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Rawat S, Trius Béjar J, Wang A. Characterization of Optical, Thermal, and Viscoelastic Properties of Pollenkitt in Angiosperm Pollen Using In-Line Digital Holographic Microscopy. ACS APPLIED BIO MATERIALS 2024; 7:4029-4038. [PMID: 38756048 DOI: 10.1021/acsabm.4c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Pollen grains are remarkable material composites, with various organelles in their fragile interior protected by a strong shell made of sporopollenin. The outermost layer of angiosperm pollen grains contains a lipid-rich substance called pollenkitt, which is a natural bioadhesive that helps preserve structural integrity when the pollen grain is exposed to external environmental stresses. In addition, its viscous nature enables it to adhere to various floral and insect surfaces, facilitating the pollination process. To examine the physicochemical properties of aqueous pollenkitt droplets, we used in-line digital holographic microscopy to capture light scattering from individual pollenkitt particles. Comparison of pollenkitt holograms to those modeled using the Lorenz-Mie theory enables investigations into the minute variations in the refractive index and size resulting from changes in local temperature and pollen aging.
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Affiliation(s)
- Siddharth Rawat
- School of Chemistry, UNSW Sydney, Sydney, New South Wales 2052, Australia
- School of Physics, UNSW Sydney, Sydney, New South Wales 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, New South Wales 2052, Australia
- ARC CoE in Synthetic Biology, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Juan Trius Béjar
- Departament de Física, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, New South Wales 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, New South Wales 2052, Australia
- ARC CoE in Synthetic Biology, UNSW Sydney, Sydney, New South Wales 2052, Australia
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2
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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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3
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Matthews SA, Coelho C, Rodriguez Salas EE, Brock EE, Hodge VJ, Walker JA, Wilson LG. Real-time 3D tracking of swimming microbes using digital holographic microscopy and deep learning. PLoS One 2024; 19:e0301182. [PMID: 38669245 PMCID: PMC11051601 DOI: 10.1371/journal.pone.0301182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
The three-dimensional swimming tracks of motile microorganisms can be used to identify their species, which holds promise for the rapid identification of bacterial pathogens. The tracks also provide detailed information on the cells' responses to external stimuli such as chemical gradients and physical objects. Digital holographic microscopy (DHM) is a well-established, but computationally intensive method for obtaining three-dimensional cell tracks from video microscopy data. We demonstrate that a common neural network (NN) accelerates the analysis of holographic data by an order of magnitude, enabling its use on single-board computers and in real time. We establish a heuristic relationship between the distance of a cell from the focal plane and the size of the bounding box assigned to it by the NN, allowing us to rapidly localise cells in three dimensions as they swim. This technique opens the possibility of providing real-time feedback in experiments, for example by monitoring and adapting the supply of nutrients to a microbial bioreactor in response to changes in the swimming phenotype of microbes, or for rapid identification of bacterial pathogens in drinking water or clinical samples.
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Affiliation(s)
- Samuel A. Matthews
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | - Carlos Coelho
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | - Erick E. Rodriguez Salas
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | - Emma E. Brock
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | | | - James A. Walker
- Department of Computer Science, Deramore Lane, York, United Kingdom
| | - Laurence G. Wilson
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
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4
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Dubay MM, Acres J, Riekeles M, Nadeau JL. Recent advances in experimental design and data analysis to characterize prokaryotic motility. J Microbiol Methods 2023; 204:106658. [PMID: 36529156 DOI: 10.1016/j.mimet.2022.106658] [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: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying run distances and speeds, turn angles and behavior by surfaces or cell-cell interactions) remains a challenging task. A qualitative and quantitative understanding of bacterial motility is needed to bridge the gap between experimentation, omics analysis, and bacterial motility theory. In this review, we discuss the strengths and limitations of how phase contrast microscopy, fluorescence microscopy, and digital holographic microscopy have been used to quantify bacterial motility. Approaches to automated software analysis, including cell recognition, tracking, and track analysis, are also discussed with a view to providing a guide for experimenters to setting up the appropriate imaging and analysis system for their needs.
