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Huang Z, Cao L. Quantitative phase imaging based on holography: trends and new perspectives. LIGHT, SCIENCE & APPLICATIONS 2024; 13:145. [PMID: 38937443 PMCID: PMC11211409 DOI: 10.1038/s41377-024-01453-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 06/29/2024]
Abstract
In 1948, Dennis Gabor proposed the concept of holography, providing a pioneering solution to a quantitative description of the optical wavefront. After 75 years of development, holographic imaging has become a powerful tool for optical wavefront measurement and quantitative phase imaging. The emergence of this technology has given fresh energy to physics, biology, and materials science. Digital holography (DH) possesses the quantitative advantages of wide-field, non-contact, precise, and dynamic measurement capability for complex-waves. DH has unique capabilities for the propagation of optical fields by measuring light scattering with phase information. It offers quantitative visualization of the refractive index and thickness distribution of weak absorption samples, which plays a vital role in the pathophysiology of various diseases and the characterization of various materials. It provides a possibility to bridge the gap between the imaging and scattering disciplines. The propagation of wavefront is described by the complex amplitude. The complex-value in the complex-domain is reconstructed from the intensity-value measurement by camera in the real-domain. Here, we regard the process of holographic recording and reconstruction as a transformation between complex-domain and real-domain, and discuss the mathematics and physical principles of reconstruction. We review the DH in underlying principles, technical approaches, and the breadth of applications. We conclude with emerging challenges and opportunities based on combining holographic imaging with other methodologies that expand the scope and utility of holographic imaging even further. The multidisciplinary nature brings technology and application experts together in label-free cell biology, analytical chemistry, clinical sciences, wavefront sensing, and semiconductor production.
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Affiliation(s)
- Zhengzhong Huang
- Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Liangcai Cao
- Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.
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2
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Shanmugavel SC, Zhu Y. Structured illumination contrast transfer function for high resolution quantitative phase imaging. OPTICS EXPRESS 2023; 31:40151-40165. [PMID: 38041322 DOI: 10.1364/oe.504961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023]
Abstract
We report a sub-diffraction resolution imaging of non-fluorescent samples through quantitative phase imaging. This is achieved through a novel application of structured illumination microscopy (SIM), a super-resolution imaging technique established primarily for fluorescence microscopy. Utilizing our contrast transfer function formalism with SIM, we extract the high spatial frequency components of the phase profile from the defocused intensity images, enabling the reconstruction of a quantitative phase image with a frequency spectrum that surpasses the diffraction limit imposed by the imaging system. Our approach offers several advantages including a deterministic, phase-unwrapping-free algorithm and an easily implementable, non-interferometric setup. We validate the proposed technique for high-resolution phase imaging through both simulation and experimental results, demonstrating a two-fold enhancement in resolution. A lateral resolution of 0.814 µm is achieved for the phase imaging of human cheek cells using a 0.42 NA objective lens and an illumination wavelength of 660 nm, highlighting the efficacy of our approach for high-resolution quantitative phase imaging.
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3
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Wen K, Gao Z, Liu R, Fang X, Ma Y, Zheng J, An S, Kozacki T, Gao P. Structured illumination phase and fluorescence microscopy for bioimaging. APPLIED OPTICS 2023; 62:4871-4879. [PMID: 37707263 DOI: 10.1364/ao.486718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/14/2023] [Indexed: 09/15/2023]
Abstract
This study presents a dual-modality microscopic imaging approach that combines quantitative phase microscopy and fluorescence microscopy based on structured illumination (SI) to provide structural and functional information for the same sample. As the first imaging modality, structured illumination digital holographic microscopy (SI-DHM) is implemented along the transmission beam path. SI-DHM acts as a label-free, noninvasive approach and provides high-contrast and quantitative phase images utilizing the refractive index contrast of the inner structures of samples against the background. As the second imaging modality, structured illumination (fluorescence) microscopy (SIM) is constructed along the reflection beam path. SIM utilizes fluorescent labeling and provides super-resolution images for specific functional structures of samples. We first experimentally demonstrated phase imaging of SI-DHM on rice leaves and fluorescence (SIM) imaging on mouse kidney sections. Then, we demonstrated dual-modality imaging of biological samples, using DHM to acquire the overall cell morphology and SIM to obtain specific functional structures. These results prove that the proposed technique is of great importance in biomedical studies, such as providing insight into cell physiology by visualizing and quantifying subcellular structures.
