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Aziz JAB, Smith-Dryden S, E A Saleh B, Li G. Three-dimensional tomographic reconstruction using Voronoi weighting. OPTICS EXPRESS 2024; 32:20256-20267. [PMID: 38859140 DOI: 10.1364/oe.521968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/21/2024] [Indexed: 06/12/2024]
Abstract
Three-dimensional tomographic reconstruction requires careful selection of the illumination angles, often under certain measurement constraints. When the angular distribution must be nonuniform, appropriate selection of the reconstruction weights is necessary. We show that Voronoi weighting can significantly improve the fidelity of optical diffraction tomography.
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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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Taddese AM, Lo M, Verrier N, Debailleul M, Haeberlé O. Jones tomographic diffractive microscopy with a polarized array sensor. OPTICS EXPRESS 2023; 31:9034-9051. [PMID: 36860005 DOI: 10.1364/oe.483050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Tomographic diffractive microscopy (TDM) based on scalar light-field approximation is widely implemented. Samples exhibiting anisotropic structures, however, necessitate accounting for the vectorial nature of light, leading to 3-D quantitative polarimetric imaging. In this work, we have developed a high-numerical aperture (at both illumination and detection) Jones TDM system, with detection multiplexing via a polarized array sensor (PAS), for imaging optically birefringent samples at high resolution. The method is first studied through image simulations. To validate our setup, an experiment using a sample containing both birefringent and non-birefringent objects is performed. Araneus diadematus spider silk fiber and Pinna nobilis oyster shell crystals are finally studied, allowing us to assess both birefringence and fast-axis orientation maps.
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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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He Y, Zhou N, Ziemczonok M, Wang Y, Lei L, Duan L, Zhou R. Standardizing image assessment in optical diffraction tomography. OPTICS LETTERS 2023; 48:395-398. [PMID: 36638466 DOI: 10.1364/ol.478554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Optical diffraction tomography (ODT) has gradually become a popular label-free imaging technique that offers diffraction-limited resolution by mapping an object's three-dimensional (3D) refractive index (RI) distribution. However, there is a lack of comprehensive quantitative image assessment metrics in ODT for studying how various experimental conditions influence image quality, and subsequently optimizing the experimental conditions. In this Letter, we propose to standardize the image assessment in ODT by proposing a set of metrics, including signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and structural distinguishability (SD). To test the feasibility of the metrics, we performed experiments on angle-scanning ODT by varying the number of illumination angles, RI contrast of samples, sample feature sizes, and sample types (e.g., standard polystyrene beads and 3D printed structures) and evaluated the RI tomograms with SNR, CNR, and SD. We further quantitatively studied how image quality can be improved, and tested the image assessment metrics on subcellular structures of living cells. We envision the proposed image assessment metrics may greatly benefit end-users for assessing the RI tomograms, as well as experimentalists for optimizing ODT instruments.
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Ossowski P, Kuś A, Krauze W, Tamborski S, Ziemczonok M, Kuźbicki Ł, Szkulmowski M, Kujawińska M. Near-infrared, wavelength, and illumination scanning holographic tomography. BIOMEDICAL OPTICS EXPRESS 2022; 13:5971-5988. [PMID: 36733741 PMCID: PMC9872886 DOI: 10.1364/boe.468046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 06/18/2023]
Abstract
We present a holographic tomography technique in which the projections are acquired using both wavelength and illumination scanning in the near-infrared region. We show how to process the acquired data to obtain correct values of three-dimensional refractive index distributions in both single-wavelength and multi-wavelength data acquisition schemes and how to properly account for the dispersion of the sample. We perform numerical and experimental comparisons of different illumination scenarios to determine the most efficient measurement protocol. We show that the multi-wavelength protocol is advantageous in terms of signal-to-noise ratio and contrast-to-noise ratio over single-wavelength protocols, even for the same number of projections used for reconstructions. Finally, we show that this approach is suitable for providing high-quality refractive index distributions of relatively thick colon cancer samples.
