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Kim J, Lee SJ. Digital in-line holographic microscopy for label-free identification and tracking of biological cells. Mil Med Res 2024; 11:38. [PMID: 38867274 PMCID: PMC11170804 DOI: 10.1186/s40779-024-00541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Digital in-line holographic microscopy (DIHM) is a non-invasive, real-time, label-free technique that captures three-dimensional (3D) positional, orientational, and morphological information from digital holographic images of living biological cells. Unlike conventional microscopies, the DIHM technique enables precise measurements of dynamic behaviors exhibited by living cells within a 3D volume. This review outlines the fundamental principles and comprehensive digital image processing procedures employed in DIHM-based cell tracking methods. In addition, recent applications of DIHM technique for label-free identification and digital tracking of various motile biological cells, including human blood cells, spermatozoa, diseased cells, and unicellular microorganisms, are thoroughly examined. Leveraging artificial intelligence has significantly enhanced both the speed and accuracy of digital image processing for cell tracking and identification. The quantitative data on cell morphology and dynamics captured by DIHM can effectively elucidate the underlying mechanisms governing various microbial behaviors and contribute to the accumulation of diagnostic databases and the development of clinical treatments.
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Affiliation(s)
- Jihwan Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sang Joon Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.
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2
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Huang HY, Yue QY, Yang Y, Wang RX, Guo CS. Single-exposure multi-wavelength optical diffraction tomography based on space-angle dual multiplexing holography. OPTICS LETTERS 2024; 49:3066-3069. [PMID: 38824329 DOI: 10.1364/ol.519248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
We present a space-angle dual multiplexing holographic recording system for realizing single-exposure multi-wavelength optical diffraction tomographic (ODT) imaging. This system is achieved by combining the principle of single-exposure multi-wavelength holographic imaging technique based on angle-division multiplexing with the principle of single-exposure ODT imaging technique based on microlens array multi-angle illuminations and space-division multiplexing. Compared with the existing multi-wavelength ODT imaging methods, it enables the holographic recording of all the diffraction tomography information of a measured specimen at multiple illumination wavelengths in a single camera exposure without any scan mechanism. Using our proposed data processing method, the multi-wavelength three-dimensional (3D) refractive index tomograms of a specimen can be eventually reconstructed from single recorded multiplexing hologram. Experimental results of a static polystyrene bead and a living C. elegans worm demonstrate the feasibility of this system.
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Huang CH, Lai YJ, Chen LN, Hung YH, Tu HY, Cheng CJ. Label-Free Three-Dimensional Morphological Characterization of Cell Death Using Holographic Tomography. SENSORS (BASEL, SWITZERLAND) 2024; 24:3435. [PMID: 38894226 PMCID: PMC11174527 DOI: 10.3390/s24113435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
This study presents a novel label-free approach for characterizing cell death states, eliminating the need for complex molecular labeling that may yield artificial or ambiguous results due to technical limitations in microscope resolution. The proposed holographic tomography technique offers a label-free avenue for capturing precise three-dimensional (3D) refractive index morphologies of cells and directly analyzing cellular parameters like area, height, volume, and nucleus/cytoplasm ratio within the 3D cellular model. We showcase holographic tomography results illustrating various cell death types and elucidate distinctive refractive index correlations with specific cell morphologies complemented by biochemical assays to verify cell death states. These findings hold promise for advancing in situ single cell state identification and diagnosis applications.
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Affiliation(s)
- Chung-Hsuan Huang
- Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
| | - Yun-Ju Lai
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; (L.-N.C.); (Y.-H.H.)
| | - Li-Nian Chen
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; (L.-N.C.); (Y.-H.H.)
| | - Yu-Hsuan Hung
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; (L.-N.C.); (Y.-H.H.)
| | - Han-Yen Tu
- Department of Electrical Engineering, Chinese Culture University, Taipei 11114, Taiwan;
| | - Chau-Jern Cheng
- Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
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4
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Verrier N, Debailleul M, Haeberlé O. Recent Advances and Current Trends in Transmission Tomographic Diffraction Microscopy. SENSORS (BASEL, SWITZERLAND) 2024; 24:1594. [PMID: 38475130 DOI: 10.3390/s24051594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Optical microscopy techniques are among the most used methods in biomedical sample characterization. In their more advanced realization, optical microscopes demonstrate resolution down to the nanometric scale. These methods rely on the use of fluorescent sample labeling in order to break the diffraction limit. However, fluorescent molecules' phototoxicity or photobleaching is not always compatible with the investigated samples. To overcome this limitation, quantitative phase imaging techniques have been proposed. Among these, holographic imaging has demonstrated its ability to image living microscopic samples without staining. However, for a 3D assessment of samples, tomographic acquisitions are needed. Tomographic Diffraction Microscopy (TDM) combines holographic acquisitions with tomographic reconstructions. Relying on a 3D synthetic aperture process, TDM allows for 3D quantitative measurements of the complex refractive index of the investigated sample. Since its initial proposition by Emil Wolf in 1969, the concept of TDM has found a lot of applications and has become one of the hot topics in biomedical imaging. This review focuses on recent achievements in TDM development. Current trends and perspectives of the technique are also discussed.
