Advanced Motion Compensation Methods for Intravital Optical Microscopy

Serial intravital 2-photon microscopy and analysis of the kidney using upright microscopes

Serial intravital 2-photon microscopy of the kidney and other abdominal organs is a powerful technique to assess tissue function and structure simultaneously and over time. Thus, serial intravital microscopy can capture dynamic tissue changes during health and disease and holds great potential to characterize (patho-) physiological processes with subcellular resolution. However, successful image acquisition and analysis require significant expertise and impose multiple potential challenges. Abdominal organs are rhythmically displaced by breathing movements which hamper high-resolution imaging. Traditionally, kidney intravital imaging is performed on inverted microscopes where breathing movements are partly compensated by the weight of the animal pressing down. Here, we present a custom and easy-to-implement setup for intravital imaging of the kidney and other abdominal organs on upright microscopes. Furthermore, we provide image processing protocols and a new plugin for the free image analysis software FIJI to process multichannel fluorescence microscopy data. The proposed image processing pipelines cover multiple image denoising algorithms, sample drift correction using 2D registration, and alignment of serial imaging data collected over several weeks using landmark-based 3D registration. The provided tools aim to lower the barrier of entry to intravital microscopy of the kidney and are readily applicable by biomedical practitioners.

Minimizing Motion Artifacts in Intravital Microscopy Using the Sedative Effect of Dexmedetomidine

Among intravital imaging instruments, the intravital two-photon fluorescence excitation microscope has the advantage of enabling real-time 3D fluorescence imaging deep into cells and tissues, with reduced photobleaching and photodamage compared with conventional intravital confocal microscopes. However, excessive motion of organs due to involuntary movement such as breathing may result in out-of-focus images and severe fluorescence intensity fluctuations, which hinder meaningful imaging and analysis. The clinically approved alpha-2 adrenergic receptor agonist dexmedetomidine was administered to mice during two-photon fluorescence intravital imaging to alleviate this problem. As dexmedetomidine blocks the release of the neurotransmitter norepinephrine, pain is suppressed, blood pressure is reduced, and a sedation effect is observed. By tracking the quality of focus and stability of detected fluorescence in two-photon fluorescence images of fluorescein isothiocyanate-sensitized liver vasculature in vivo, we demonstrated that intravascular dexmedetomidine can reduce fluorescence fluctuations caused by respiration on a timescale of minutes in mice, improving image quality and resolution. The results indicate that short-term dexmedetomidine treatment is suitable for reducing involuntary motion in preclinical intravital imaging studies. This method may be applicable to other animal models.

Endoscopic Optical Imaging Technologies and Devices for Medical Purposes: State of the Art

The growth and development of optical components and, in particular, the miniaturization of micro-electro-mechanical systems (MEMSs), has motivated and enabled researchers to design smaller and smaller endoscopes. The overarching goal of this work has been to image smaller previously inaccessible luminal organs in real time, at high resolution, in a minimally invasive manner that does not compromise the comfort of the subject, nor introduce additional risk. Thus, an initial diagnosis can be made, or a small precancerous lesion may be detected, in a small-diameter luminal organ that would not have otherwise been possible. Continuous advancement in the field has enabled a wide range of optical scanners. Different scanning techniques, working principles, and the applications of endoscopic scanners are summarized in this review.

A Compact High-Speed Image-Based Method for Measuring the Longitudinal Motion of Living Tissues

Intraoperative imaging of living tissue at the cell level by endomicroscopy might help surgeons optimize surgical procedures and provide individualized treatments. However, the resolution of the microscopic image is limited by the motion of living tissue caused by heartbeat and respiration. An active motion compensation (AMC) strategy has been recognized as an effective way to reduce, or even eliminate, the influence of tissue movement for intravital fluorescence microscopy (IVM). To realize the AMC system, a high-speed sensor for measuring the motion of tissues is needed. At present, state-of-the-art commercialized displacement sensors are not suitable to apply in minimally invasive imaging instruments to measure the motion of living tissues because of the size problem, range of measurement or the update rate. In this study, a compact high-speed image-based method for measuring the longitudinal motion of living tissues is proposed. The complexity of the proposed method is the same as that of the traditional wide-field fluorescent microscopy (WFFM) system, which makes it easy to be miniaturized and integrated into a minimally invasive imaging instrument. Experimental results reveal that the maximum indication error, range of measurement and the sensitivity of the laboratory-built experimental prototype is 150 μm, 6 mm and −211.46 mm−1 respectively. Experimental results indicate that the proposed optical method is expected to be used in minimally invasive imaging instruments to build an AMC system.

