Rapid, high-throughput tracking of bacterial motility in 3D via phase-contrast holographic video microscopy

Digital in-line holographic microscopy for label-free identification and tracking of biological cells

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.

Real-time 3D tracking of swimming microbes using digital holographic microscopy and deep learning

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.

All-optical dual module platform for motility-based functional scrutiny of microencapsulated probiotic bacteria

Probiotic bacteria are widely used in pharmaceutics to offer health benefits. Microencapsulation is used to deliver probiotics into the human body. Capsules in the stomach have to keep bacteria constrained until release occurs in the intestine. Once outside, bacteria must maintain enough motility to reach the intestine walls. Here, we develop a platform based on two label-free optical modules for rapidly screening and ranking probiotic candidates in the laboratory. Bio-speckle dynamics assay tests the microencapsulation effectiveness by simulating the gastrointestinal transit. Then, a digital holographic microscope 3D-tracks their motility profiles at a single element level to rank the strains.

Silver Ions Inhibit Bacterial Movement and Stall Flagellar Motor

Silver (Ag) in different forms has been gaining broad attention due to its antimicrobial activities and the increasing resistance of bacteria to commonly prescribed antibiotics. However, various aspects of the antimicrobial mechanism of Ag have not been understood, including how Ag affects bacterial motility, a factor intimately related to bacterial virulence. Here, we report our study on how Ag⁺ ions affect the motility of E. coli bacteria using swimming, tethering, and rotation assays. We observed that the bacteria slowed down dramatically by >70% when subjected to Ag⁺ ions, providing direct evidence that Ag⁺ ions inhibit the motility of bacteria. In addition, through tethering and rotation assays, we monitored the rotation of flagellar motors and observed that the tumbling/pausing frequency of bacteria increased significantly by 77% in the presence of Ag⁺ ions. Furthermore, we analyzed the results from the tethering assay using the hidden Markov model (HMM) and found that Ag⁺ ions decreased bacterial tumbling/pausing-to-running transition rate significantly by 75%. The results suggest that the rotation of bacterial flagellar motors was stalled by Ag⁺ ions. This work provided a new quantitative understanding of the mechanism of Ag-based antimicrobial agents in bacterial motility.

High-Speed and Low-Latency 3D Fluorescence Imaging for Robotic Microscope

In this study, we propose a high-speed and low-latency 3D fluorescence imaging method for robotic microscopes. The prototype system consists of a focus-tunable lens called a TAG lens, which operates at several hundred kHz, an image intensifier (I.I.) that enhances faint light such as fluorescence, and a high-speed vision system that can transfer acquired images to the host PC in 500 Hz. The proposed method can acquire images at arbitrary focal lengths at frame rates on the order of 1 kHz by synchronizing the focal-length fluctuation of the TAG lens and the exposure timing of the I.I., whose duration is a few hundred nanoseconds. The low-latency we aim for in this paper is on the order of a few milliseconds. A prototype system was developed to validate the proposed method. High-speed 3D tracking of the Brownian motion of a fluorescent bead of 0.5 μm diameter was demonstrated to verify the feedback performance of the proposed low-latency 3D fluorescence imaging method.

Label-free viability assay using in-line holographic video microscopy

Total holographic characterization (THC) is presented here as an efficient, automated, label-free method of accurately identifying cell viability. THC is a single-particle characterization technology that determines the size and index of refraction of individual particles using the Lorenz-Mie theory of light scattering. Although assessment of cell viability is a challenge in many applications, including biologics manufacturing, traditional approaches often include unreliable labeling with dyes and/or time consuming methods of manually counting cells. In this work we measured the viability of Saccharomyces cerevisiae yeast in the presence of various concentrations of isopropanol as a function of time. All THC measurements were performed in the native environment of the sample with no dilution or addition of labels. Holographic measurements were made with an in-line holographic microscope using a 40[Formula: see text] objective lens with plane wave illumination. We compared our results with THC to manual counting of living and dead cells as distinguished with trypan blue dye. Our findings demonstrate that THC can effectively distinguish living and dead yeast cells by the index of refraction of individual cells.

Methods to Evaluate Bacterial Motility and Its Role in Bacterial–Host Interactions

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.

Improving axial localization of weak phase particles in digital in-line holography

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.

Holographic characterization and tracking of colloidal dimers in the effective-sphere approximation

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.