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Affiliation(s)
- Nicolas Verrier
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, 68093 Mulhouse, France
| | - Matthieu Debailleul
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, 68093 Mulhouse, France
| | - Olivier Haeberlé
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, 68093 Mulhouse, France
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5
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Astratov VN, Sahel YB, Eldar YC, Huang L, Ozcan A, Zheludev N, Zhao J, Burns Z, Liu Z, Narimanov E, Goswami N, Popescu G, Pfitzner E, Kukura P, Hsiao YT, Hsieh CL, Abbey B, Diaspro A, LeGratiet A, Bianchini P, Shaked NT, Simon B, Verrier N, Debailleul M, Haeberlé O, Wang S, Liu M, Bai Y, Cheng JX, Kariman BS, Fujita K, Sinvani M, Zalevsky Z, Li X, Huang GJ, Chu SW, Tzang O, Hershkovitz D, Cheshnovsky O, Huttunen MJ, Stanciu SG, Smolyaninova VN, Smolyaninov II, Leonhardt U, Sahebdivan S, Wang Z, Luk’yanchuk B, Wu L, Maslov AV, Jin B, Simovski CR, Perrin S, Montgomery P, Lecler S. Roadmap on Label-Free Super-Resolution Imaging. LASER & PHOTONICS REVIEWS 2023; 17:2200029. [PMID: 38883699 PMCID: PMC11178318 DOI: 10.1002/lpor.202200029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 06/18/2024]
Abstract
Label-free super-resolution (LFSR) imaging relies on light-scattering processes in nanoscale objects without a need for fluorescent (FL) staining required in super-resolved FL microscopy. The objectives of this Roadmap are to present a comprehensive vision of the developments, the state-of-the-art in this field, and to discuss the resolution boundaries and hurdles which need to be overcome to break the classical diffraction limit of the LFSR imaging. The scope of this Roadmap spans from the advanced interference detection techniques, where the diffraction-limited lateral resolution is combined with unsurpassed axial and temporal resolution, to techniques with true lateral super-resolution capability which are based on understanding resolution as an information science problem, on using novel structured illumination, near-field scanning, and nonlinear optics approaches, and on designing superlenses based on nanoplasmonics, metamaterials, transformation optics, and microsphere-assisted approaches. To this end, this Roadmap brings under the same umbrella researchers from the physics and biomedical optics communities in which such studies have often been developing separately. The ultimate intent of this paper is to create a vision for the current and future developments of LFSR imaging based on its physical mechanisms and to create a great opening for the series of articles in this field.
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Affiliation(s)
- Vasily N. Astratov
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223-0001, USA
| | - Yair Ben Sahel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yonina C. Eldar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, California 90095, USA
- Bioengineering Department, University of California, Los Angeles, California 90095, USA
- California Nano Systems Institute (CNSI), University of California, Los Angeles, California 90095, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, California 90095, USA
- Bioengineering Department, University of California, Los Angeles, California 90095, USA
- California Nano Systems Institute (CNSI), University of California, Los Angeles, California 90095, USA
- David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Nikolay Zheludev
- Optoelectronics Research Centre, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Disruptive Photonic Technologies, The Photonics Institute, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Junxiang Zhao
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zachary Burns
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zhaowei Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Material Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Evgenii Narimanov
- School of Electrical Engineering, and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - Neha Goswami
- Quantitative Light Imaging Laboratory, Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Gabriel Popescu
- Quantitative Light Imaging Laboratory, Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Emanuel Pfitzner
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Philipp Kukura
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica 1, Roosevelt Rd. Sec. 4, Taipei 10617 Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica 1, Roosevelt Rd. Sec. 4, Taipei 10617 Taiwan
| | - Brian Abbey
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia
| | - Alberto Diaspro
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Aymeric LeGratiet
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- Université de Rennes, CNRS, Institut FOTON - UMR 6082, F-22305 Lannion, France
| | - Paolo Bianchini
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Natan T. Shaked
- Tel Aviv University, Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv 6997801, Israel
| | - Bertrand Simon
- LP2N, Institut d’Optique Graduate School, CNRS UMR 5298, Université de Bordeaux, Talence France
| | - Nicolas Verrier
- IRIMAS UR UHA 7499, Université de Haute-Alsace, Mulhouse, France
| | | | - Olivier Haeberlé
- IRIMAS UR UHA 7499, Université de Haute-Alsace, Mulhouse, France
| | - Sheng Wang
- School of Physics and Technology, Wuhan University, China
- Wuhan Institute of Quantum Technology, China
| | - Mengkun Liu
- Department of Physics and Astronomy, Stony Brook University, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, USA
| | - Yeran Bai
- Boston University Photonics Center, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Boston University Photonics Center, Boston, MA 02215, USA
| | - Behjat S. Kariman
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Katsumasa Fujita
- Department of Applied Physics and the Advanced Photonics and Biosensing Open Innovation Laboratory (AIST); and the Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Moshe Sinvani
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Zeev Zalevsky
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Xiangping Li
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Guan-Jie Huang
- Department of Physics and Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shi-Wei Chu
- Department of Physics and Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Omer Tzang
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Dror Hershkovitz
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Ori Cheshnovsky
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Mikko J. Huttunen
- Laboratory of Photonics, Physics Unit, Tampere University, FI-33014, Tampere, Finland
| | - Stefan G. Stanciu
- Center for Microscopy – Microanalysis and Information Processing, Politehnica University of Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
| | - Vera N. Smolyaninova
- Department of Physics Astronomy and Geosciences, Towson University, 8000 York Rd., Towson, MD 21252, USA
| | - Igor I. Smolyaninov
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD 20742, USA
| | - Ulf Leonhardt
- Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sahar Sahebdivan
- EMTensor GmbH, TechGate, Donau-City-Strasse 1, 1220 Wien, Austria
| | - Zengbo Wang
- School of Computer Science and Electronic Engineering, Bangor University, Bangor, LL57 1UT, United Kingdom
| | - Boris Luk’yanchuk
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Limin Wu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Alexey V. Maslov
- Department of Radiophysics, University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - Boya Jin
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223-0001, USA
| | - Constantin R. Simovski
- Department of Electronics and Nano-Engineering, Aalto University, FI-00076, Espoo, Finland
- Faculty of Physics and Engineering, ITMO University, 199034, St-Petersburg, Russia
| | - Stephane Perrin
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
| | - Paul Montgomery
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
| | - Sylvain Lecler
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
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Mazur M, Krauze W. Volumetric segmentation of biological cells and subcellular structures for optical diffraction tomography images. BIOMEDICAL OPTICS EXPRESS 2023; 14:5022-5035. [PMID: 37854559 PMCID: PMC10581803 DOI: 10.1364/boe.498275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 10/20/2023]
Abstract
Three-dimensional, quantitative imaging of biological cells and their internal structures performed by optical diffraction tomography (ODT) is an important part of biomedical research. However, conducting quantitative analysis of ODT images requires performing 3D segmentation with high accuracy, often unattainable with available segmentation methods. Therefore, in this work, we present a new semi-automatic method, called ODT-SAS, which combines several non-machine-learning techniques to segment cells and 2 types of their organelles: nucleoli and lipid structures (LS). ODT-SAS has been compared with Cellpose and slice-by-slice manual segmentation, respectively, in cell segmentation and organelles segmentation. The comparison shows superiority of ODT-SAS over Cellpose and reveals the potential of our technique in detecting cells, nucleoli and LS.