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Affiliation(s)
- Megan Marie Dubay
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Jacqueline Acres
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Max Riekeles
- Astrobiology Group, Center of Astronomy and Astrophysics, Technical University Berlin, Hardenbergstraße 36A, 10623 Berlin, Germany
| | - Jay L Nadeau
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America.
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5
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Elius M, Ling H. Effect of hologram plane position on particle tracking using digital holographic microscopy. APPLIED OPTICS 2022; 61:9415-9422. [PMID: 36606887 DOI: 10.1364/ao.473763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
This paper discusses the effect of hologram plane position on the tracking of particle motions in a 3D suspension using digital holography microscopy. We compare two optical configurations where the hologram plane is located either just outside the particle suspension or in the middle of the suspension. In both cases, we record two axially separated holograms using two cameras and subsequently adopt an iterative phase retrieval approach to solve the virtual image problem. We measure the settling motions of 2 µm spheres in a 2 mm thick sample containing 300 to 1500p a r t i c l e s/m m 3. We show that the optical setup where the hologram plane is located in the middle of the sample provides superior tracking results compared to the other, including higher accuracy in the measurement of particle displacement and longer particle trajectories. The accuracy of particle displacement increases by a maximum of 18%, and the trajectory length increases by a maximum of 16%. This superior outcome is due to the less overlapping of the diffraction patterns on the holograms when the separation distance between particles and the hologram plane is minimized.
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6
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Cheng Z, Zhang Y, Liu X, Guo C, He C, Liu G, Song H. Time-Resolved Four-Channel Jones Matrix Measurement of Birefringent Materials Using an Ultrafast Laser. MATERIALS (BASEL, SWITZERLAND) 2022; 15:7813. [PMID: 36363406 PMCID: PMC9654291 DOI: 10.3390/ma15217813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
A method for ultrafast time-resolved four-channel Jones matrix measurement of birefringent materials using an ultrafast laser is investigated. This facilitated the acquisition of a four-channel angular multiplexing hologram in a single shot. The Jones matrix information of a birefringent sample was retrieved from the spatial spectrum of a hologram. The feasibility of this approach was established by measuring the Jones matrix of starch granules in microfluidic chips and the complex amplitude distribution and phase delay distribution of liquid crystal cell at different voltages. Moreover, when the picosecond laser was switched to a femtosecond laser, ultrafast measurements were possible provided that the time interval between two detection pulses was larger than the pulse width.
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Affiliation(s)
- Zhenjia Cheng
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Yuqin Zhang
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Xuan Liu
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Chengshan Guo
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Changwei He
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Guiyuan Liu
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Hongsheng Song
- School of Science, Shandong Jianzhu University, Jinan 250101, China
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7
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Zhang J, Huang L, Chen B, Yan L. Accurate extraction of the +1 term spectrum with spurious spectrum elimination in off-axis digital holography. OPTICS EXPRESS 2022; 30:28142-28157. [PMID: 36236968 DOI: 10.1364/oe.464491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
In off-axis digital holography, spatial filtering is a key problem limiting the quality of reconstructed image, especially in the case of spurious spectrum generated by coherent noise in the hologram spectrum. In this paper, a new spatial filtering method with spurious spectrum elimination is proposed. Side band centering judgment is firstly implemented to locate the center point of the +1 term in the hologram spectrum. Then by roughly recognizing the region of +1 term spectrum, most of the -1 term, 0 term and the spurious spectral components are eliminated. Finally, Butterworth filtering is performed to extract the +1 term spectrum as enough as possible without introducing the spurious spectrum. Simulated hologram of E-shaped specimen with the spurious spectrum is generated to evaluate the performance of the proposed method. Experimental data of USAF 1951 resolution target, ovarian slice and microlens array are adopted to verify the effectiveness of the proposed method. Simulation and experimental results demonstrated that the proposed method is able to accurately extract the +1 term spectrum with spurious spectrum elimination and achieve a relatively good balance between the structural detail characterization and noise suppression.