Automatic Tumor Segmentation With a Convolutional Neural Network in Multiparametric MRI: Influence of Distortion Correction

Precise tumor segmentation is a crucial task in radiation therapy planning. Convolutional neural networks (CNNs) are among the highest scoring automatic approaches for tumor segmentation. We investigate the difference in segmentation performance of geometrically distorted and corrected diffusion-weighted data using data of patients with head and neck tumors; 18 patients with head and neck tumors underwent multiparametric magnetic resonance imaging, including T2w, T1w, T2*, perfusion (k_trans), and apparent diffusion coefficient (ADC) measurements. Owing to strong geometrical distortions in diffusion-weighted echo planar imaging in the head and neck region, ADC data were additionally distortion corrected. To investigate the influence of geometrical correction, first 14 CNNs were trained on data with geometrically corrected ADC and another 14 CNNs were trained using data without the correction on different samples of 13 patients for training and 4 patients for validation each. The different sets were each trained from scratch using randomly initialized weights, but the training data distributions were pairwise equal for corrected and uncorrected data. Segmentation performance was evaluated on the remaining 1 test-patient for each of the 14 sets. The CNN segmentation performance scored an average Dice coefficient of 0.40 ± 0.18 for data including distortion-corrected ADC and 0.37 ± 0.21 for uncorrected data. Paired t test revealed that the performance was not significantly different (P = .313). Thus, geometrical distortion on diffusion-weighted imaging data in patients with head and neck tumor does not significantly impair CNN segmentation performance in use.

Intravital imaging of host-parasite interactions in organs of the thoracic and abdominopelvic cavities

Infections with protozoan and helminthic parasites affect multiple organs in the mammalian host. Imaging pathogens in their natural environment takes a more holistic view on biomedical aspects of parasitic infections. Here, we focus on selected organs of the thoracic and abdominopelvic cavities most commonly affected by parasites. Parasitic infections of these organs are often associated with severe medical complications or have health implications beyond the infected individual. Intravital imaging has provided a more dynamic picture of the host-parasite interplay and contributed not only to our understanding of the various disease pathologies, but has also provided fundamental insight into the biology of the parasites.

Reprint of "Multi-modal image cytometry approach - From dynamic to whole organ imaging"

Optical imaging is a valuable tool to visualise biological processes in the context of the tissue. Each imaging modality provides the biologist with different types of information - cell dynamics and migration over time can be tracked with time-lapse imaging (e.g. intra-vital imaging); an overview of whole tissues can be acquired using optical clearing in conjunction with light sheet microscopy; finer details such as cellular morphology and fine nerve tortuosity can be imaged at higher resolution using the confocal microscope. Multi-modal imaging combined with image cytometry - a form of quantitative analysis of image datasets - provides an objective basis for comparing between sample groups. Here, we provide an overview of technical aspects to look out for in an image cytometry workflow, and discuss issues related to sample preparation, image post-processing and analysis for intra-vital and whole organ imaging.