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4
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Nguyen TL, Pradeep S, Judson-Torres RL, Reed J, Teitell MA, Zangle TA. Quantitative Phase Imaging: Recent Advances and Expanding Potential in Biomedicine. ACS NANO 2022; 16:11516-11544. [PMID: 35916417 PMCID: PMC10112851 DOI: 10.1021/acsnano.1c11507] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Quantitative phase imaging (QPI) is a label-free, wide-field microscopy approach with significant opportunities for biomedical applications. QPI uses the natural phase shift of light as it passes through a transparent object, such as a mammalian cell, to quantify biomass distribution and spatial and temporal changes in biomass. Reported in cell studies more than 60 years ago, ongoing advances in QPI hardware and software are leading to numerous applications in biology, with a dramatic expansion in utility over the past two decades. Today, investigations of cell size, morphology, behavior, cellular viscoelasticity, drug efficacy, biomass accumulation and turnover, and transport mechanics are supporting studies of development, physiology, neural activity, cancer, and additional physiological processes and diseases. Here, we review the field of QPI in biology starting with underlying principles, followed by a discussion of technical approaches currently available or being developed, and end with an examination of the breadth of applications in use or under development. We comment on strengths and shortcomings for the deployment of QPI in key biomedical contexts and conclude with emerging challenges and opportunities based on combining QPI with other methodologies that expand the scope and utility of QPI even further.
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5
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Single-Shot 3D Topography of Transmissive and Reflective Samples with a Dual-Mode Telecentric-Based Digital Holographic Microscope. SENSORS 2022; 22:s22103793. [PMID: 35632202 PMCID: PMC9144696 DOI: 10.3390/s22103793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023]
Abstract
Common path DHM systems are the most robust DHM systems as they are based on self-interference and are thus less prone to external fluctuations. A common issue amongst these DHM systems is that the two replicas of the sample’s information overlay due to self-interference, making them only suitable for imaging sparse samples. This overlay has restricted the use of common-path DHM systems in material science. The overlay can be overcome by limiting the sample’s field of view to occupy only half of the imaging field of view or by using an optical spatial filter. In this work, we have implemented optical spatial filtering in a common-path DHM system using a Fresnel biprism. We have analyzed the optimal pinhole size by evaluating the frequency content of the reconstructed phase images of a star target. We have also measured the accuracy of the system and the sensitivity to noise for different pinhole sizes. Finally, we have proposed the first dual-mode common-path DHM system using a Fresnel biprism. The performance of the dual-model DHM system has been evaluated experimentally using transmissive and reflective microscopic samples.
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Chen X, Kandel ME, Popescu G. Spatial light interference microscopy: principle and applications to biomedicine. ADVANCES IN OPTICS AND PHOTONICS 2021; 13:353-425. [PMID: 35494404 PMCID: PMC9048520 DOI: 10.1364/aop.417837] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this paper, we review spatial light interference microscopy (SLIM), a common-path, phase-shifting interferometer, built onto a phase-contrast microscope, with white-light illumination. As one of the most sensitive quantitative phase imaging (QPI) methods, SLIM allows for speckle-free phase reconstruction with sub-nanometer path-length stability. We first review image formation in QPI, scattering, and full-field methods. Then, we outline SLIM imaging from theory and instrumentation to diffraction tomography. Zernike's phase-contrast microscopy, phase retrieval in SLIM, and halo removal algorithms are discussed. Next, we discuss the requirements for operation, with a focus on software developed in-house for SLIM that enables high-throughput acquisition, whole slide scanning, mosaic tile registration, and imaging with a color camera. We introduce two methods for solving the inverse problem using SLIM, white-light tomography, and Wolf phase tomography. Lastly, we review the applications of SLIM in basic science and clinical studies. SLIM can study cell dynamics, cell growth and proliferation, cell migration, mass transport, etc. In clinical settings, SLIM can assist with cancer studies, reproductive technology, blood testing, etc. Finally, we review an emerging trend, where SLIM imaging in conjunction with artificial intelligence brings computational specificity and, in turn, offers new solutions to outstanding challenges in cell biology and pathology.