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8
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Rawat S, Wendoloski J, Wang A. cGAN-assisted imaging through stationary scattering media. OPTICS EXPRESS 2022; 30:18145-18155. [PMID: 36221621 DOI: 10.1364/oe.450321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/03/2022] [Indexed: 06/16/2023]
Abstract
Analyzing images taken through scattering media is challenging, owing to speckle decorrelations from perturbations in the media. For in-line imaging modalities, which are appealing because they are compact, require no moving parts, and are robust, negating the effects of such scattering becomes particularly challenging. Here we explore the use of conditional generative adversarial networks (cGANs) to mitigate the effects of the additional scatterers in in-line geometries, including digital holographic microscopy. Using light scattering simulations and experiments on objects of interest with and without additional scatterers, we find that cGANs can be quickly trained with minuscule datasets and can also efficiently learn the one-to-one statistical mapping between the cross-domain input-output image pairs. Importantly, the output images are faithful enough to enable quantitative feature extraction. We also show that with rapid training using only 20 image pairs, it is possible to negate this undesired scattering to accurately localize diffraction-limited impulses with high spatial accuracy, therefore transforming a shift variant system to a linear shift invariant (LSI) system.
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9
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Palma V, Gutiérrez MS, Vargas O, Parthasarathy R, Navarrete P. Methods to Evaluate Bacterial Motility and Its Role in Bacterial–Host Interactions. Microorganisms 2022; 10:microorganisms10030563. [PMID: 35336138 PMCID: PMC8953368 DOI: 10.3390/microorganisms10030563] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial motility is a widespread characteristic that can provide several advantages for the cell, allowing it to move towards more favorable conditions and enabling host-associated processes such as colonization. There are different bacterial motility types, and their expression is highly regulated by the environmental conditions. Because of this, methods for studying motility under realistic experimental conditions are required. A wide variety of approaches have been developed to study bacterial motility. Here, we present the most common techniques and recent advances and discuss their strengths as well as their limitations. We classify them as macroscopic or microscopic and highlight the advantages of three-dimensional imaging in microscopic approaches. Lastly, we discuss methods suited for studying motility in bacterial–host interactions, including the use of the zebrafish model.
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Affiliation(s)
- Victoria Palma
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, El Líbano 5524, Santiago 7830490, Chile; (V.P.); (M.S.G.); (O.V.)
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, El Líbano 5524, Santiago 7830490, Chile; (V.P.); (M.S.G.); (O.V.)
- Millennium Science Initiative Program, Milenium Nucleus in the Biology of the Intestinal Microbiota, National Agency for Research and Development (ANID), Moneda 1375, Santiago 8200000, Chile
| | - Orlando Vargas
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, El Líbano 5524, Santiago 7830490, Chile; (V.P.); (M.S.G.); (O.V.)
| | - Raghuveer Parthasarathy
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA;
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, El Líbano 5524, Santiago 7830490, Chile; (V.P.); (M.S.G.); (O.V.)
- Millennium Science Initiative Program, Milenium Nucleus in the Biology of the Intestinal Microbiota, National Agency for Research and Development (ANID), Moneda 1375, Santiago 8200000, Chile
- Correspondence:
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10
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Kaddour H, Tranquille M, Okeoma CM. The Past, the Present, and the Future of the Size Exclusion Chromatography in Extracellular Vesicles Separation. Viruses 2021; 13:2272. [PMID: 34835078 PMCID: PMC8618570 DOI: 10.3390/v13112272] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/13/2023] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membranous particles secreted by all cell types (including virus infected and uninfected cells) into the extracellular milieu. EVs carry, protect, and transport a wide array of bioactive cargoes to recipient/target cells. EVs regulate physiological and pathophysiological processes in recipient cells and are important in therapeutics/drug delivery. Despite these great attributes of EVs, an efficient protocol for EV separation from biofluids is lacking. Numerous techniques have been adapted for the separation of EVs with size exclusion chromatography (SEC)-based methods being the most promising. Here, we review the SEC protocols used for EV separation, and discuss opportunities for significant improvements, such as the development of novel particle purification liquid chromatography (PPLC) system capable of tandem purification and characterization of biological and synthetic particles with near-single vesicle resolution. Finally, we identify future perspectives and current issues to make PPLC a tool capable of providing a unified, automated, adaptable, yet simple and affordable particle separation resource.
