-micrometre tomography from scattering data. IUCrJ 2020; 7:893-900. [PMID: 32939281 PMCID: PMC7467166 DOI: 10.1107/s2052252520010295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/24/2020] [Indexed: 06/01/2023]
Abstract
Neutrons are valuable probes for various material samples across many areas of research. Neutron imaging typically has a spatial resolution of larger than 20 µm, whereas neutron scattering is sensitive to smaller features but does not provide a real-space image of the sample. A computed-tomography technique is demonstrated that uses neutron-scattering data to generate an image of a periodic sample with a spatial resolution of ∼300 nm. The achieved resolution is over an order of magnitude smaller than the resolution of other forms of neutron tomography. This method consists of measuring neutron diffraction using a double-crystal diffractometer as a function of sample rotation and then using a phase-retrieval algorithm followed by tomographic reconstruction to generate a map of the sample's scattering-length density. Topological features found in the reconstructions are confirmed with scanning electron micrographs. This technique should be applicable to any sample that generates clear neutron-diffraction patterns, including nanofabricated samples, biological membranes and magnetic materials, such as skyrmion lattices.
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Affiliation(s)
- B. Heacock
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
- Triangle Universities Nuclear Laboratory, Durham, NC 27708, USA
| | - D. Sarenac
- Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
- Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
| | - D. G. Cory
- Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
- Perimeter Institute for Theoretical Physics, Waterloo, Ontario, Canada N2L2Y5
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada M5G 1Z8
| | - M. G. Huber
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - J. P. W. MacLean
- Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
- Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
| | - H. Miao
- Biophysics and Biochemistry Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - H. Wen
- Biophysics and Biochemistry Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - D. A. Pushin
- Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
- Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L3G1
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43
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Blackburn AM, McLeod RA. Practical implementation of high-resolution electron ptychography and comparison with off-axis electron holography. Microscopy (Oxf) 2020; 70:131-147. [PMID: 32986121 DOI: 10.1093/jmicro/dfaa055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 11/13/2022] Open
Abstract
Ptychography is a coherent diffractive imaging technique that can determine how an electron wave is transmitted through an object by probing it in many small overlapping regions and processing the diffraction data obtained at each point. The resulting electron transmission model describes both phase and amplitude changes to the electron wave. Ptychography has been adopted in transmission electron microscopy in recent years following advances in high-speed direct electron detectors and computer algorithms which now make the technique suitable for practical applications. Its ability to retrieve quantitative phase information at high spatial resolution makes it a plausible alternative or complement to electron holography. Furthermore, unlike off-axis electron holography, it can provide phase information without an electron bi-prism assembly or the requirement of a minimally structured region adjacent to the region of interest in the object. However, it does require a well-calibrated scanning transmission electron microscope and a well-managed workflow to manage the calibration, data acquisition and reconstruction process to yield a practical technique. Here we detail this workflow and highlight how this is greatly assisted by acquisition management software. Through experimental data and modelling we also explore the similarities and differences between high-resolution ptychography and electron holography. Both techniques show a dependence of the recovered phase on the crystalline orientation of the material which is attributable to dynamical scattering. However, the exact nature of the variation differs reflecting fundamental expectations, but nonetheless equally useful information is obtained from electron holography and the ptychographically determined object transmission function.
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Affiliation(s)
- Arthur M Blackburn
- Department of Physics and Astronomy, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Robert A McLeod
- Nano Accessories Product Group, Hitachi High Technologies Canada, Inc., Etobicoke, ON M9W 6A4, Canada
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44
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Abstract
A method is presented for the measurement of the phase gradient of a wavefront by tracking the relative motion of speckles in projection holograms as a sample is scanned across the wavefront. By removing the need to obtain an undistorted reference image of the sample, this method is suitable for the metrology of highly divergent wavefields. Such wavefields allow for large magnification factors that, according to current imaging capabilities, will allow for nanoradian angular sensitivity and nanoscale sample projection imaging. Both the reconstruction algorithm and the imaging geometry are nearly identical to that of ptychography, except that the sample is placed downstream of the beam focus and that no coherent propagation is explicitly accounted for. Like other X-ray speckle tracking methods, it is robust to low-coherence X-ray sources, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology. A modified form of the speckle tracking approximation is also presented, based on a second-order local expansion of the Fresnel integral. This result extends the validity of the speckle tracking approximation and may be useful for similar approaches in the field.