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Affiliation(s)
- Martyna Mazur
- Warsaw University of Technology, 8 Boboli Str., Warsaw, 02-525, Poland
| | - Wojciech Krauze
- Warsaw University of Technology, 8 Boboli Str., Warsaw, 02-525, Poland
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7
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Bazow B, Phan T, Raub CB, Nehmetallah G. Three-dimensional refractive index estimation based on deep-inverse non-interferometric optical diffraction tomography (ODT-Deep). OPTICS EXPRESS 2023; 31:28382-28399. [PMID: 37710893 DOI: 10.1364/oe.491707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/27/2023] [Indexed: 09/16/2023]
Abstract
Optical diffraction tomography (ODT) solves an inverse scattering problem to obtain label-free, 3D refractive index (RI) estimation of biological specimens. This work demonstrates 3D RI retrieval methods suitable for partially-coherent ODT systems supported by intensity-only measurements consisting of axial and angular illumination scanning. This framework allows for access to 3D quantitative RI contrast using a simplified non-interferometric technique. We consider a traditional iterative tomographic solver based on a multiple in-plane representation of the optical scattering process and gradient descent optimization adapted for focus-scanning systems, as well as an approach that relies solely on 3D convolutional neural networks (CNNs) to invert the scattering process. The approaches are validated using simulations of the 3D scattering potential for weak phase 3D biological samples.
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8
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Bogdanov G, Chatterjee A, Makeeva N, Farrukh A, Gorodetsky AA. Squid leucophore-inspired engineering of optically dynamic human cells. iScience 2023; 26:106854. [PMID: 37519901 PMCID: PMC10372739 DOI: 10.1016/j.isci.2023.106854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 03/17/2023] [Accepted: 05/05/2023] [Indexed: 08/01/2023] Open
Abstract
Cephalopods (e.g., squids, octopuses, and cuttlefishes) possess remarkable dynamic camouflage abilities and therefore have emerged as powerful sources of inspiration for the engineering of dynamic optical technologies. Within this context, we have focused on the development of engineered living systems that can emulate the tunable optical characteristics of some squid skin cells. Herein, we expand our ability to controllably incorporate reflectin-based structures within mammalian cells via genetic engineering methods, and demonstrate that such structures can facilitate holotomographic and standard microscopy imaging of the cells. Moreover, we show that the reflectin-based structures within our cells can be reconfigured with a straightforward chemical stimulus, and we quantify the stimulus-induced changes observed for the structures at the single cell level. The reported findings may enable a better understanding of the color- and appearance-changing capabilities of some cephalopod skin cells and could afford opportunities for reflectins as molecular probes in the fields of cell biology and biomedical optics.
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Affiliation(s)
- Georgii Bogdanov
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Atrouli Chatterjee
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Nataliya Makeeva
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Aleeza Farrukh
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Alon A Gorodetsky
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697, USA
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9
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Gontarz M, Dutta V, Kujawińska M, Krauze W. Phase unwrapping using deep learning in holographic tomography. OPTICS EXPRESS 2023; 31:18964-18992. [PMID: 37381325 DOI: 10.1364/oe.486984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 06/30/2023]
Abstract
Holographic tomography (HT) is a measurement technique that generates phase images, often containing high noise levels and irregularities. Due to the nature of phase retrieval algorithms within the HT data processing, the phase has to be unwrapped before tomographic reconstruction. Conventional algorithms lack noise robustness, reliability, speed, and possible automation. In order to address these problems, this work proposes a convolutional neural network based pipeline consisting of two steps: denoising and unwrapping. Both steps are carried out under the umbrella of a U-Net architecture; however, unwrapping is aided by introducing Attention Gates (AG) and Residual Blocks (RB) to the architecture. Through the experiments, the proposed pipeline makes possible the phase unwrapping of highly irregular, noisy, and complex experimental phase images captured in HT. This work proposes phase unwrapping carried out by segmentation with a U-Net network, that is aided by a pre-processing denoising step. It also discusses the implementation of the AGs and RBs in an ablation study. What is more, this is the first deep learning based solution that is trained solely on real images acquired with HT.
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10
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Moser S, Jesacher A, Ritsch-Marte M. Efficient and accurate intensity diffraction tomography of multiple-scattering samples. OPTICS EXPRESS 2023; 31:18274-18289. [PMID: 37381541 DOI: 10.1364/oe.486296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/25/2023] [Indexed: 06/30/2023]
Abstract
Optical Diffraction Tomography (ODT) is a label-free method to quantitatively estimate the 3D refractive index (RI) distributions of microscopic samples. Recently, significant efforts were directed towards methods to model multiple-scattering objects. The fidelity of reconstructions rely on accurately modelling light-matter interactions, but the efficient simulation of light propagation through high-RI structures over a large range of illumination angles is still challenging. Here we present a solution dealing with these problems, proposing a method that allows one to efficiently model the tomographic image formation for strongly scattering objects illuminated over a wide range of angles. Instead of propagating tilted plane waves we apply rotations on the illuminated object and optical field and formulate a new and robust multi-slice model suitable for high-RI contrast structures. We test reconstructions made by our approach against simulations and experiments, using rigorous solutions to Maxwell's equations as ground truth. We find the proposed method to produce reconstructions of higher fidelity compared to conventional multi-slice methods, especially for the challenging case of strongly scattering samples where conventional reconstruction methods fail.