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Affiliation(s)
- Hussein Kaddour
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Malik Tranquille
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Chioma M. Okeoma
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
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11
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Shangraw M, Ling H. Improving axial localization of weak phase particles in digital in-line holography. APPLIED OPTICS 2021; 60:7099-7106. [PMID: 34612994 DOI: 10.1364/ao.435021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/18/2021] [Indexed: 06/13/2023]
Abstract
One shortcoming of digital in-line holography (DIH) is the low axial position accuracy due to the elongated particle traces in the reconstruction field. Here, we propose a method that improves the axial localization of DIH when applying it to track the motion of weak phase particles in dense suspensions. The proposed method detects particle positions based on local intensities in the reconstruction field consisting of scattering and incident waves. We perform both numerical and experimental tests and demonstrate that the proposed method has a higher axial position accuracy than the previous method based on the local intensities in the reconstructed scattered field. We show that the proposed method has an axial position error below 1.5 particle diameters for holograms with a particle concentration of 4700particles/mm3. The proposed method is further validated by tracking the Brownian motion of 1µmparticles in dense suspensions.
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12
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Wong GCL, Antani JD, Lele PP, Chen J, Nan B, Kühn MJ, Persat A, Bru JL, Høyland-Kroghsbo NM, Siryaporn A, Conrad JC, Carrara F, Yawata Y, Stocker R, V Brun Y, Whitfield GB, Lee CK, de Anda J, Schmidt WC, Golestanian R, O'Toole GA, Floyd KA, Yildiz FH, Yang S, Jin F, Toyofuku M, Eberl L, Nomura N, Zacharoff LA, El-Naggar MY, Yalcin SE, Malvankar NS, Rojas-Andrade MD, Hochbaum AI, Yan J, Stone HA, Wingreen NS, Bassler BL, Wu Y, Xu H, Drescher K, Dunkel J. Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Phys Biol 2021; 18. [PMID: 33462162 PMCID: PMC8506656 DOI: 10.1088/1478-3975/abdc0e] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/14/2021] [Indexed: 11/29/2022]
Abstract
Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.
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Affiliation(s)
- Gerard C L Wong
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA24061, United States of America
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, Texas, TX 77845, United States of America
| | - Marco J Kühn
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-Louis Bru
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America
| | | | - Albert Siryaporn
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Physics & Astronomy, University of California-Irvine, California, CA 92697, United States of America
| | - Jacinta C Conrad
- William A Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, TX 77204, United States of America
| | - Francesco Carrara
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yutaka Yawata
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves V Brun
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Gregory B Whitfield
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Calvin K Lee
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jaime de Anda
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - William C Schmidt
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), D-37077 Göttingen, Germany.,Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States of America
| | - Kyle A Floyd
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Shuai Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Biological Sciences, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Mauricio D Rojas-Andrade
- Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America
| | - Allon I Hochbaum
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America.,Department of Chemistry, University of California-Irvine, Irvine, California, CA 92697, United States of America.,Department of Chemical and Biomolecular Engineering, University of California-Irvine, Irvine, California, CA 92697, United States of America
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, CT 06511, United States of America
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,The Howard Hughes Medical Institute, Chevy Chase, Maryland MD 20815, United States of America
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139-4307, United States of America
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13
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Martin C, Leahy B, Manoharan VN. Improving holographic particle characterization by modeling spherical aberration. OPTICS EXPRESS 2021; 29:18212-18223. [PMID: 34154082 DOI: 10.1364/oe.424043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Holographic microscopy combined with forward modeling and inference allows colloidal particles to be characterized and tracked in three dimensions with high precision. However, current models ignore the effects of optical aberrations on hologram formation. We investigate the effects of spherical aberration on the structure of single-particle holograms and on the accuracy of particle characterization. We find that in a typical experimental setup, spherical aberration can result in systematic shifts of about 2% in the inferred refractive index and radius. We show that fitting with a model that accounts for spherical aberration decreases this aberration-dependent error by a factor of two or more, even when the level of spherical aberration in the optical train is unknown. With the new generative model, the inferred parameters are consistent across different levels of aberration, making particle characterization more robust.