Multiphoton intravital microscopy in small animals: motion artefact challenges and technical solutions

Since its invention 29 years ago, two‐photon laser‐scanning microscopy has evolved from a promising imaging technique, to an established widely available imaging modality used throughout the biomedical research community. The establishment of two‐photon microscopy as the preferred method for imaging fluorescently labelled cells and structures in living animals can be attributed to the biophysical mechanism by which the generation of fluorescence is accomplished. The use of powerful lasers capable of delivering infrared light pulses within femtosecond intervals, facilitates the nonlinear excitation of fluorescent molecules only at the focal plane and determines by objective lens position. This offers numerous benefits for studies of biological samples at high spatial and temporal resolutions with limited photo‐damage and superior tissue penetration. Indeed, these attributes have established two‐photon microscopy as the ideal method for live‐animal imaging in several areas of biology and have led to a whole new field of study dedicated to imaging biological phenomena in intact tissues and living organisms. However, despite its appealing features, two‐photon intravital microscopy is inherently limited by tissue motion from heartbeat, respiratory cycles, peristalsis, muscle/vascular tone and physiological functions that change tissue geometry. Because these movements impede temporal and spatial resolution, they must be properly addressed to harness the full potential of two‐photon intravital microscopy and enable accurate data analysis and interpretation. In addition, the sources and features of these motion artefacts are varied, sometimes unpredictable and unique to specific organs and multiple complex strategies have previously been devised to address them. This review will discuss these motion artefacts requirement and technical solutions for their correction and after intravital two‐photon microscopy.

Fluorescence anisotropy imaging in drug discovery

Non-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting has proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs.

Tify: A quality-based frame selection tool for improving the output of unstable biomedical imaging

The ability to image biological tissues is critical to our understanding of a range of systems and processes. In the case of in situ living tissue, such imaging is hampered by the innate mechanical properties of the tissue. In many cases, this provides challenges in how to process large amounts of image data which may contain aberrations from movement. Generally, current tools require the provision of reference images and are unable to maintain temporal correlations within an image set. Here, we describe a tool-Tify-which can accurately predict a numerical quality score versus human scoring and can analyse image sets in a manner that allows the maintenance of temporal relationships. The tool uses regression-based techniques to link image statistics to image quality based on user provided scores from a sample of images. Scores calculated by the software correlate strongly with the scores provided by human users. We identified that, in most cases, the software requires users to score between 20-30 frames in order to be able to accurately calculate the remaining images. Importantly, our results suggest that the software can use coefficients generated from consolidated image sets to process images without the need for additional manual scoring. Finally, the tool is able to use a frame windowing technique to identify the highest quality frame from a moving window, thus retaining macro-chronological connections between frames. In summary, Tify is able to successfully predict the quality of images in an image set based on a small number of sample scores provided by end-users. This software has the potential to improve the effectiveness of biological imaging techniques where motion artefacts, even in the presence of stabilisation, pose a significant problem.

In Vivo Imaging of Microglia With Multiphoton Microscopy

Neuroimaging has become an unparalleled tool to understand the central nervous system (CNS) anatomy, physiology and neurological diseases. While an altered immune function and microglia hyperactivation are common neuropathological features for many CNS disorders and neurodegenerative diseases, direct assessment of the role of microglial cells remains a challenging task. Non-invasive neuroimaging techniques, including magnetic resonance imaging (MRI), positron emission tomography (PET) and single positron emission computed tomography (SPECT) are widely used for human clinical applications, and a variety of ligands are available to detect neuroinflammation. In animal models, intravital imaging has been largely used, and minimally invasive multiphoton microcopy (MPM) provides high resolution detection of single microglia cells, longitudinally, in living brain. In this study, we review in vivo real-time MPM approaches to assess microglia in preclinical studies, including individual cell responses in surveillance, support, protection and restoration of brain tissue integrity, synapse formation, homeostasis, as well as in different pathological situations. We focus on in vivo studies that assess the role of microglia in mouse models of Alzheimer’s disease (AD), analyzing microglial motility and recruitment, as well as the role of microglia in anti-amyloid-β treatment, as a key therapeutic approach to treat AD. Altogether, MPM provides a high contrast and high spatial resolution approach to follow microglia chronically in vivo in complex models, supporting MPM as a powerful tool for deep intravital tissue imaging.