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11
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Ebrahimi S, Moreno-Pescador G, Persson S, Jauffred L, Bendix PM. Label-free optical interferometric microscopy to characterize morphodynamics in living plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1156478. [PMID: 37284726 PMCID: PMC10239806 DOI: 10.3389/fpls.2023.1156478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/04/2023] [Indexed: 06/08/2023]
Abstract
During the last century, fluorescence microscopy has played a pivotal role in a range of scientific discoveries. The success of fluorescence microscopy has prevailed despite several shortcomings like measurement time, photobleaching, temporal resolution, and specific sample preparation. To bypass these obstacles, label-free interferometric methods have been developed. Interferometry exploits the full wavefront information of laser light after interaction with biological material to yield interference patterns that contain information about structure and activity. Here, we review recent studies in interferometric imaging of plant cells and tissues, using techniques such as biospeckle imaging, optical coherence tomography, and digital holography. These methods enable quantification of cell morphology and dynamic intracellular measurements over extended periods of time. Recent investigations have showcased the potential of interferometric techniques for precise identification of seed viability and germination, plant diseases, plant growth and cell texture, intracellular activity and cytoplasmic transport. We envision that further developments of these label-free approaches, will allow for high-resolution, dynamic imaging of plants and their organelles, ranging in scales from sub-cellular to tissue and from milliseconds to hours.
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Affiliation(s)
- Samira Ebrahimi
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Guillermo Moreno-Pescador
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liselotte Jauffred
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Poul Martin Bendix
- Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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12
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Pirone D, Montella A, Sirico DG, Mugnano M, Villone MM, Bianco V, Miccio L, Porcelli AM, Kurelac I, Capasso M, Iolascon A, Maffettone PL, Memmolo P, Ferraro P. Label-free liquid biopsy through the identification of tumor cells by machine learning-powered tomographic phase imaging flow cytometry. Sci Rep 2023; 13:6042. [PMID: 37055398 PMCID: PMC10101968 DOI: 10.1038/s41598-023-32110-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/21/2023] [Indexed: 04/15/2023] Open
Abstract
Image-based identification of circulating tumor cells in microfluidic cytometry condition is one of the most challenging perspectives in the Liquid Biopsy scenario. Here we show a machine learning-powered tomographic phase imaging flow cytometry system capable to provide high-throughput 3D phase-contrast tomograms of each single cell. In fact, we show that discrimination of tumor cells against white blood cells is potentially achievable with the aid of artificial intelligence in a label-free flow-cyto-tomography method. We propose a hierarchical machine learning decision-maker, working on a set of features calculated from the 3D tomograms of the cells' refractive index. We prove that 3D morphological features are adequately distinctive to identify tumor cells versus the white blood cell background in the first stage and, moreover, in recognizing the tumor type at the second decision step. Proof-of-concept experiments are shown, in which two different tumor cell lines, namely neuroblastoma cancer cells and ovarian cancer cells, are used against monocytes. The reported results allow claiming the identification of tumor cells with a success rate higher than 97% and with an accuracy over 97% in discriminating between the two cancer cell types, thus opening in a near future the route to a new Liquid Biopsy tool for detecting and classifying circulating tumor cells in blood by stain-free method.
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Affiliation(s)
- Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Annalaura Montella
- CEINGE Advanced Biotechnologies, Naples, Italy
- DMMBM, Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Daniele G Sirico
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Martina Mugnano
- Department of Chemical, Materials and Production Engineering, DICMaPI, University of Naples "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy
| | - Massimiliano M Villone
- Department of Chemical, Materials and Production Engineering, DICMaPI, University of Naples "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy
| | - Vittorio Bianco
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Lisa Miccio
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
- Interdepartmental Centre for Industrial Research 'Scienze Della Vita e Tecnologie per La Salute', University of Bologna, Bologna, Italy
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Ivana Kurelac
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
- DIMEC, Department of Medical and Surgical Sciences, Centro di Studio e Ricerca Sulle Neoplasie (CSR) Ginecologiche, Alma Mater Studiorum-University of Bologna, 40138, Bologna, Italy
| | - Mario Capasso
- CEINGE Advanced Biotechnologies, Naples, Italy
- DMMBM, Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Achille Iolascon
- CEINGE Advanced Biotechnologies, Naples, Italy
- DMMBM, Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Pier Luca Maffettone
- Department of Chemical, Materials and Production Engineering, DICMaPI, University of Naples "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy
| | - Pasquale Memmolo
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy.
| | - Pietro Ferraro
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy.
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13
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Rajora S, Butola M, Khare K. 3D reconstruction of unstained weakly scattering cells from a single defocused hologram. APPLIED OPTICS 2023; 62:D146-D156. [PMID: 37132780 DOI: 10.1364/ao.478351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We investigate the problem of 3D complex field reconstruction corresponding to unstained red blood cells (RBCs) with a single defocused off-axis digital hologram. The main challenge in this problem is the localization of cells to the correct axial range. While investigating the volume recovery problem for a continuous phase object like the RBC, we observe an interesting feature of the backpropagated field that it does not show a clear focusing effect. Therefore, sparsity enforcement within the iterative optimization framework using a single hologram data frame cannot effectively restrict the reconstruction to the true object volume. For phase objects, it is known that the amplitude contrast of the backpropagated object field at the focus plane is minimum. We use this information available in the recovered object field in the hologram plane to device depth-dependent weights that are proportional to the inverse of amplitude contrast. This weight function is employed in the iterative steps of the optimization algorithm to assist the object volume localization. The overall reconstruction process is performed using the mean gradient descent (MGD) framework. Experimental illustrations of 3D volume reconstruction of the healthy as well as malaria-infected RBCs are presented. A test sample of polystyrene microsphere bead is also used to validate the axial localization capability of the proposed iterative technique. The proposed methodology is simple to implement experimentally and provides an approximate tomographic solution, which is axially restricted and consistent with the object field data.