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14
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Altman LE, Quddus R, Cheong FC, Grier DG. Holographic characterization and tracking of colloidal dimers in the effective-sphere approximation. SOFT MATTER 2021; 17:2695-2703. [PMID: 33630984 DOI: 10.1039/d0sm02262d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An in-line hologram of a colloidal sphere can be analyzed with the Lorenz-Mie theory of light scattering to measure the sphere's three-dimensional position with nanometer-scale precision while also measuring its diameter and refractive index with part-per-thousand precision. Applying the same technique to aspherical or inhomogeneous particles yields measurements of the position, diameter and refractive index of an effective sphere that represents an average over the particle's geometry and composition. This effective-sphere interpretation has been applied successfully to porous, dimpled and coated spheres, as well as to fractal clusters of nanoparticles, all of whose inhomogeneities appear on length scales smaller than the wavelength of light. Here, we combine numerical and experimental studies to investigate effective-sphere characterization of symmetric dimers of micrometer-scale spheres, a class of aspherical objects that appear commonly in real-world dispersions. Our studies demonstrate that the effective-sphere interpretation usefully distinguishes small colloidal clusters in holographic characterization studies of monodisperse colloidal spheres. The effective-sphere estimate for a dimer's axial position closely follows the ground truth for its center of mass. Trends in the effective-sphere diameter and refractive index, furthermore, can be used to measure a dimer's three-dimensional orientation. When applied to colloidal dimers transported in a Poiseuille flow, the estimated orientation distribution is consistent with expectations for Brownian particles undergoing Jeffery orbits.
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Affiliation(s)
- Lauren E Altman
- Department of Physics and Center for Soft Matter Research, New York University, New York, NY 10003, USA.
| | - Rushna Quddus
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | | - David G Grier
- Department of Physics and Center for Soft Matter Research, New York University, New York, NY 10003, USA.
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15
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Gibson T, Bedrossian M, Serabyn E, Lindensmith C, Nadeau JL. Using the Gouy phase anomaly to localize and track bacteria in digital holographic microscopy 4D images. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:A11-A18. [PMID: 33690523 DOI: 10.1364/josaa.404004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
Described over 100 years ago, the Gouy phase anomaly refers to the additional π phase shift that is accumulated as a wave passes through focus. It is potentially useful in analyzing any type of phase-sensitive imaging; in light microscopy, digital holographic microscopy (DHM) provides phase information in the encoded hologram. One limitation of DHM is the weak contrast generated by many biological cells, especially unpigmented bacteria. We demonstrate here that the Gouy phase anomaly may be detected directly in the phase image using the z-derivative of the phase, allowing for precise localization of unlabeled, micrometer-sized bacteria. The use of dyes that increase phase contrast does not improve detectability. This approach is less computationally intensive than other procedures such as deconvolution and is relatively insensitive to reconstruction parameters. The software is implemented in an open-source FIJI plug-in.
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16
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Shangraw M, Ling H. Separating twin images in digital holographic microscopy using weak scatterers. APPLIED OPTICS 2021; 60:626-634. [PMID: 33690444 DOI: 10.1364/ao.410167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
When using inline digital holographic microscopy (DHM) and placing the hologram plane within a particle suspension, both real and virtual images come into focus during reconstruction, limiting our ability to resolve three-dimensional (3D) particle distribution. Here, we propose a new method to distinguish between real and virtual images in the 3D reconstruction field. This new method is based on the use of weak scatterers, and the fact that the real and virtual images of weak scatterers display distinct intensity distributions along the optical axis. We experimentally demonstrate this method by localizing and tracking 1 µm particles in a 3D volume with a particle concentration ranging from 200 to 6000particles/mm3. Unlike previous approaches to address the virtual image problem, this method does not require the recording of multiple holograms or the insertion of additional optical components. The proposed method allows the hologram plane to be placed within the sample volume, and extends the capability of DHM to measure the 3D movements of particles in deep samples far away from the optical window.