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Affiliation(s)
- Andrew J. Morgan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Harry M. Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Saša Bajt
- DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henry N. Chapman
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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Lohse LM, Robisch AL, Töpperwien M, Maretzke S, Krenkel M, Hagemann J, Salditt T. A phase-retrieval toolbox for X-ray holography and tomography. J Synchrotron Radiat 2020; 27:852-859. [PMID: 32381790 PMCID: PMC7206550 DOI: 10.1107/s1600577520002398] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/19/2020] [Indexed: 05/10/2023]
Abstract
Propagation-based phase-contrast X-ray imaging is by now a well established imaging technique, which - as a full-field technique - is particularly useful for tomography applications. Since it can be implemented with synchrotron radiation and at laboratory micro-focus sources, it covers a wide range of applications. A limiting factor in its development has been the phase-retrieval step, which was often performed using methods with a limited regime of applicability, typically based on linearization. In this work, a much larger set of algorithms, which covers a wide range of cases (experimental parameters, objects and constraints), is compiled into a single toolbox - the HoloTomoToolbox - which is made publicly available. Importantly, the unified structure of the implemented phase-retrieval functions facilitates their use and performance test on different experimental data.
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Affiliation(s)
- Leon M. Lohse
- Institut für Röntgenphysik, Universität Göttingen, Germany
| | | | | | - Simon Maretzke
- Institut für Röntgenphysik, Universität Göttingen, Germany
| | - Martin Krenkel
- Institut für Röntgenphysik, Universität Göttingen, Germany
| | - Johannes Hagemann
- Institut für Röntgenphysik, Universität Göttingen, Germany
- Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Universität Göttingen, Germany
- Correspondence e-mail:
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Wakonig K, Stadler HC, Odstrčil M, Tsai EHR, Diaz A, Holler M, Usov I, Raabe J, Menzel A, Guizar-Sicairos M. PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data. J Appl Crystallogr 2020; 53:574-586. [PMID: 32280327 PMCID: PMC7133065 DOI: 10.1107/s1600576720001776] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/07/2020] [Indexed: 11/25/2022] Open
Abstract
A new computer program for analysing ptychographic data combines both high-level simplicity and high-performance computing on large-scale computing clusters. It is available with a royalty-free non-exclusive licence for academic and non-commercial purposes. Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen’s transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.
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Affiliation(s)
- Klaus Wakonig
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.,ETH and University of Zürich, Institute for Biomedical Engineering, 8093 Zürich, Switzerland
| | | | | | | | - Ana Diaz
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Mirko Holler
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Ivan Usov
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jörg Raabe
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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Nakano M, Miyashita O, Tama F. Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching. Biophys Physicobiol 2020; 16:367-376. [PMID: 31984191 PMCID: PMC6975998 DOI: 10.2142/biophysico.16.0_367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/09/2019] [Indexed: 12/01/2022] Open
Abstract
Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL.
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Affiliation(s)
- Miki Nakano
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aich 464-8602, Japan
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48
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Robisch AL, Eckermann M, Töpperwien M, van der Meer F, Stadelmann C, Salditt T. Nanoscale x-ray holotomography of human brain tissue with phase retrieval based on multienergy recordings. J Med Imaging (Bellingham) 2020; 7:013501. [PMID: 32016134 PMCID: PMC6975131 DOI: 10.1117/1.jmi.7.1.013501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/24/2019] [Indexed: 11/14/2022] Open
Abstract
X-ray cone-beam holotomography of unstained tissue from the human central nervous system reveals details down to subcellular length scales. This visualization of variations in the electron density of the sample is based on phase-contrast techniques using intensities formed by self-interference of the beam between object and detector. Phase retrieval inverts diffraction and overcomes the phase problem by constraints such as several measurements at different Fresnel numbers for a single projection. Therefore, the object-to-detector distance (defocus) can be varied. However, for cone-beam geometry, changing defocus changes magnification, which can be problematic in view of image processing and resolution. Alternatively, the photon energy can be altered (multi-E). Far from absorption edges, multi-E data yield the wavelength-independent electron density. We present the multi-E holotomography at the Göttingen Instrument for Nano-Imaging with X-Rays (GINIX) setup of the P10 beamline at Deutsches Elektronen-Synchrotron. The instrument is based on a combined optics of elliptical mirrors and an x-ray waveguide positioned in the focal plane for further coherence, spatial filtering, and high numerical aperture. Previous results showed the suitability of this instrument for nanoscale tomography of unstained brain tissue. We demonstrate that upon energy variation, the focal spot is stable enough for imaging. To this end, a double-crystal monochromator and automated alignment routines are required. Three tomograms of human brain tissue were recorded and jointly analyzed using phase retrieval based on the contrast transfer function formalism generalized to multiple photon energies. Variations of the electron density of the sample are successfully reconstructed.