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Brown PT, Kruithoff R, Seedorf GJ, Shepherd DP. Multicolor structured illumination microscopy and quantitative control of polychromatic light with a digital micromirror device. BIOMEDICAL OPTICS EXPRESS 2021; 12:3700-3716. [PMID: 34221689 PMCID: PMC8221958 DOI: 10.1364/boe.422703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 05/10/2023]
Abstract
Linear structured illumination microscopy (SIM) is a super-resolution microscopy technique that does not impose photophysics requirements on fluorescent samples. Multicolor SIM implementations typically rely on liquid crystal on silicon (LCoS) spatial light modulators (SLM's) for patterning the excitation light, but digital micromirror devices (DMD's) are a promising alternative, owing to their lower cost and higher speed. However, existing coherent DMD SIM implementations use only a single wavelength of light, limited by the lack of efficient approaches for solving the blazed grating effect for polychromatic light. We develop the requisite quantitative tools, including a closed form solution of the blaze and diffraction conditions, forward models of DMD diffraction and pattern projection, and a model of DMD aberrations. Based on these advances, we constructed a three-color DMD microscope, quantified the effect of aberrations from the DMD, developed a high-resolution optical transfer function measurement technique, and demonstrated SIM on fixed and live cells. This opens the door to applying DMD's in polychromatic applications previously restricted to LCoS SLM's.
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Affiliation(s)
- Peter T. Brown
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Gregory J. Seedorf
- Department of Pediatrics and Pediatric Heart Lung Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Douglas P. Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
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8
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Brown PT, Kruithoff R, Seedorf GJ, Shepherd DP. Multicolor structured illumination microscopy and quantitative control of polychromatic light with a digital micromirror device. BIOMEDICAL OPTICS EXPRESS 2021. [PMID: 34221689 DOI: 10.1101/2020.07.27.223941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Linear structured illumination microscopy (SIM) is a super-resolution microscopy technique that does not impose photophysics requirements on fluorescent samples. Multicolor SIM implementations typically rely on liquid crystal on silicon (LCoS) spatial light modulators (SLM's) for patterning the excitation light, but digital micromirror devices (DMD's) are a promising alternative, owing to their lower cost and higher speed. However, existing coherent DMD SIM implementations use only a single wavelength of light, limited by the lack of efficient approaches for solving the blazed grating effect for polychromatic light. We develop the requisite quantitative tools, including a closed form solution of the blaze and diffraction conditions, forward models of DMD diffraction and pattern projection, and a model of DMD aberrations. Based on these advances, we constructed a three-color DMD microscope, quantified the effect of aberrations from the DMD, developed a high-resolution optical transfer function measurement technique, and demonstrated SIM on fixed and live cells. This opens the door to applying DMD's in polychromatic applications previously restricted to LCoS SLM's.
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Affiliation(s)
- Peter T Brown
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Gregory J Seedorf
- Department of Pediatrics and Pediatric Heart Lung Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
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9
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Konda PC, Loetgering L, Zhou KC, Xu S, Harvey AR, Horstmeyer R. Fourier ptychography: current applications and future promises. OPTICS EXPRESS 2020; 28:9603-9630. [PMID: 32225565 DOI: 10.1364/oe.386168] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/30/2020] [Indexed: 05/18/2023]
Abstract
Traditional imaging systems exhibit a well-known trade-off between the resolution and the field of view of their captured images. Typical cameras and microscopes can either "zoom in" and image at high-resolution, or they can "zoom out" to see a larger area at lower resolution, but can rarely achieve both effects simultaneously. In this review, we present details about a relatively new procedure termed Fourier ptychography (FP), which addresses the above trade-off to produce gigapixel-scale images without requiring any moving parts. To accomplish this, FP captures multiple low-resolution, large field-of-view images and computationally combines them in the Fourier domain into a high-resolution, large field-of-view result. Here, we present details about the various implementations of FP and highlight its demonstrated advantages to date, such as aberration recovery, phase imaging, and 3D tomographic reconstruction, to name a few. After providing some basics about FP, we list important details for successful experimental implementation, discuss its relationship with other computational imaging techniques, and point to the latest advances in the field while highlighting persisting challenges.