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14
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Zhang Y, Huang Z, Jin S, Cao L. Hough transform-based multi-object autofocusing compressive holography. APPLIED OPTICS 2023; 62:D23-D30. [PMID: 37132766 DOI: 10.1364/ao.478473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reconstruction of multiple objects from one hologram can be affected by the focus metric judgment of autofocusing. Various segmentation algorithms are applied to obtain a single object in the hologram. Each object is unambiguously reconstructed to acquire its focal position, which produces complicated calculations. Herein, Hough transform (HT)-based multi-object autofocusing compressive holography is presented. The sharpness of each reconstructed image is computed by using a focus metric such as entropy or variance. According to the characteristics of the object, the standard HT is further used for calibration to remove redundant extreme points. The compressive holographic imaging framework with a filter layer can eliminate the inherent noise in in-line reconstruction including cross talk noise of different depth layers, two-order noise, and twin image noise. The proposed method can effectively obtain 3D information on multiple objects and achieve noise elimination by only reconstructing from one hologram.
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15
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Chatterjee A, Pratakshya P, Kwansa AL, Kaimal N, Cannon AH, Sartori B, Marmiroli B, Orins H, Feng Z, Drake S, Couvrette J, Le L, Bernstorff S, Yingling YG, Gorodetsky AA. Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures. ACS Biomater Sci Eng 2023; 9:978-990. [PMID: 36692450 DOI: 10.1021/acsbiomaterials.2c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The fascination with the optical properties of naturally occurring systems has been driven in part by nature's ability to produce a diverse palette of vibrant colors from a relatively small number of common structural motifs. Within this context, some cephalopod species have evolved skin cells called iridophores and leucophores whose constituent ultrastructures reflect light in different ways but are composed of the same high refractive index material─a protein called reflectin. Although such natural optical systems have attracted much research interest, measuring the refractive indices of biomaterial-based structures across multiple different environments and establishing theoretical frameworks for accurately describing the obtained refractive index values has proven challenging. Herein, we employ a synergistic combination of experimental and computational methodologies to systematically map the three-dimensional refractive index distributions of model self-assembled reflectin-based structures both in vivo and in vitro. When considered together, our findings may improve understanding of squid skin cell functionality, augment existing methods for characterizing protein-based optical materials, and expand the utility of emerging holotomographic microscopy techniques.
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Affiliation(s)
- Atrouli Chatterjee
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Preeta Pratakshya
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Albert L Kwansa
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nikhil Kaimal
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Andrew H Cannon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Graz 8010, Austria
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, Graz 8010, Austria
| | - Helen Orins
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Zhijing Feng
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Samantha Drake
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Justin Couvrette
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - LeAnn Le
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | | | - Yaroslava G Yingling
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Alon A Gorodetsky
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
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16
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Verrier N, Taddese AM, Abbessi R, Debailleul M, Haeberlé O. 3D differential interference contrast microscopy using polarisation-sensitive tomographic diffraction microscopy. J Microsc 2023; 289:128-133. [PMID: 36408663 PMCID: PMC10107843 DOI: 10.1111/jmi.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/18/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022]
Abstract
Tomographic diffraction microscopy (TDM) is a generalisation of digital holographic microscopy (DHM), for which the illumination angle onto the sample is fully controlled, which has become a tool of choice for 3D, high-resolution imaging of unlabelled samples. TDM makes it possible to obtain the optical field in both amplitude and phase for each illumination angle. Proper information reallocation eventually allows for 3D reconstruction of the complex refractive index map. On the other hand, polarisation array sensors (PAS) paves new way for TDM, as vectorial information assessment about the investigated sample. In this contribution, we show an alternative use of this polarisation information based on the phase sensitive nature of TDM. Here, we demonstrated that TDM coupled with PAS can lead to a 3D differential interference contrast (DIC) microscope with almost no experimental configuration modification.
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Affiliation(s)
- Nicolas Verrier
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, Mulhouse Cedex, France
| | - Asemare Mengistie Taddese
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, Mulhouse Cedex, France
| | - Riadh Abbessi
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, Mulhouse Cedex, France
| | - Matthieu Debailleul
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, Mulhouse Cedex, France
| | - Olivier Haeberlé
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, Mulhouse Cedex, France
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17
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Stępień P, Ziemczonok M, Kujawińska M, Baczewska M, Valenti L, Cherubini A, Casirati E, Krauze W. Numerical refractive index correction for the stitching procedure in tomographic quantitative phase imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:5709-5720. [PMID: 36733760 PMCID: PMC9872904 DOI: 10.1364/boe.466403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 06/18/2023]
Abstract
Tomographic quantitative phase imaging (QPI) lacks an absolute refractive index value baseline, which poses a problem when large dense objects extending over multiple fields of view are measured volume by volume and stitched together. Some of the measurements lack the natural baseline value that is provided by the mounting medium with a known refractive index. In this work, we discuss the problem of the refractive index (RI) baseline of individual reconstructed volumes that are deprived of access to mounting medium due to the extent of the object. The solution of this problem is provided by establishing the RI offsets based on the overlapping regions. We have proven that the process of finding the offset RI values may be justifiably reduced to the analogous procedure in the 2D baseline correction (2D-BC). Finally, we proposed the enhancement of the state-of-the-art 2D-BC procedure previously introduced in the context of 2D QPI. The processing is validated at the examples of a synthetic dataset and a liver organoid.