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17
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Abstract
<abstract>
<p>Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fashion. However, computational tools for tracking large 4D datasets remain lacking. In this paper, we examine the errors introduced by tracking bacterial motion as 2D projections vs. 3D volumes under different circumstances: bacteria free in liquid media and bacteria near a glass surface. We find that while XYZ speeds are generally equal to or larger than XY speeds, they are still within empirical uncertainties. Additionally, when studying dynamic surface behavior, the Z coordinate cannot be neglected.</p>
</abstract>
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18
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Barkley S, Dimiduk TG, Fung J, Kaz DM, Manoharan VN, McGorty R, Perry RW, Wang A. Holographic Microscopy With Python and HoloPy. Comput Sci Eng 2020. [DOI: 10.1109/mcse.2019.2923974] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Kaddour H, Lyu Y, Shouman N, Mohan M, Okeoma CM. Development of Novel High-Resolution Size-Guided Turbidimetry-Enabled Particle Purification Liquid Chromatography (PPLC): Extracellular Vesicles and Membraneless Condensates in Focus. Int J Mol Sci 2020; 21:ijms21155361. [PMID: 32731547 PMCID: PMC7432554 DOI: 10.3390/ijms21155361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Acellular particles (extracellular vesicles and membraneless condensates) have important research, drug discovery, and therapeutic implications. However, their isolation and retrieval have faced enormous challenges, impeding their use. Here, a novel size-guided particle purification liquid chromatography (PPLC) is integrated into a turbidimetry-enabled system for dye-free isolation, online characterization, and retrieval of intact acellular particles from biofluids. The chromatographic separation of particles from different biofluids—semen, blood, urine, milk, and cell culture supernatants—is achieved using a first-in-class gradient size exclusion column (gSEC). Purified particles are collected using a fraction collector. Online UV–Vis monitoring reveals biofluid-dependent particle spectral differences, with semen being the most complex. Turbidimetry provides the accurate physical characterization of seminal particle (Sp) lipid contents, sizes, and concentrations, validated by a nanoparticle tracking analysis, transmission electron microscopy, and naphthopyrene assay. Furthermore, different fractions of purified Sps contain distinct DNA, RNA species, and protein compositions. The integration of Sp physical and compositional properties identifies two archetypal membrane-encased seminal extracellular vesicles (SEV)—notably SEV large (SEVL), SEV small (SEVS), and a novel non-archetypal-membraneless Sps, herein named membraneless condensates (MCs). This study demonstrates a comprehensive yet affordable platform for isolating, collecting, and analyzing acellular particles to facilitate extracellular particle research and applications in drug delivery and therapeutics. Ongoing efforts focus on increased resolution by tailoring bead/column chemistry for each biofluid type.
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Affiliation(s)
- Hussein Kaddour
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794-8651, USA; (H.K.); (Y.L.); (N.S.)
| | - Yuan Lyu
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794-8651, USA; (H.K.); (Y.L.); (N.S.)
| | - Nadia Shouman
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794-8651, USA; (H.K.); (Y.L.); (N.S.)
| | - Mahesh Mohan
- Host Pathogen Interaction Program Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Chioma M. Okeoma
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794-8651, USA; (H.K.); (Y.L.); (N.S.)
- Correspondence: ; Tel.: +1-631-444-3014
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20
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Leahy B, Alexander R, Martin C, Barkley S, Manoharan VN. Large depth-of-field tracking of colloidal spheres in holographic microscopy by modeling the objective lens. OPTICS EXPRESS 2020; 28:1061-1075. [PMID: 32121823 DOI: 10.1364/oe.382159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Holographic microscopy has developed into a powerful tool for 3D particle tracking, yielding nanometer-scale precision at high frame rates. However, current particle tracking algorithms ignore the effect of the microscope objective on the formation of the recorded hologram. As a result, particle tracking in holographic microscopy is currently limited to particles well above the microscope focus. Here, we show that modeling the effect of an aberration-free lens allows tracking of particles above, near, and below the focal plane in holographic microscopy, doubling the depth of field. Finally, we use our model to determine the conditions under which ignoring the effect of the lens is justified and in what conditions it leads to systematic errors.