Dynamic swimming pattern of Pseudomonas aeruginosa near a vertical wall during initial attachment stages of biofilm formation

Studying the swimming behaviour of bacteria in 3 dimensions (3D) allows us to understand critical biological processes, such as biofilm formation. It is still unclear how near wall swimming behaviour may regulate the initial attachment and biofilm formation. It is challenging to address this as visualizing the movement of bacteria with reasonable spatial and temporal resolution in a high-throughput manner is technically difficult. Here, we compared the near wall (vertical) swimming behaviour of P. aeruginosa (PAO1) and its mutants ΔdipA (reduced in swarming motility and increased in biofilm formation) and ΔfimX (deficient in twitching motility and reduced in biofilm formation) using our new imaging technique based on light sheet microscopy. We found that P. aeruginosa (PAO1) increases its speed and changes its swimming angle drastically when it gets closer to a wall. In contrast, ΔdipA mutant moves toward the wall with steady speed without changing of swimming angle. The near wall behavior of ΔdipA allows it to be more effective to interact with the wall or wall-attached cells, thus leading to more adhesion events and a larger biofilm volume during initial attachment when compared with PAO1. Furthermore, we found that ΔfimX has a similar near wall swimming behavior as PAO1. However, it has a higher dispersal frequency and smaller biofilm formation when compared with PAO1 which can be explained by its poor twitching motility. Together, we propose that near wall swimming behavior of P. aeruginosa plays an important role in the regulation of initial attachment and biofilm formation.

2D vs 3D tracking in bacterial motility analysis

<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>

Adaptive behaviors of planktonic Pseudomonas aeruginosa in response to the surface-deposited dead siblings

In this study, the 3D motion behaviors and the underlying adaptation mechanism of planktonic Pseudomonas aeruginosa (PAO1) in response to the deposited dead siblings nearby were explored. Utilizing a real-time 3D tracking technique, digital holographic microscopy (DHM), we demonstrate that planktonic cells near the surface covered with dead siblings have a lower density and a reduced 3D velocity compared with those upon viable ones. As a sign of chemosensory responses, bacteria swimming near the dead siblings exhibit increase in frequency of the 'flick' motion. Transcriptomic analysis by RNA-seq reveals an upregulated expression of dgcM and dgcE inhibited the movement of PAO1, accompanied by increased transcriptional levels of the virulence factor-related genes hcp1, clpV1, and vgrG1. Moreover, the decrease in l-glutamate and the increase in succinic acid in the metabolites of the dead bacteria layer promote the dispersion of planktonic bacteria. As a result, the dead siblings on a surface inhibit the bacterial accumulation and activate the adaptive defensive responses of planktonic PAO1 in the vicinity.

A multi-mode digital holographic microscope

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.

Simultaneous two-color imaging in digital holographic microscopy

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.

High-Speed "4D" Computational Microscopy of Bacterial Surface Motility

Bacteria exhibit surface motility modes that play pivotal roles in early-stage biofilm community development, such as type IV pili-driven "twitching" motility and flagellum-driven "spinning" and "swarming" motility. Appendage-driven motility is controlled by molecular motors, and analysis of surface motility behavior is complicated by its inherently 3D nature, the speed of which is too fast for confocal microscopy to capture. Here, we combine electromagnetic field computation and statistical image analysis to generate 3D movies close to a surface at 5 ms time resolution using conventional inverted microscopes. We treat each bacterial cell as a spherocylindrical lens and use finite element modeling to solve Maxwell's equations and compute the diffracted light intensities associated with different angular orientations of the bacterium relative to the surface. By performing cross-correlation calculations between measured 2D microscopy images and a library of computed light intensities, we demonstrate that near-surface 3D movies of Pseudomonas aeruginosa translational and rotational motion are possible at high temporal resolution. Comparison between computational reconstructions and detailed hydrodynamic calculations reveals that P. aeruginosa act like low Reynolds number spinning tops with unstable orbits, driven by a flagellum motor with a torque output of ∼2 pN μm. Interestingly, our analysis reveals that P. aeruginosa can undergo complex flagellum-driven dynamical behavior, including precession, nutation, and an unexpected taxonomy of surface motility mechanisms, including upright-spinning bacteria that diffuse laterally across the surface, and horizontal bacteria that follow helicoidal trajectories and exhibit superdiffusive movements parallel to the surface.

Visualizing Flagella while Tracking Bacteria

A complete description of the swimming behavior of a bacterium requires measurement of the displacement and orientation of the cell body together with a description of the movement of the flagella. We rebuilt a tracking microscope so that we could visualize flagellar filaments of tracked cells by fluorescence. We studied Escherichia coli (cells of various lengths, including swarm cells), Bacillus subtilis (wild-type and a mutant with fewer flagella), and a motile Streptococcus (now Enterococcus). The run-and-tumble statistics were nearly the same regardless of cell shape, length, and flagellation; however, swarm cells rarely tumbled, and cells of Enterococcus tended to swim in loops when moving slowly. There were events in which filaments underwent polymorphic transformations but remained in bundles, leading to small deflections in direction of travel. Tumble speeds were ∼2/3 as large as run speeds, and the rates of change of swimming direction while running or tumbling were smaller when cells swam more rapidly. If a smaller fraction of filaments were involved in tumbles, the tumble intervals were shorter and the angles between runs were smaller.