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10
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Chowdhury S, Chen M, Eckert R, Ren D, Wu F, Repina N, Waller L. High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images. OPTICA 2019; 6:1211-1219. [PMID: 38515960 PMCID: PMC10956703 DOI: 10.1364/optica.6.001211] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/01/2019] [Indexed: 03/23/2024]
Abstract
Optical diffraction tomography (ODT) reconstructs a sample's volumetric refractive index (RI) to create high-contrast, quantitative 3D visualizations of biological samples. However, standard implementations of ODT use interferometric systems, and so are sensitive to phase instabilities, complex mechanical design, and coherent noise. Furthermore, their reconstruction framework is typically limited to weakly scattering samples, and thus excludes a whole class of multiple-scattering samples. Here, we implement a new 3D RI microscopy technique that utilizes a computational multi-slice beam propagation method to invert the optical scattering process and reconstruct high-resolution (NA > 1.0) 3D RI distributions of multiple-scattering samples. The method acquires intensity-only measurements from different illumination angles and then solves a nonlinear optimization problem to recover the sample's 3D RI distribution. We experimentally demonstrate the reconstruction of samples with varying amounts of multiple-scattering: a 3T3 fibroblast cell, a cluster of C. elegans embryos, and a whole C. elegans worm, with lateral and axial resolutions of ≤ 240 nm and ≤ 900 nm, respectively. The results of this work lays groundwork for future studies into using optical wavelengths to probe 3D RI distributions of highly scattering biological organisms.
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Affiliation(s)
- Shwetadwip Chowdhury
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - Michael Chen
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - Regina Eckert
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - David Ren
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - Fan Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Nicole Repina
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Laura Waller
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
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11
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Yeh LH, Chowdhury S, Repina NA, Waller L. Speckle-structured illumination for 3D phase and fluorescence computational microscopy. BIOMEDICAL OPTICS EXPRESS 2019; 10:3635-3653. [PMID: 31467796 PMCID: PMC6706021 DOI: 10.1364/boe.10.003635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 05/29/2023]
Abstract
High-content biological microscopy targets high-resolution imaging across large fields-of-view, often achieved by computational imaging approaches. Previously, we demonstrated 2D multimodal high-content microscopy via structured illumination microscopy (SIM) with resolution > 2 × the diffraction limit, using speckle illumination from Scotch tape. In this work, we extend the method to 3D by leveraging the fact that the speckle illumination is in fact a 3D structured pattern. We use both a coherent and an incoherent imaging model to develop algorithms for joint retrieval of the 3D super-resolved fluorescent and complex-field distributions of the sample. Our reconstructed images resolve features beyond the physical diffraction-limit set by the system's objective and demonstrate 3D multimodal imaging with ∼ 0.6 × 0.6 × 6 μ m3 resolution over a volume of ∼ 314 × 500 × 24 μ m3.
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Affiliation(s)
- Li-Hao Yeh
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720,
USA
| | - Shwetadwip Chowdhury
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720,
USA
| | - Nicole A. Repina
- Graduate Program in Bioengineering, University of California, Berkeley, CA 94720,
USA
| | - Laura Waller
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720,
USA
- Graduate Program in Bioengineering, University of California, Berkeley, CA 94720,
USA
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12
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LEE KYEOREH, SHIN SEUNGWOO, YAQOOB ZAHID, SO PETERTC, PARK YONGKEUN. Low-coherent optical diffraction tomography by angle-scanning illumination. JOURNAL OF BIOPHOTONICS 2019; 12:e201800289. [PMID: 30597743 PMCID: PMC6470054 DOI: 10.1002/jbio.201800289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/27/2018] [Accepted: 12/28/2018] [Indexed: 05/20/2023]
Abstract
Temporally low-coherent optical diffraction tomography (ODT) is proposed and demonstrated based on angle-scanning Mach-Zehnder interferometry. Using a digital micromirror device based on diffractive tilting, the full-field interference of incoherent light is successfully maintained during every angle-scanning sequences. Further, current ODT reconstruction principles for temporally incoherent illuminations are thoroughly reviewed and developed. Several limitations of incoherent illumination are also discussed, such as the nondispersive assumption, optical sectioning capacity and illumination angle limitation. Using the proposed setup and reconstruction algorithms, low-coherent ODT imaging of plastic microspheres, human red blood cells and rat pheochromocytoma cells is experimentally demonstrated.