Visualizing Viral Infection In Vivo by Multi-Photon Intravital Microscopy

Viral pathogens have adapted to the host organism to exploit the cellular machinery for virus replication and to modulate the host cells for efficient systemic dissemination and immune evasion. Much of our knowledge of the effects that virus infections have on cells originates from in vitro imaging studies using experimental culture systems consisting of cell lines and primary cells. Recently, intravital microscopy using multi-photon excitation of fluorophores has been applied to observe virus dissemination and pathogenesis in real-time under physiological conditions in living organisms. Critical steps during viral infection and pathogenesis could be studied by direct visualization of fluorescent virus particles, virus-infected cells, and the immune response to viral infection. In this review, I summarize the latest research on in vivo studies of viral infections using multi-photon intravital microscopy (MP-IVM). Initially, the underlying principle of multi-photon microscopy is introduced and experimental challenges during microsurgical animal preparation and fluorescent labeling strategies for intravital imaging are discussed. I will further highlight recent studies that combine MP-IVM with optogenetic tools and transcriptional analysis as a powerful approach to extend the significance of in vivo imaging studies of viral pathogens.

Molecular mobility and activity in an intravital imaging setting - implications for cancer progression and targeting

Molecular mobility, localisation and spatiotemporal activity are at the core of cell biological processes and deregulation of these dynamic events can underpin disease development and progression. Recent advances in intravital imaging techniques in mice are providing new avenues to study real-time molecular behaviour in intact tissues within a live organism and to gain exciting insights into the intricate regulation of live cell biology at the microscale level. The monitoring of fluorescently labelled proteins and agents can be combined with autofluorescent properties of the microenvironment to provide a comprehensive snapshot of in vivo cell biology. In this Review, we summarise recent intravital microscopy approaches in mice, in processes ranging from normal development and homeostasis to disease progression and treatment in cancer, where we emphasise the utility of intravital imaging to observe dynamic and transient events in vivo We also highlight the recent integration of advanced subcellular imaging techniques into the intravital imaging pipeline, which can provide in-depth biological information beyond the single-cell level. We conclude with an outlook of ongoing developments in intravital microscopy towards imaging in humans, as well as provide an overview of the challenges the intravital imaging community currently faces and outline potential ways for overcoming these hurdles.

A permanent window for the murine lung enables high-resolution imaging of cancer metastasis

Stable, high-resolution intravital imaging of the lung has become possible through the utilization of vacuum-stabilized imaging windows. However, this technique is extremely invasive and limited to only hours in duration. Here we describe a minimally invasive, permanently implantable window for high-resolution intravital imaging of the murine lung that allows the mouse to survive surgery, recover from anesthesia, and breathe independently. Compared to vacuum-stabilized windows, this window produces the same high-quality images without vacuum-induced artifacts; it is also less invasive, which allows imaging of the same lung tissue over a period of weeks. We further adapt the technique of microcartography for reliable relocalization of the same cells longitudinally. Using commonly employed experimental, as well as more clinically relevant, spontaneous metastasis models, we visualize all stages of metastatic seeding, including: tumor cell arrival; extravasation; growth and progression to micrometastases; as well as tumor microenvironment of metastasis function, the hallmark of hematogenous dissemination of tumor cells.

Motion characterization scheme to minimize motion artifacts in intravital microscopy

Respiratory- and cardiac-induced motion artifacts pose a major challenge for in vivo optical imaging, limiting the temporal and spatial imaging resolution in fluorescence laser scanning microscopy. Here, we present an imaging platform developed for in vivo characterization of physiologically induced axial motion. The motion characterization system can be straightforwardly implemented on any conventional laser scanning microscope and can be used to evaluate the effectiveness of different motion stabilization schemes. This method is particularly useful to improve the design of novel tissue stabilizers and to facilitate stabilizer positioning in real time, therefore facilitating optimal tissue immobilization and minimizing motion induced artifacts.