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Affiliation(s)
- Anna-Lena Robisch
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany
| | - Marina Eckermann
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," Göttingen, Germany
| | - Mareike Töpperwien
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany
| | - Franziska van der Meer
- Universitätsmedizin Göttingen, Institut für Neuropathologie, Klinik für Neurologie, Göttingen, Germany
| | - Christine Stadelmann
- Universitätsmedizin Göttingen, Institut für Neuropathologie, Klinik für Neurologie, Göttingen, Germany
| | - Tim Salditt
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," Göttingen, Germany
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49
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Abstract
Plasmonic microscopy is a powerful tool for nanoscopic bio- and chemical sample analysis due to its high sensitivity. Phase quantification in plasmonic microscopy would provide inherent information, i.e., refractive index, for identification of nanomaterials. However, it usually relies on complex optics to acquire quantitative phase images. Here, we demonstrated the quantitative amplitude and phase imaging capabilities through holographical reconstructions of the plasmonic patterns recorded in the interferometric plasmonic microscopy. Operating the plasmonic microscopy over the surface plasmon resonance angle separates the twin images and allows for accurate mapping of the amplitude and phase distribution of surface plasmon near fields. Results show that the imaging capabilities enable direct visualization of complex surface plasmon fields arising from interactions with nanoparticles and nanowires, without the need for nanoscopic scanning probes. Theoretical and experimental analysis also suggests future applications in the identification of nanoparticles and super-resolution imaging. The proposed technology is thus promising for nanoplasmonic study and various sensing purposes.
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Affiliation(s)
- Yuting Yang
- Institute for Personalized Medicine, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200030 , China
| | - Chunhui Zhai
- Institute for Personalized Medicine, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200030 , China
| | - Qiang Zeng
- Institute for Personalized Medicine, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200030 , China
| | - Ab Lateef Khan
- Institute for Personalized Medicine, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200030 , China
| | - Hui Yu
- Institute for Personalized Medicine, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200030 , China
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50
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Zhang S, Zhou G, Wang Y, Hu Y, Hao Q. A Simply Equipped Fourier Ptychography Platform Based on an Industrial Camera and Telecentric Objective. Sensors (Basel) 2019; 19:s19224913. [PMID: 31717982 PMCID: PMC6891469 DOI: 10.3390/s19224913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 06/01/2023]
Abstract
Fourier ptychography microscopy (FPM) is a recently emerged computational imaging method, which combines the advantages of synthetic aperture and phase retrieval to achieve super-resolution microscopic imaging. FPM can bypass the diffraction limit of the numerical aperture (NA) system and achieve complex images with wide field of view and high resolution (HR) on the basis of the existing microscopic platform, which has low resolution and wide field of view. Conventional FPM platforms are constructed based on basic microscopic platform and a scientific complementary metal-oxide-semiconductor (sCMOS) camera, which has ultrahigh dynamic range. However, sCMOS, or even the microscopic platform, is too expensive to afford for some researchers. Furthermore, the fixed microscopic platform limits the space for function expansion and system modification. In this work, we present a simply equipped FPM platform based on an industrial camera and telecentric objective, which is much cheaper than sCMOS camera and microscopic platform and has accurate optical calibration. A corresponding algorithm was embedded into a conventional FP framework to overcome the low dynamic range of industrial cameras. Simulation and experimental results showed the feasibility and good performance of the designed FPM platform and algorithms.
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