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21
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Bianchi S, Saglimbeni F, Frangipane G, Dell'Arciprete D, Di Leonardo R. 3D dynamics of bacteria wall entrapment at a water-air interface. SOFT MATTER 2019; 15:3397-3406. [PMID: 30933209 DOI: 10.1039/c9sm00077a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Swimming bacteria can be trapped for prolonged times at the surface of an impenetrable boundary. The subsequent surface confined motility is found to be very sensitive to the physico-chemical properties of the interfaces which determine the boundary conditions for the flow. The quantitative understanding of this complex dynamics requires detailed and systematic experimental data to validate theoretical models for both flagellar propulsion and interfacial dynamics. Using a combination of optical trapping and holographic imaging we study the 3D dynamics of wall entrapment of swimming bacteria that are sequentially released towards a surfactant-covered liquid-air interface. We find that an incompressible surfactant model for the interface quantitatively accounts for the observed normal and tangential speed of bacteria as they approach the boundary. Surprisingly we also find that, although bacteria circulate over the air phase in counterclockwise circular trajectories, typical of free-slip interfaces, the body axis is still tilted "nose down" as found for no-slip interfaces.
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Affiliation(s)
- Silvio Bianchi
- CNR-NANOTEC, Soft and Living Matter Laboratory, Rome, I-00185 Roma, Italy.
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22
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Flewellen JL, Zaid IM, Berry RM. A multi-mode digital holographic microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:023705. [PMID: 30831696 DOI: 10.1063/1.5066556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
We present a transmission-mode digital holographic microscope that can switch easily between three different imaging modes: inline, dark field off-axis, and bright field off-axis. Our instrument can be used: to track through time in three dimensions microscopic dielectric objects, such as motile micro-organisms; localize brightly scattering nanoparticles, which cannot be seen under conventional bright field illumination; and recover topographic information and measure the refractive index and dry mass of samples via quantitative phase recovery. Holograms are captured on a digital camera capable of high-speed video recording of up to 2000 frames per second. The inline mode of operation can be easily configurable to a large range of magnifications. We demonstrate the efficacy of the inline mode in tracking motile bacteria in three dimensions in a 160 μm × 160 μm × 100 μm volume at 45× magnification. Through the use of a novel physical mask in a conjugate Fourier plane in the imaging path, we use our microscope for high magnification, dark field off-axis holography, demonstrated by localizing 100 nm gold nanoparticles at 225× magnification up to at least 16 μm from the imaging plane. Finally, the bright field off-axis mode facilitates quantitative phase microscopy, which we employ to measure the refractive index of a standard resolution test target and to measure the dry mass of human erythrocytes.
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Affiliation(s)
- James L Flewellen
- Immune Receptor Activation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Irwin M Zaid
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Richard M Berry
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
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23
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Zhang H, Stangner T, Wiklund K, Andersson M. Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holography. APPLIED OPTICS 2018; 57:9855-9862. [PMID: 30462021 DOI: 10.1364/ao.57.009855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/15/2018] [Indexed: 06/09/2023]
Abstract
Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolved by iterative reconstruction routines. However, recovering the phase properties of an object in a hologram requires an object plane to be chosen correctly for reconstruction. In this work, we present a novel multi-wavelength iterative algorithm to determine the object plane using single-shot holograms recorded at multiple wavelengths in an in-line holographic microscope. Using micro-sized objects, we verify the object positioning capabilities of the method for various shapes and derive the phase information using synthetic and experimental data. Experimentally, we built a compact digital in-line holographic microscopy setup around a standard optical microscope with a regular RGB-CCD camera and acquired holograms of micro-spheres, E. coli, and red blood cells, which are illuminated using three lasers operating at 491 nm, 532 nm, and 633 nm, respectively. We demonstrate that our method provides accurate object plane detection and phase retrieval under noisy conditions, e.g., using low-contrast holograms with an inhomogeneous background. This method allows for automatic positioning and phase retrieval suitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research.