A multispectral microscope for in vivo oximetry of rat dorsal spinal cord vasculature

Quantification of blood oxygen saturation (SO₂) in vivo is essential for understanding the pathogenesis of diseases in which hypoxia is thought to play a role, including inflammatory disorders such as multiple sclerosis (MS) and rheumatoid arthritis (RA). We describe a low-cost multispectral microscope and oximetry technique for calibration-free absolute oximetry of surgically exposed blood vessels in vivo. We imaged the vasculature of the dorsal spinal cord in healthy rats, and varied inspired oxygen (FiO₂) in order to evaluate the sensitivity of the imaging system to changes in SO₂. The venous SO₂ was calculated as 67.8  ±  10.4% (average  ±  standard deviation), increasing to 83.1  ±  11.6% under hyperoxic conditions (100% FiO₂) and returning to 67.4  ±  10.9% for a second normoxic period; the venous SO₂ was 50.9  ±  15.5% and 29.2  ±  24.6% during subsequent hypoxic states (18% and 15% FiO₂ respectively). We discuss the design and performance of our multispectral imaging system, and the future scope for extending this oximetry technique to quantification of hypoxia in inflamed tissue.

Motion quantification during multi-photon functional imaging in behaving animals

Functional imaging in behaving animals is essential to understanding brain function. However, artifacts resulting from animal motion, including locomotion, can severely corrupt functional measurements. To dampen tissue motion, we designed a new optical window with minimal optical aberrations. Using the newly developed high-speed continuous volumetric imaging system based on an optical phase-locked ultrasound lens, we quantified motion of the cerebral cortex and hippocampal surface during two-photon functional imaging in behaving mice. We find that the out-of-plane motion is generally greater than the axial dimension of the point-spread-function during mouse locomotion, which indicates that high-speed continuous volumetric imaging is necessary to minimize motion artifacts.

Live cell imaging to understand monocyte, macrophage, and dendritic cell function in atherosclerosis

Ley et al. provide a review of the technology and accomplishments of dynamic imaging of myeloid cells in atherosclerosis.

Intravital imaging is an invaluable tool for understanding the function of cells in healthy and diseased tissues. It provides a window into dynamic processes that cannot be studied by other techniques. This review will cover the benefits and limitations of various techniques for labeling and imaging myeloid cells, with a special focus on imaging cells in atherosclerotic arteries. Although intravital imaging is a powerful tool for understanding cell function, it alone does not provide a complete picture of the cell. Other techniques, such as flow cytometry and transcriptomics, must be combined with intravital imaging to fully understand a cell's phenotype, lineage, and function.

Intravital imaging reveals new ancillary mechanisms co-opted by cancer cells to drive tumor progression

Intravital imaging is providing new insights into the dynamics of tumor progression in native tissues and has started to reveal the layers of complexity found in cancer. Recent advances in intravital imaging have allowed us to look deeper into cancer behavior and to dissect the interactions between tumor cells and the ancillary host niche that promote cancer development. In this review, we provide an insight into the latest advances in cancer biology achieved by intravital imaging, focusing on recently discovered mechanisms by which tumor cells manipulate normal tissue to facilitate disease progression.

In vivo nonlinear optical imaging to monitor early microscopic changes in a murine cutaneous squamous cell carcinoma model

Early detection of cutaneous squamous cell carcinoma (cSCC) can enable timely therapeutic and preventive interventions for patients. In this study, in vivo nonlinear optical imaging (NLOI) based on two-photon excitation fluorescence (TPEF) and second harmonic generation (SHG), was used to non-invasively detect microscopic changes occurring in murine skin treated topically with 7,12-dimethylbenz(a)anthracene (DMBA). The optical microscopic findings and the measured TPEF-SHG index show that NLOI was able to clearly detect early cytostructural changes in DMBA treated skin that appeared clinically normal. This suggests that in vivo NLOI could be a non-invasive tool to monitor early signs of cSCC. In vivo axial NLOI scans of normal murine skin (upper left), murine skin with preclinical hyperplasia (upper right), early clinical murine skin lesion (lower left) and late or advanced murine skin lesion (lower right).