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Affiliation(s)
- Piotr Stępień
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Michał Ziemczonok
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Małgorzata Kujawińska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Maria Baczewska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Luca Valenti
- Università degli Studi di Milano, Department of Pathophysiology and Transplantation, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Transfusion Medicine and Hematology, Milan, Italy
| | - Alessandro Cherubini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Transfusion Medicine and Hematology, Milan, Italy
| | - Elia Casirati
- Università degli Studi di Milano, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Wojciech Krauze
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
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18
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Tang M, He H, Yu L. Real-time 3D imaging of ocean algae with crosstalk suppressed single-shot digital holographic microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:4455-4467. [PMID: 36032587 PMCID: PMC9408253 DOI: 10.1364/boe.463678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Digital holographic microscopy (DHM) has the potential to reconstruct the 3D shape of volumetric samples from a single-shot hologram in a label-free and noninvasive manner. However, the holographic reconstruction is significantly compromised by the out-of-focus image resulting from the crosstalk between refocused planes, leading to the low fidelity of the results. In this paper, we propose a crosstalk suppression algorithm-assisted 3D imaging method combined with a home built DHM system to achieve accurate 3D imaging of ocean algae using only a single hologram. As a key step in the algorithm, a hybrid edge detection strategy using gradient-based and deep learning-based methods is proposed to offer accurate boundary information for the downstream processing. With this information, the crosstalk of each refocused plane can be estimated with adjacent refocused planes. Empowered by this method, we demonstrated successful 3D imaging of six kinds of ocean algae that agree well with the ground truth; we further demonstrated that this method could achieve real-time 3D imaging of the quick swimming ocean algae in the water environment. To our knowledge, this is the first time single-shot DHM is reported in 3D imaging of ocean algae, paving the way for on-site monitoring of the ocean algae.
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Affiliation(s)
- Ming Tang
- School of Advanced Manufacturing, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Hao He
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Longkun Yu
- School of Advanced Manufacturing, Nanchang University, Nanchang, Jiangxi 330031, China
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19
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Advances in Digital Holographic Interferometry. J Imaging 2022; 8:jimaging8070196. [PMID: 35877640 PMCID: PMC9323567 DOI: 10.3390/jimaging8070196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Holographic interferometry is a well-established field of science and optical engineering. It has a half-century history of successful implementation as the solution to numerous technical tasks and problems. However, fast progress in digital and computer holography has promoted it to a new level of possibilities and has opened brand new fields of its application. In this review paper, we consider some such new techniques and applications.
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20
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Zhang J, Yang D, Lv W, Jin X, Shi Y. Three-dimensional phase and intensity reconstruction from coherent modulation imaging measurements. OPTICS EXPRESS 2022; 30:20415-20430. [PMID: 36224787 DOI: 10.1364/oe.460648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/11/2022] [Indexed: 06/16/2023]
Abstract
Coherent modulation imaging is a lensless imaging technique, where a complex-valued image can be recovered from a single diffraction pattern using the iterative algorithm. Although mostly applied in two dimensions, it can be tomographically combined to produce three-dimensional (3D) images. Here we present a 3D reconstruction procedure for the sample's phase and intensity from coherent modulation imaging measurements. Pre-processing methods to remove illumination probe, inherent ambiguities in phase reconstruction results, and intensity fluctuation are given. With the projections extracted by our method, standard tomographic reconstruction frameworks can be used to recover accurate quantitative 3D phase and intensity images. Numerical simulations and optical experiments validate our method.
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21
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At the Intersection of Natural Structural Coloration and Bioengineering. Biomimetics (Basel) 2022; 7:biomimetics7020066. [PMID: 35645193 PMCID: PMC9149877 DOI: 10.3390/biomimetics7020066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Most of us get inspired by and interact with the world around us based on visual cues such as the colors and patterns that we see. In nature, coloration takes three primary forms: pigmentary coloration, structural coloration, and bioluminescence. Typically, pigmentary and structural coloration are used by animals and plants for their survival; however, few organisms are able to capture the nearly instantaneous and visually astounding display that cephalopods (e.g., octopi, squid, and cuttlefish) exhibit. Notably, the structural coloration of these cephalopods critically relies on a unique family of proteins known as reflectins. As a result, there is growing interest in characterizing the structure and function of such optically-active proteins (e.g., reflectins) and to leverage these materials across a broad range of disciplines, including bioengineering. In this review, I begin by briefly introducing pigmentary and structural coloration in animals and plants as well as highlighting the extraordinary appearance-changing capabilities of cephalopods. Next, I outline recent advances in the characterization and utilization of reflectins for photonic technologies and and discuss general strategies and limitations for the structural and optical characterization of proteins. Finally, I explore future directions of study for optically-active proteins and their potential applications. Altogether, this review aims to bring together an interdisciplinary group of researchers who can resolve the fundamental questions regarding the structure, function, and self-assembly of optically-active protein-based materials.