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24
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Jung J, Kim J, Seo MK, Park Y. Measurements of polarization-dependent angle-resolved light scattering from individual microscopic samples using Fourier transform light scattering. OPTICS EXPRESS 2018; 26:7701-7711. [PMID: 29609322 DOI: 10.1364/oe.26.007701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/24/2018] [Indexed: 05/27/2023]
Abstract
We present a method to measure the vector-field light scattering of individual microscopic objects. The polarization-dependent optical field images are measured with quantitative phase imaging at the sample plane, and then numerically propagated to the far-field plane. This approach allows the two-dimensional polarization-dependent angle-resolved light scattered patterns from individual object to be obtained with high precision and sensitivity. Using this method, we present the measurements of the polarization-dependent light scattering of a liquid crystal droplet and individual silver nanowires over scattering angles of 50°. In addition, the spectroscopic extension of the polarization-dependent angle-resolved light scattering is demonstrated using wavelength-scanning illumination.
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25
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Farthing NE, Findlay RC, Jikeli JF, Walrad PB, Bees MA, Wilson LG. Simultaneous two-color imaging in digital holographic microscopy. OPTICS EXPRESS 2017; 25:28489-28500. [PMID: 31956278 PMCID: PMC6968951 DOI: 10.1364/oe.25.028489] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/14/2017] [Indexed: 05/24/2023]
Abstract
We demonstrate the use of two-color digital holographic microscopy (DHM) for imaging microbiological subjects. The use of two wavelengths significantly reduces artifacts present in the reconstructed data, allowing us to image weakly-scattering objects in close proximity to strongly-scattering objects. We demonstrate this by reconstructing the shape of the flagellum of a unicellular eukaryotic parasite Leishmania mexicana in close proximity to a more strongly-scattering cell body. Our approach also yields a reduction of approximately one third in the axial position uncertainty when tracking the motion of swimming cells at low magnification, which we demonstrate with a sample of Escherichia coli bacteria mixed with polystyrene beads. The two-wavelength system that we describe introduces minimal additional complexity into the optical system, and provides significant benefits.
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Affiliation(s)
- Nicola E. Farthing
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Rachel C. Findlay
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Jan F. Jikeli
- Biophysical Imaging, Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Pegine B. Walrad
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Martin A. Bees
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Laurence G. Wilson
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK
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26
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Vandewiele S, Strubbe F, Schreuer C, Neyts K, Beunis F. Low coherence digital holography microscopy based on the Lorenz-Mie scattering model. OPTICS EXPRESS 2017; 25:25853-25866. [PMID: 29041248 DOI: 10.1364/oe.25.025853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/30/2017] [Indexed: 06/07/2023]
Abstract
We demonstrate the use of low spatial and temporal coherence holography microscopy, based on the Lorenz-Mie model, using the standard tungsten-halogen lamp present in an inverted microscope. An optical model is put forward to incorporate the effect of spectral width and different incidence angles of the incident light determined by the aperture at the back focal plane of the condenser lens. The model is validated for 899 nm diameter polystyrene microspheres in glycerol, giving a resolution of 0.4% for the index of refraction and 2.2% for the diameter of the particles.
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27
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Gao Y, Yu Y, Sanchez L, Yu Y. Seeing the unseen: Imaging rotation in cells with designer anisotropic particles. Micron 2017; 101:123-131. [PMID: 28711013 DOI: 10.1016/j.micron.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 01/27/2023]
Abstract
Cellular functions are enabled by cascades of transient biological events. Imaging and tracking the dynamics of these events have proven to be a powerful means of understanding the principles of cellular processes. These studies have typically focused on translational dynamics. By contrast, investigations of rotational dynamics have been scarce, despite emerging evidence that rotational dynamics are an inherent feature of many cellular processes and may also provide valuable clues to understanding those cell functions. Such studies have been impeded by the limited availability of suitable rotational imaging probes. This has recently changed thanks to the advances in the development of anisotropic particles for rotational imaging. In this review, we will summarize current techniques for imaging rotation using particle probes that are anisotropic in shape or optical properties. We will highlight two studies that demonstrate how these techniques can be applied to explore important facets of cellular functions.
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Affiliation(s)
- Yuan Gao
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Yanqi Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Lucero Sanchez
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States.
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28
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Lemoine A, Delvigne F, Bockisch A, Neubauer P, Junne S. Tools for the determination of population heterogeneity caused by inhomogeneous cultivation conditions. J Biotechnol 2017; 251:84-93. [DOI: 10.1016/j.jbiotec.2017.03.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 01/01/2023]
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