Single-objective high-resolution confocal light sheet fluorescence microscopy for standard biological sample geometries

In Vivo Microrheology Reveals Local Elastic and Plastic Responses Inside 3D Bacterial Biofilms

Bacterial biofilms are highly abundant 3D living materials capable of performing complex biomechanical and biochemical functions, including programmable growth, self-repair, filtration, and bioproduction. Methods to measure internal mechanical properties of biofilms in vivo with spatial resolution on the cellular scale have been lacking. Here, thousands of cells are tracked inside living 3D biofilms of the bacterium Vibrio cholerae during and after the application of shear stress, for a wide range of stress amplitudes, periods, and biofilm sizes, which revealed anisotropic elastic and plastic responses of both cell displacements and cell reorientations. Using cellular tracking to infer parameters of a general mechanical model, spatially-resolved measurements of the elastic modulus inside the biofilm are obtained, which correlate with the spatial distribution of the polysaccharides within the biofilm matrix. The noninvasive microrheology and force-inference approach introduced here provides a general framework for studying mechanical properties with high spatial resolution in living materials.

Graded arc beam in light needle microscopy for axially resolved, rapid volumetric imaging without nonlinear processes

High-speed three-dimensional (3D) imaging is essential for revealing the structure and functions of biological specimens. Confocal laser scanning microscopy has been widely employed for this purpose. However, it requires a time-consuming image-stacking procedure. As a solution, we previously developed light needle microscopy using a Bessel beam with a wavefront-engineered approach [Biomed. Opt. Express13, 1702 (2022)10.1364/BOE.449329]. However, this method applies only to multiphoton excitation microscopy because of the requirement to reduce the sidelobes of the Bessel beam. Here, we introduce a beam that produces a needle spot while eluding the intractable artifacts due to the sidelobes. This beam can be adopted even in one-photon excitation fluorescence 3D imaging. The proposed method can achieve real-time, rapid 3D observation of 200-nm particles in water at a rate of over 50 volumes per second. In addition, fine structures, such as the spines of neurons in fixed mouse brain tissue, can be visualized in 3D from a single raster scan of the needle spot. The proposed method can be applied to various modalities in biological imaging, enabling rapid 3D image acquisition.

Harnessing the power of optical microscopy for visualization and analysis of histopathological images

Histopathology is the foundation and gold standard for identifying diseases, and precise quantification of histopathological images can provide the pathologist with objective clues to make a more convincing diagnosis. Optical microscopy (OM), an important branch of optical imaging technology that provides high-resolution images of tissue cytology and structural morphology, has been used in the diagnosis of histopathology and evolved into a new disciplinary direction of optical microscopic histopathology (OMH). There are a number of ex-vivo studies providing applicability of different OMH approaches, and a transfer of these techniques toward in vivo diagnosis is currently in progress. Furthermore, combined with advanced artificial intelligence algorithms, OMH allows for improved diagnostic reliability and convenience due to the complementarity of retrieval information. In this review, we cover recent advances in OMH, including the exploration of new techniques in OMH as well as their applications, and look ahead to new challenges in OMH. These typical application examples well demonstrate the application potential and clinical value of OMH techniques in histopathological diagnosis.

Advances in linking single-cell bacterial stress response to population-level survival

Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.

BCM3D 2.0: accurate segmentation of single bacterial cells in dense biofilms using computationally generated intermediate image representations

Accurate detection and segmentation of single cells in three-dimensional (3D) fluorescence time-lapse images is essential for observing individual cell behaviors in large bacterial communities called biofilms. Recent progress in machine-learning-based image analysis is providing this capability with ever-increasing accuracy. Leveraging the capabilities of deep convolutional neural networks (CNNs), we recently developed bacterial cell morphometry in 3D (BCM3D), an integrated image analysis pipeline that combines deep learning with conventional image analysis to detect and segment single biofilm-dwelling cells in 3D fluorescence images. While the first release of BCM3D (BCM3D 1.0) achieved state-of-the-art 3D bacterial cell segmentation accuracies, low signal-to-background ratios (SBRs) and images of very dense biofilms remained challenging. Here, we present BCM3D 2.0 to address this challenge. BCM3D 2.0 is entirely complementary to the approach utilized in BCM3D 1.0. Instead of training CNNs to perform voxel classification, we trained CNNs to translate 3D fluorescence images into intermediate 3D image representations that are, when combined appropriately, more amenable to conventional mathematical image processing than a single experimental image. Using this approach, improved segmentation results are obtained even for very low SBRs and/or high cell density biofilm images. The improved cell segmentation accuracies in turn enable improved accuracies of tracking individual cells through 3D space and time. This capability opens the door to investigating time-dependent phenomena in bacterial biofilms at the cellular level.

Lightsheet Microscopy

In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

Wavefront engineered light needle microscopy for axially resolved rapid volumetric imaging

Increasing the acquisition speed of three-dimensional volumetric images is important-particularly in biological imaging-to unveil the structural dynamics and functionalities of specimens in detail. In conventional laser scanning fluorescence microscopy, volumetric images are constructed from optical sectioning images sequentially acquired by changing the observation plane, limiting the acquisition speed. Here, we present a novel method to realize volumetric imaging from two-dimensional raster scanning of a light needle spot without sectioning, even in the traditional framework of laser scanning microscopy. Information from multiple axial planes is simultaneously captured using wavefront engineering for fluorescence signals, allowing us to readily survey the entire depth range while maintaining spatial resolution. This technique is applied to real-time and video-rate three-dimensional tracking of micrometer-sized particles, as well as the prompt visualization of thick fixed biological specimens, offering substantially faster volumetric imaging.

Optically Accessible Microfluidic Flow Channels for Noninvasive High-Resolution Biofilm Imaging Using Lattice Light Sheet Microscopy

Imaging platforms that enable long-term, high-resolution imaging of biofilms are required to study cellular level dynamics within bacterial biofilms. By combining high spatial and temporal resolution and low phototoxicity, lattice light sheet microscopy (LLSM) has made critical contributions to the study of cellular dynamics. However, the power of LLSM has not yet been leveraged for biofilm research because the open-on-top imaging geometry using water-immersion objective lenses is not compatible with living bacterial specimens; bacterial growth on the microscope's objective lenses makes long-term time-lapse imaging impossible and raises considerable safety concerns for microscope users. To make LLSM compatible with pathogenic bacterial specimens, we developed hermetically sealed, but optically accessible, microfluidic flow channels that can sustain bacterial biofilm growth for multiple days under precisely controllable physical and chemical conditions. To generate a liquid- and gas-tight seal, we glued a thin polymer film across a 3D-printed channel, where the top wall had been omitted. We achieved negligible optical aberrations by using polymer films that precisely match the refractive index of water. Bacteria do not adhere to the polymer film itself, so that the polymer window provides unobstructed optical access to the channel interior. Inside the flow channels, biofilms can be grown on arbitrary, even nontransparent, surfaces. By integrating this flow channel with LLSM, we were able to record the growth of S. oneidensis MR-1 biofilms over several days at cellular resolution without any observable phototoxicity or photodamage.