Intravital live cell triggered imaging system reveals monocyte patrolling and macrophage migration in atherosclerotic arteries

Intravital multiphoton imaging of arteries is technically challenging because the artery expands with every heartbeat, causing severe motion artifacts. To study leukocyte activity in atherosclerosis, we developed the intravital live cell triggered imaging system (ILTIS). This system implements cardiac triggered acquisition as well as frame selection and image registration algorithms to produce stable movies of myeloid cell movement in atherosclerotic arteries in live mice. To minimize tissue damage, no mechanical stabilization is used and the artery is allowed to expand freely. ILTIS performs multicolor high frame-rate two-dimensional imaging and full-thickness three-dimensional imaging of beating arteries in live mice. The external carotid artery and its branches (superior thyroid and ascending pharyngeal arteries) were developed as a surgically accessible and reliable model of atherosclerosis. We use ILTIS to demonstrate Cx3cr1GFP monocytes patrolling the lumen of atherosclerotic arteries. Additionally, we developed a new reporter mouse (Apoe−/−Cx3cr1GFP/+Cd11cYFP) to image GFP+ and GFP+YFP + macrophages “dancing on the spot” and YFP+ macrophages migrating within intimal plaque. ILTIS will be helpful to answer pertinent open questions in the field, including monocyte recruitment and transmigration, macrophage and dendritic cell activity, and motion of other immune cells.

Optically gated beating-heart imaging

The constant motion of the beating heart presents an obstacle to clear optical imaging, especially 3D imaging, in small animals where direct optical imaging would otherwise be possible. Gating techniques exploit the periodic motion of the heart to computationally "freeze" this movement and overcome motion artifacts. Optically gated imaging represents a recent development of this, where image analysis is used to synchronize acquisition with the heartbeat in a completely non-invasive manner. This article will explain the concept of optical gating, discuss a range of different implementation strategies and their strengths and weaknesses. Finally we will illustrate the usefulness of the technique by discussing applications where optical gating has facilitated novel biological findings by allowing 3D in vivo imaging of cardiac myocytes in their natural environment of the beating heart.

Motion compensation for in vivo subcellular optical microscopy

In this review, we focus on the impact of tissue motion on attempting to conduct subcellular resolution optical microscopy, in vivo. Our position is that tissue motion is one of the major barriers in conducting these studies along with light induced damage, optical probe loading as well as absorbing and scattering effects on the excitation point spread function and collection of emitted light. Recent developments in the speed of image acquisition have reached the limit, in most cases, where the signal from a subcellular voxel limits the speed and not the scanning rate of the microscope. Different schemes for compensating for tissue displacements due to rigid body and deformation are presented from tissue restriction, gating, adaptive gating and active tissue tracking. We argue that methods that minimally impact the natural physiological motion of the tissue are desirable because the major reason to perform in vivo studies is to evaluate normal physiological functions. Towards this goal, active tracking using the optical imaging data itself to monitor tissue displacement and either prospectively or retrospectively correct for the motion without affecting physiological processes is desirable. Critical for this development was the implementation of near real time image processing in conjunction with the control of the microscope imaging parameters. Clearly, the continuing development of methods of motion compensation as well as significant technological solutions to the other barriers to tissue subcellular optical imaging in vivo, including optical aberrations and overall signal-to-noise ratio, will make major contributions to the understanding of cell biology within the body.

Imaging windows for long-term intravital imaging: General overview and technical insights

Intravital microscopy is increasingly used to visualize and quantitate dynamic biological processes at the (sub)cellular level in live animals. By visualizing tissues through imaging windows, individual cells (e.g., cancer, host, or stem cells) can be tracked and studied over a time-span of days to months. Several imaging windows have been developed to access tissues including the brain, superficial fascia, mammary glands, liver, kidney, pancreas, and small intestine among others. Here, we review the development of imaging windows and compare the most commonly used long-term imaging windows for cancer biology: the cranial imaging window, the dorsal skin fold chamber, the mammary imaging window, and the abdominal imaging window. Moreover, we provide technical details, considerations, and trouble-shooting tips on the surgical procedures and microscopy setups for each imaging window and explain different strategies to assure imaging of the same area over multiple imaging sessions. This review aims to be a useful resource for establishing the long-term intravital imaging procedure.