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22
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Pirone D, Sirico D, Miccio L, Bianco V, Mugnano M, Ferraro P, Memmolo P. Speeding up reconstruction of 3D tomograms in holographic flow cytometry via deep learning. LAB ON A CHIP 2022; 22:793-804. [PMID: 35076055 DOI: 10.1039/d1lc01087e] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tomographic flow cytometry by digital holography is an emerging imaging modality capable of collecting multiple views of moving and rotating cells with the aim of recovering their refractive index distribution in 3D. Although this modality allows us to access high-resolution imaging with high-throughput, the huge amount of time-lapse holographic images to be processed (hundreds of digital holograms per cell) constitutes the actual bottleneck. This prevents the system from being suitable for lab-on-a-chip platforms in real-world applications, where fast analysis of measured data is mandatory. Here we demonstrate a significant speeding-up reconstruction of phase-contrast tomograms by introducing in the processing pipeline a multi-scale fully-convolutional context aggregation network. Although it was originally developed in the context of semantic image analysis, we demonstrate for the first time that it can be successfully adapted to a holographic lab-on-chip platform for achieving 3D tomograms through a faster computational process. We trained the network with input-output image pairs to reproduce the end-to-end holographic reconstruction process, i.e. recovering quantitative phase maps (QPMs) of single cells from their digital holograms. Then, the sequence of QPMs of the same rotating cell is used to perform the tomographic reconstruction. The proposed approach significantly reduces the computational time for retrieving tomograms, thus making them available in a few seconds instead of tens of minutes, while essentially preserving the high-content information of tomographic data. Moreover, we have accomplished a compact deep convolutional neural network parameterization that can fit into on-chip SRAM and a small memory footprint, thus demonstrating its possible exploitation to provide onboard computations for lab-on-chip devices with low processing hardware resources.
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Affiliation(s)
- Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
- DIETI, Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", via Claudio 21, 80125 Napoli, Italy
| | - Daniele Sirico
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Lisa Miccio
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Vittorio Bianco
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Martina Mugnano
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Pietro Ferraro
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Pasquale Memmolo
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
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23
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Bazow B, Phan T, Raub CB, Nehmetallah G. Computational multi-wavelength phase synthesis using convolutional neural networks [Invited]. APPLIED OPTICS 2022; 61:B132-B146. [PMID: 35201134 DOI: 10.1364/ao.439323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/13/2021] [Indexed: 05/22/2023]
Abstract
Multi-wavelength digital holographic microscopy (MWDHM) provides indirect measurements of the refractive index for non-dispersive samples. Successive-shot MWDHM is not appropriate for dynamic samples and single-shot MWDHM significantly increases the complexity of the optical setup due to the need for multiple lasers or a wavelength tunable source. Here we consider deep learning convolutional neural networks for computational phase synthesis to obtain high-speed simultaneous phase estimates on different wavelengths and thus single-shot estimates of the integral refractive index without increased experimental complexity. This novel, to the best of our knowledge, computational concept is validated using cell phantoms consisting of internal refractive index variations representing cytoplasm and membrane-bound organelles, respectively, and a simulation of a realistic holographic recording process. Specifically, in this work we employed data-driven computational techniques to perform accurate dual-wavelength hologram synthesis (hologram-to-hologram prediction), dual-wavelength phase synthesis (unwrapped phase-to-phase prediction), direct phase-to-index prediction using a single wavelength, hologram-to-phase prediction, and 2D phase unwrapping with sharp discontinuities (wrapped-to-unwrapped phase prediction).
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24
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Trolinger JD, Mansoor MM. History and metrology applications of a game-changing technology: digital holography [Invited]. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:A29-A43. [PMID: 35200948 DOI: 10.1364/josaa.440610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
In digital holography (DH), information in the hologram is recorded and stored in digital format in discrete bits. Like its parent, holography, DH evolved over many years with periods of dormancy and revival. Almost abandoned, multiple times, unanticipated events or developments in separate industries revived it with explosive, quantum jumps, making it useful and popular to a wide audience. Although its history has been treated in many papers and books, the field is dynamic and constantly providing new opportunities. Having been born long before low-cost, fast, powerful digital computers and digital detectors were available, DH was confined to the academic world, where practical applications and commercial opportunities were few if any. Consumer demand that led to low-cost personal computers, high-resolution digital cameras, supporting software, and related products changed the situation drastically by providing every potential researcher affordable, powerful hardware and software needed to apply image processing algorithms and move DH to new practical application levels. In this paper, as part of the sixtieth anniversary of off-axis holography, we include a brief introduction to the fundamentals of DH and examine the history and evolution of DH during its periods of rise and fall. We summarize many new emerging techniques, applications, and potential future applications along with additional details for metrological examples from the authors' research.
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25
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Muhamad RK, Stępień P, Kujawińska M, Schelkens P. Off-axis image plane hologram compression in holographic tomography - metrological assessment. OPTICS EXPRESS 2022; 30:4261-4273. [PMID: 35209666 DOI: 10.1364/oe.449932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
In this paper, we present a novel study on the impact of lossy data compression on the metrological properties of holographic tomography reconstruction of the refractive index (RI). We use a spatial bandwidth-optimized compression procedure that leverages the properties of image plane off-axis holograms and standardized compression codecs, both widely applied in research and industry. The compression procedure is tested at multiple bitrates, for four different objects and against three reconstruction algorithms. The metrological evaluation is primarily done by comparison to the reconstruction from original data using the root-mean-squared error (RMSE). We show that due to differences between objects and different noise sensitivities of the reconstruction algorithms, the rate-distortion behaviour varies, but in most cases allows for the compression below 1 bit per pixel, while maintaining an RI RMSE less than 10-4.
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Roadmap on Digital Holography-Based Quantitative Phase Imaging. J Imaging 2021; 7:jimaging7120252. [PMID: 34940719 PMCID: PMC8703719 DOI: 10.3390/jimaging7120252] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 12/02/2022] Open
Abstract
Quantitative Phase Imaging (QPI) provides unique means for the imaging of biological or technical microstructures, merging beneficial features identified with microscopy, interferometry, holography, and numerical computations. This roadmap article reviews several digital holography-based QPI approaches developed by prominent research groups. It also briefly discusses the present and future perspectives of 2D and 3D QPI research based on digital holographic microscopy, holographic tomography, and their applications.