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Affiliation(s)
- KYEOREH LEE
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon 34141, Republic of Korea
| | - SEUNGWOO SHIN
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon 34141, Republic of Korea
| | - ZAHID YAQOOB
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - PETER T. C. SO
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - YONGKEUN PARK
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon 34051, Republic of Korea
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13
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Yeh LH, Chowdhury S, Waller L. Computational structured illumination for high-content fluorescence and phase microscopy. BIOMEDICAL OPTICS EXPRESS 2019; 10:1978-1998. [PMID: 31061769 PMCID: PMC6485002 DOI: 10.1364/boe.10.001978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/17/2019] [Accepted: 03/13/2019] [Indexed: 05/05/2023]
Abstract
High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample's super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4× the objective's diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 μm QP resolution, across a FOV of 2 × 2.7 mm 2 , giving a space-bandwidth product (SBP) of 60 megapixels.
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Affiliation(s)
- Li-Hao Yeh
- Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720,
USA
| | - Shwetadwip Chowdhury
- Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720,
USA
| | - Laura Waller
- Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720,
USA
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14
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He K, Wang Z, Huang X, Wang X, Yoo S, Ruiz P, Gdor I, Selewa A, Ferrier NJ, Scherer N, Hereld M, Katsaggelos AK, Cossairt O. Computational multifocal microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:6477-6496. [PMID: 31065444 PMCID: PMC6491004 DOI: 10.1364/boe.9.006477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/27/2023]
Abstract
Despite recent advances, high performance single-shot 3D microscopy remains an elusive task. By introducing designed diffractive optical elements (DOEs), one is capable of converting a microscope into a 3D "kaleidoscope," in which case the snapshot image consists of an array of tiles and each tile focuses on different depths. However, the acquired multifocal microscopic (MFM) image suffers from multiple sources of degradation, which prevents MFM from further applications. We propose a unifying computational framework which simplifies the imaging system and achieves 3D reconstruction via computation. Our optical configuration omits optical elements for correcting chromatic aberrations and redesigns the multifocal grating to enlarge the tracking area. Our proposed setup features only one single grating in addition to a regular microscope. The aberration correction, along with Poisson and background denoising, are incorporated in our deconvolution-based fully-automated algorithm, which requires no empirical parameter-tuning. In experiments, we achieve spatial resolutions of 0.35um (lateral) and 0.5um (axial), which are comparable to the resolution that can be achieved with confocal deconvolution microscopy. We demonstrate a 3D video of moving bacteria recorded at 25 frames per second using our proposed computational multifocal microscopy technique.
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Affiliation(s)
- Kuan He
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Zihao Wang
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Xiang Huang
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Xiaolei Wang
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
| | - Seunghwan Yoo
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Pablo Ruiz
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Itay Gdor
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
| | - Alan Selewa
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Nicola J. Ferrier
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Norbert Scherer
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
- James Franck Institute, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
| | - Mark Hereld
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Aggelos K. Katsaggelos
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Oliver Cossairt
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
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15
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Kim YS, Lee S, Jung J, Shin S, Choi HG, Cha GH, Park W, Lee S, Park Y. Combining Three-Dimensional Quantitative Phase Imaging and Fluorescence Microscopy for the Study of Cell Pathophysiology. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2018; 91:267-277. [PMID: 30258314 PMCID: PMC6153632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Quantitative phase imaging (QPI) has emerged as one of the powerful imaging tools for the study of live cells in a non-invasive manner. In particular, multimodal approaches combining QPI and fluorescence microscopic techniques have been recently developed for superior spatiotemporal resolution as well as high molecular specificity. In this review, we briefly summarize recent advances in three-dimensional QPI combined with fluorescence techniques for the correlative study of cell pathophysiology. Through this review, biologists and clinicians can be provided with insights on this rapidly growing field of research and may find broader applications to investigate unrevealed nature in cell physiology and related diseases.