Landing Dynamics of Swimming Bacteria on a Polymeric Surface: Effect of Surface Properties

Landing of bacteria for adhesion on a surface is a common phenomenon in our life. However, how surface properties are involved in this process remains largely unclear. Using digital holographic microscopy, we investigated the three-dimensional motions of flagellate Escherichia coli swimming near polymeric surfaces with different properties in aqueous solution before adhesion. We monitored the bacteria landing dynamics, which shows that the density distribution, the probability, and the orientation for collisions of the bacteria are determined by their motility but are slightly affected by the surface properties. However, surface hydrophobicity reduces the near-wall velocity of the bacteria through collisions and slightly increases the collision duration. This promotes the landing and adhesion of bacteria. By contrast, most bacteria collide with the surface using their flagella, which resist adhesion.

An all-glass 12 μm ultra-thin and flexible micro-fluidic chip fabricated by femtosecond laser processing

This study investigated and established a method, using femtosecond laser processing, to fabricate a 100%-glass-based 12 μm ultra-thin and flexible micro-fluidic chip. First we investigated the suitable pulse energy of the laser to fabricate ultra-thin glass sheets and then we fabricated a prototype glass micro-fluidic chip. Two 1 mm-in-diameter orifices for facilitating alignment in the bonding step and one channel with a width of 20 μm and a length of 25 mm were fabricated in a 4 μm thickness ultra-thin glass sheet using the femtosecond laser; this forms layer 2 in the completed device. Next, the glass sheet with the channel was sandwiched between another glass sheet having an inlet hole and an outlet hole (layer 1) and a base glass sheet (layer 3); the three sheets were bonded to each other, resulting in a flexible, 100%-glass micro-fluidic chip with a thickness of approximately 12 μm and a weight of 3.6 mg. The basic function of the glass micro-fluidic chip was confirmed by flowing 1 and 2 μm in-diameter bead particles through the channel. The fabrication method clearly scales down the thickness limitation of flexible glass devices and offers a possible element technology for fabricating ultra-thin glass devices that can be applied to convection-enhanced delivery, implantable medical devices, wearable devices, and high-resolution imaging of small biological objects such as bacteria and proteins in the channel.

Large-Scale Integration of All-Glass Valves on a Microfluidic Device

In this study, we developed a method for fabricating a microfluidic device with integrated large-scale all-glass valves and constructed an actuator system to control each of the valves on the device. Such a microfluidic device has advantages that allow its use in various fields, including physical, chemical, and biochemical analyses and syntheses. However, it is inefficient and difficult to integrate the large-scale all-glass valves in a microfluidic device using conventional glass fabrication methods, especially for the through-hole fabrication step. Therefore, we have developed a fabrication method for the large-scale integration of all-glass valves in a microfluidic device that contains 110 individually controllable diaphragm valve units on a 30 mm × 70 mm glass slide. This prototype device was fabricated by first sandwiching a 0.4-mm-thick glass slide that contained 110 1.5-mm-diameter shallow chambers, each with two 50-μm-diameter through-holes, between an ultra-thin glass sheet (4 μm thick) and another 0.7-mm-thick glass slide that contained etched channels. After the fusion bonding of these three layers, the large-scale microfluidic device was obtained with integrated all-glass valves consisting of 110 individual diaphragm valve units. We demonstrated its use as a pump capable of generating a flow rate of approximately 0.06–5.33 μL/min. The maximum frequency of flow switching was approximately 12 Hz.

Improved Tracking and Resolution of Bacteria in Holographic Microscopy Using Dye and Fluorescent Protein Labeling

Digital holographic microscopy (DHM) is an emerging imaging technique that permits instantaneous capture of a relatively large sample volume. However, large volumes usually come at the expense of lower spatial resolution, and the technique has rarely been used with prokaryotic cells due to their small size and low contrast. In this paper we demonstrate the use of a Mach-Zehnder dual-beam instrument for imaging of labeled and unlabeled bacteria and microalgae. Spatial resolution of 0.3 μm is achieved, providing a sampling of several pixels across a typical prokaryotic cell. Both cellular motility and morphology are readily recorded. The use of dyes provides both amplitude and phase contrast improvement and is of use to identify cells in dense samples.

High-throughput 3D tracking of bacteria on a standard phase contrast microscope

Bacteria employ diverse motility patterns in traversing complex three-dimensional (3D) natural habitats. 2D microscopy misses crucial features of 3D behaviour, but the applicability of existing 3D tracking techniques is constrained by their performance or ease of use. Here we present a simple, broadly applicable, high-throughput 3D bacterial tracking method for use in standard phase contrast microscopy. Bacteria are localized at micron-scale resolution over a range of 350 × 300 × 200 μm by maximizing image cross-correlations between their observed diffraction patterns and a reference library. We demonstrate the applicability of our technique to a range of bacterial species and exploit its high throughput to expose hidden contributions of bacterial individuality to population-level variability in motile behaviour. The simplicity of this powerful new tool for bacterial motility research renders 3D tracking accessible to a wider community and paves the way for investigations of bacterial motility in complex 3D environments.

Microscopy techniques used to study the movement of swimming microbes are limited to two dimensions or require sophisticated devices. Here, Taute et al. present a simple method for high-throughput 3D tracking of bacteria using standard phase contrast microscopy.