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Meteyer E, Foucart F, Pezerat C, Picart P. Modeling of speckle decorrelation in digital Fresnel holographic interferometry. OPTICS EXPRESS 2021; 29:36180-36200. [PMID: 34809036 DOI: 10.1364/oe.438346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
This paper presents analytical modeling of the speckle decorrelation noise in digital Fresnel holographic interferometry. The theoretical analysis is carried out by considering the complex coherence factor between two speckled images from two digitally reconstructed holograms at two different instants. The expression giving the modulus of the coherence factor is established and depends on the local surface deformation and parameters from the holographic setup. The analysis is supported by realistic simulations and experiments. Both simulations and experimental results exhibit a very good agreement with the theoretical prediction.
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Javidi B, Carnicer A, Anand A, Barbastathis G, Chen W, Ferraro P, Goodman JW, Horisaki R, Khare K, Kujawinska M, Leitgeb RA, Marquet P, Nomura T, Ozcan A, Park Y, Pedrini G, Picart P, Rosen J, Saavedra G, Shaked NT, Stern A, Tajahuerce E, Tian L, Wetzstein G, Yamaguchi M. Roadmap on digital holography [Invited]. OPTICS EXPRESS 2021; 29:35078-35118. [PMID: 34808951 DOI: 10.1364/oe.435915] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/04/2021] [Indexed: 05/22/2023]
Abstract
This Roadmap article on digital holography provides an overview of a vast array of research activities in the field of digital holography. The paper consists of a series of 25 sections from the prominent experts in digital holography presenting various aspects of the field on sensing, 3D imaging and displays, virtual and augmented reality, microscopy, cell identification, tomography, label-free live cell imaging, and other applications. Each section represents the vision of its author to describe the significant progress, potential impact, important developments, and challenging issues in the field of digital holography.
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Wang Z, Bianco V, Pirone D, Memmolo P, Villone MM, Maffettone PL, Ferraro P. Dehydration of plant cells shoves nuclei rotation allowing for 3D phase-contrast tomography. LIGHT, SCIENCE & APPLICATIONS 2021; 10:187. [PMID: 34526484 PMCID: PMC8443563 DOI: 10.1038/s41377-021-00626-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/15/2021] [Accepted: 08/27/2021] [Indexed: 05/07/2023]
Abstract
Single-cell phase-contrast tomography promises to become decisive for studying 3D intracellular structures in biology. It involves probing cells with light at wide angles, which unfortunately requires complex systems. Here we show an intriguing concept based on an inherent natural process for plants biology, i.e., dehydration, allowing us to easily obtain 3D-tomography of onion-epidermal cells' nuclei. In fact, the loss of water reduces the turgor pressure and we recognize it induces significant rotation of cells' nuclei. Thanks to the holographic focusing flexibility and an ad-hoc angles' tracking algorithm, we combine different phase-contrast views of the nuclei to retrieve their 3D refractive index distribution. Nucleolus identification capability and a strategy for measuring morphology, dry mass, biovolume, and refractive index statistics are reported and discussed. This new concept could revolutionize the investigation in plant biology by enabling dynamic 3D quantitative and label-free analysis at sub-nuclear level using a conventional holographic setup.
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Affiliation(s)
- Zhe Wang
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Vittorio Bianco
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione, Università degli Studi di Napoli "Federico II", via Claudio 21, 80125, Napoli, Italy
| | - Pasquale Memmolo
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Massimiliano Maria Villone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pier Luca Maffettone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pietro Ferraro
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
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Taddese AM, Verrier N, Debailleul M, Courbot JB, Haeberlé O. Optimizing sample illumination scanning for reflection and 4Pi tomographic diffractive microscopy. APPLIED OPTICS 2021; 60:7745-7753. [PMID: 34613246 DOI: 10.1364/ao.435721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Tomographic diffractive microscopy (TDM) is increasingly gaining attention, owing to its high-resolution, label-free imaging capability. Fast acquisitions necessitate limiting the number of holograms to be recorded. Reconstructions then rely on optimal Fourier space filling to retain image quality and resolution, that is, they rely on optimal scanning of the tomographic illuminations. In this work, we theoretically study reflection TDM, and then the 4Pi TDM, a combination of transmission and reflection systems. Image simulations are conducted to determine optimal angular sweeping. We found that three-dimensional uniform scanning fills Fourier space the best for both reflection and 4Pi configurations, providing a better refractive index estimation for the observed sample.
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Zdańkowski P, Winnik J, Patorski K, Gocłowski P, Ziemczonok M, Józwik M, Kujawińska M, Trusiak M. Common-path intrinsically achromatic optical diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:4219-4234. [PMID: 34457410 PMCID: PMC8367224 DOI: 10.1364/boe.428828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
In this work we propose an open-top like common-path intrinsically achromatic optical diffraction tomography system. It operates as a total-shear interferometer and employs Ronchi-type amplitude diffraction grating, positioned in between the camera and the tube lens without an additional 4f system, generating three-beam interferograms with achromatic second harmonic. Such configuration makes the proposed system low cost, compact and immune to vibrations. We present the results of the measurements of 3D-printed cell phantom using laser diode (coherent) and superluminescent diode (partially coherent) light sources. Broadband light sources can be naturally employed without the need for any cumbersome compensation because of the intrinsic achromaticity of the interferometric recording (holograms generated by -1st and +1st conjugated diffraction orders are not affected by the illumination wavelength). The results show that the decreased coherence offers much reduced coherent noise and higher fidelity tomographic reconstruction especially when applied nonnegativity constraint regularization procedure.
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Affiliation(s)
- Piotr Zdańkowski
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
- These authors contributed equally to this work
| | - Julianna Winnik
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
- These authors contributed equally to this work
| | - Krzysztof Patorski
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
| | - Paweł Gocłowski
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
| | - Michał Ziemczonok
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
| | - Michał Józwik
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
| | - Małgorzata Kujawińska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
| | - Maciej Trusiak
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 Św. A. Boboli st., 02-525 Warsaw, Poland
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