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Affiliation(s)
- Young Seo Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea,Tomocube Inc., Daejeon, Republic of Korea,KAIST Institute of Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - SangYun Lee
- KAIST Institute of Health Science and Technology, KAIST, Daejeon, Republic of Korea,Department of Physics, KAIST, Daejeon, Republic of Korea
| | - JaeHwang Jung
- KAIST Institute of Health Science and Technology, KAIST, Daejeon, Republic of Korea,Department of Physics, KAIST, Daejeon, Republic of Korea
| | - Seungwoo Shin
- KAIST Institute of Health Science and Technology, KAIST, Daejeon, Republic of Korea,Department of Physics, KAIST, Daejeon, Republic of Korea
| | - He-Gwon Choi
- Department of Medical Science, Chungnam National University, Daejeon, Republic of Korea
| | - Guang-Ho Cha
- Department of Medical Science, Chungnam National University, Daejeon, Republic of Korea
| | - Weisun Park
- Tomocube Inc., Daejeon, Republic of Korea,KAIST Institute of Health Science and Technology, KAIST, Daejeon, Republic of Korea,Department of Physics, KAIST, Daejeon, Republic of Korea
| | - Sumin Lee
- Tomocube Inc., Daejeon, Republic of Korea
| | - YongKeun Park
- Tomocube Inc., Daejeon, Republic of Korea,KAIST Institute of Health Science and Technology, KAIST, Daejeon, Republic of Korea,Department of Physics, KAIST, Daejeon, Republic of Korea,To whom all correspondence should be addressed: YongKeun Park, Department of Physics, KAIST, Daejeon, Republic of Korea;
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Shin S, Kim D, Kim K, Park Y. Super-resolution three-dimensional fluorescence and optical diffraction tomography of live cells using structured illumination generated by a digital micromirror device. Sci Rep 2018; 8:9183. [PMID: 29907828 PMCID: PMC6004010 DOI: 10.1038/s41598-018-27399-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/24/2018] [Indexed: 11/26/2022] Open
Abstract
We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations.
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Affiliation(s)
- Seungwoo Shin
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Doyeon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Tomocube, Inc., 48, Yuseong-daero 1184beon-gil, Yuseong-Gu, Daejeon, 34051, Republic of Korea
| | - Kyoohyun Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea.
- Tomocube, Inc., 48, Yuseong-daero 1184beon-gil, Yuseong-Gu, Daejeon, 34051, Republic of Korea.
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Steelman ZA, Eldridge WJ, Wax A. Response to Comment on "Is the nuclear refractive index lower than cytoplasm? Validation of phase measurements and implications for light scattering technologies": A Comment on "How a phase image of a cell with nucleus refractive index smaller than that of the cytoplasm should look like?", e201800033. JOURNAL OF BIOPHOTONICS 2018; 11:e201800091. [PMID: 29722169 PMCID: PMC6814151 DOI: 10.1002/jbio.201800091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 05/05/2023]
Abstract
Recently, Maxim A. Yurkin commented on our paper "Is the nuclear refractive index lower than cytoplasm? Validation of phase measurements and implications for light scattering technologies" as well as on a complementary study "Cell nuclei have lower refractive index and mass density than cytoplasm" from Schürmann et al. In his comment, Yurkin concluded that quantitative phase images of cells with nuclei that are less optically dense than the cytoplasm must exhibit a characteristic concavity, the absence of which is evidence against our conclusion of a less-dense nucleus. In this response, we suggest that Yurkin's conclusion is reached through an oversimplification of the spatial refractive index distribution within cells, which does not account for high index inclusions such as the nucleolus. We further cite recent studies in 3-dimensional refractive index imaging, in which the preponderance of studies supports our conclusion. Finally, we comment on the current state of knowledge regarding subcellular refractive index distributions in living cells.
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Affiliation(s)
- Zachary A. Steelman
- Correspondence: Zachary A. Steelman,
Department of Biomedical Engineering, Duke University, 101 Science Drive,
Durham, NC 27708,
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