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Affiliation(s)
- Paweł Ossowski
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Boboli 8 street, Warsaw, 02-525, Poland
| | - Arkadiusz Kuś
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Boboli 8 street, Warsaw, 02-525, Poland
| | - Wojciech Krauze
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Boboli 8 street, Warsaw, 02-525, Poland
| | - Szymon Tamborski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Michał Ziemczonok
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Boboli 8 street, Warsaw, 02-525, Poland
| | - Łukasz Kuźbicki
- Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Maciej Szkulmowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
| | - Małgorzata Kujawińska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Boboli 8 street, Warsaw, 02-525, Poland
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Juntunen C, Abramczyk AR, Woller IM, Sung Y. Hyperspectral three-dimensional absorption imaging using snapshot optical tomography. PHYSICAL REVIEW APPLIED 2022; 18:034055. [PMID: 37274485 PMCID: PMC10237288 DOI: 10.1103/physrevapplied.18.034055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hyperspectral imaging (HSI) records a series of two-dimensional (2D) images for different wavelengths to provide the chemical fingerprint at each pixel. Combining HSI with a tomographic data acquisition method, we can obtain the chemical fingerprint of a sample at each point in three-dimensional (3D) space. The so-called 3D HSI typically suffers from low imaging throughput due to the requirement of scanning the wavelength and rotating the beam or sample. In this paper we present an optical system which captures the entire four-dimensional (4D), i.e., 3D structure and 1D spectrum, dataset of a sample with the same throughput of conventional HSI systems. Our system works by combining snapshot projection optical tomography (SPOT) which collects multiple projection images with a single snapshot, and Fourier-transform spectroscopy (FTS) which results in superior spectral resolution by collecting and processing a series of interferogram images. Using this hyperspectral SPOT system we imaged the volumetric absorbance of dyed polystyrene microbeads, oxygenated red blood cells (RBCs), and deoxygenated RBCs. The 4D optical system demonstrated in this paper provides a tool for high-throughput chemical imaging of complex microscopic specimens.
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Affiliation(s)
- Cory Juntunen
- College of Engineering and Applied Science, University of Wisconsin, Milwaukee, Wisconsin 53211, USA
| | - Andrew R. Abramczyk
- College of Engineering and Applied Science, University of Wisconsin, Milwaukee, Wisconsin 53211, USA
| | - Isabel M. Woller
- College of Health Sciences, University of Wisconsin, Milwaukee, Wisconsin 53211, USA
| | - Yongjin Sung
- College of Engineering and Applied Science, University of Wisconsin, Milwaukee, Wisconsin 53211, USA
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Abbessi R, Verrier N, Taddese AM, Laroche S, Debailleul M, Lo M, Courbot JB, Haeberlé O. Multimodal image reconstruction from tomographic diffraction microscopy data. J Microsc 2022; 288:193-206. [PMID: 35775607 DOI: 10.1111/jmi.13131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/18/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022]
Abstract
Tomographic Diffraction Microscopy (TDM) is a tool of choice for high-resolution, marker-less 3D imaging of biological samples. Based on a generalization of Digital Holographic Microscopy (DHM) with full control of the sample's illumination, TDM measures, from many illumination directions, the diffracted fields in both phase and amplitude. Photon budget associated to TDM imaging is low. Therefore, TDM is not limited by photo-toxicity issues. The recorded information makes it possible to reconstruct 3D refractive index distribution (with both refraction and absorption contributions) of the object under scrutiny, without any staining. In this contribution, we show an alternate use of this information. A tutorial for multimodal image reconstruction is proposed. Both intensity contrasts and phase contrasts are proposed, from the image formation model to the final reconstruction with both 2D and 3D rendering, turning TDM into a kind of "universal" digital microscope. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Riadh Abbessi
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, Mulhouse Cedex, 68093, France
| | - Nicolas Verrier
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, Mulhouse Cedex, 68093, France
| | - Asemare Mengistie Taddese
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, Mulhouse Cedex, 68093, France
| | - Steve Laroche
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, Mulhouse Cedex, 68093, 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, Mulhouse Cedex, 68093, France
| | - Mohamed Lo
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, Mulhouse Cedex, 68093, France
| | - Jean-Baptiste Courbot
- Institut Recherche en Informatique, Mathématiques, Automatique et Signal (IRIMAS UR UHA 7499), Université de Haute-Alsace, IUT Mulhouse, 61 rue Albert Camus, Mulhouse Cedex, 68093, 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, Mulhouse Cedex, 68093, France
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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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