3D and 4D imaging of immune cells in vitro and in vivo

CANCOL, a Computer-Assisted Annotation Tool to Facilitate Colocalization and Tracking of Immune Cells in Intravital Microscopy

Two-photon intravital microscopy (2P-IVM) has become a widely used technique to study cell-to-cell interactions in living organisms. Four-dimensional imaging data obtained via 2P-IVM are classically analyzed by performing automated cell tracking, a procedure that computes the trajectories followed by each cell. However, technical artifacts, such as brightness shifts, the presence of autofluorescent objects, and channel crosstalking, affect the specificity of imaging channels for the cells of interest, thus hampering cell detection. Recently, machine learning has been applied to overcome a variety of obstacles in biomedical imaging. However, existing methods are not tailored for the specific problems of intravital imaging of immune cells. Moreover, results are highly dependent on the quality of the annotations provided by the user. In this study, we developed CANCOL, a tool that facilitates the application of machine learning for automated tracking of immune cells in 2P-IVM. CANCOL guides the user during the annotation of specific objects that are problematic for cell tracking when not properly annotated. Then, it computes a virtual colocalization channel that is specific for the cells of interest. We validated the use of CANCOL on challenging 2P-IVM videos from murine organs, obtaining a significant improvement in the accuracy of automated tracking while reducing the time required for manual track curation.

Recent advances in intravital microscopy for investigation of dynamic cellular behavior in vivo

Currently, most biological research relies on conventional experimental techniques that allow only static analyses at certain time points in vitro or ex vivo. However, if one could visualize cellular dynamics in living organisms, that would provide a unique opportunity to study key biological phenomena in vivo. Intravital microscopy (IVM) encompasses diverse optical systems for direct viewing of objects, including biological structures and individual cells in live animals. With the current development of devices and techniques, IVM addresses important questions in various fields of biological and biomedical sciences. In this mini-review, we provide a general introduction to IVM and examples of recent applications in the field of immunology, oncology, and vascular biology. We also introduce an advanced type of IVM, dubbed real-time IVM, equipped with video-rate resonant scanning. Since the real-time IVM can render cellular dynamics with high temporal resolution in vivo, it allows visualization and analysis of rapid biological processes.

Intravital microscopy: Imaging host-parasite interactions in lymphoid organs

Intravital microscopy allows imaging of biological phenomena within living animals, including host-parasite interactions. This has advanced our understanding of both, the function of lymphoid organs during parasitic infections, and the effect of parasites on such organs to allow their survival. In parasitic research, recent developments in this technique have been crucial for the direct study of host-parasite interactions within organs at depths, speeds and resolution previously difficult to achieve. Lymphoid organs have gained more attention as we start to understand their function during parasitic infections and the effect of parasites on them. In this review, we summarise technical and biological findings achieved by intravital microscopy with respect to the interaction of various parasites with host lymphoid organs, namely the bone marrow, thymus, lymph nodes, spleen and the mucosa-associated lymphoid tissue, and present a view into possible future applications.

Deconstructing Immune Microenvironments of Lymphoid Tissues for Reverse Engineering

The immune microenvironment presents a diverse panel of cues that impacts immune cell migration, organization, differentiation, and the immune response. Uniquely, both the liquid and solid phases of every specific immune niche within the body play an important role in defining cellular functions in immunity at that particular location. The in vivo immune microenvironment consists of biomechanical and biochemical signals including their gradients, surface topography, dimensionality, modes of ligand presentation, and cell-cell interactions, and the ability to recreate these immune biointerfaces in vitro can provide valuable insights into the immune system. This manuscript reviews the critical roles played by different immune cells and surveys the current progress of model systems for reverse engineering of immune microenvironments with a focus on lymphoid tissues.

Dynamic intravital imaging of cell-cell interactions in the lymph node

In the last decade, the application of 2-photon intravital microscopy as a tool to study cell interactions in different areas of the immune system has offered an unprecedented opportunity to understand the complexity of cell behavior in relation to immune functions. In this review we describe the latest advances in the field of live imaging in the lymph nodes, grouping the different cell populations in 2 compartments according to their motility: the sessile compartment, which is formed by resident cells of stromal origin, macrophages, and resident dendritic cells, and the motile compartment, which is mainly formed by T and B lymphocytes. Here we review how the use of in vivo imaging has contributed to our understanding of the role of these cells in the initiation of the immune response in the draining lymph nodes.

Imaging cell biology in live animals: ready for prime time

Time-lapse fluorescence microscopy is one of the main tools used to image subcellular structures in living cells. Yet for decades it has been applied primarily to in vitro model systems. Thanks to the most recent advancements in intravital microscopy, this approach has finally been extended to live rodents. This represents a major breakthrough that will provide unprecedented new opportunities to study mammalian cell biology in vivo and has already provided new insight in the fields of neurobiology, immunology, and cancer biology.

Imaging and tracking of bone marrow-derived immune and stem cells

Bone marrow (BM)-derived stem and immune cells play critical roles in maintaining the health, regeneration, and repair of many tissues. Given their important functions in tissue regeneration and therapy, tracking the dynamic behaviors of BM-derived cells has been a long-standing research goal of both biologists and engineers. Because of the complex cellular-level processes involved, real-time imaging technologies that have sufficient spatial and temporal resolution to visualize them are needed. In addition, in order to track cellular dynamics, special attention is needed to account for changes in the microenvironment where the cells reside, for example, tissue contraction, stretching, development, etc. In this chapter, we introduce methods for real-time imaging and longitudinal tracking of BM-derived immune and stem cells in in vivo three-dimensional (3-D) tissue environments with an integrated optical microscope. The integrated microscope combines multiple imaging functions derived from optical coherence tomography (OCT) and multiphoton microscopy (MPM), including optical coherence microscopy (OCM), microvasculature imaging, two-photon excited fluorescence (TPEF), and second harmonic generation (SHG) microscopy. Short- and long-term tracking of the dynamic behavior of BM-derived cells involved in cutaneous wound healing and skin grafting in green fluorescent protein (GFP) BM-transplanted mice is demonstrated. Methods and algorithms for nonrigid registration of time-lapse images are introduced, which allows for long-term tracking of cell dynamics over several months.

Automated and semi-automated cell tracking: addressing portability challenges

Cell tracking is a key task in the high-throughput quantitative study of important biological processes, such as immune system regulation and neurogenesis. Variability in cell density and dynamics in different videos, hampers portability of existing trackers across videos. We address these potability challenges in order to develop a portable cell tracking algorithm. Our algorithm can handle noise in cell segmentation as well as divisions and deaths of cells. We also propose a parameter-free variation of our tracker. In the tracker, we employ a novel method for recovering the distribution of cell displacements. Further, we present a mathematically justified procedure for determining the gating distance in relation to tracking performance. For the range of real videos tested, our tracker correctly recovers on average 96% of cell moves, and outperforms an advanced probabilistic tracker when the cell detection quality is high. The scalability of our tracker was tested on synthetic videos with up to 200 cells per frame. For more challenging tracking conditions, we propose a novel semi-automated framework that can increase the ratio of correctly recovered tracks by 12%, through selective manual inspection of only 10% of all frames in a video.

Direct observation of phagocytosis and NET-formation by neutrophils in infected lungs using 2-photon microscopy

After the gastrointestinal tract, the lung is the second largest surface for interaction between the vertebrate body and the environment. Here, an effective gas exchange must be maintained, while at the same time avoiding infection by the multiple pathogens that are inhaled during normal breathing. To achieve this, a superb set of defense strategies combining humoral and cellular immune mechanisms exists. One of the most effective measures for acute defense of the lung is the recruitment of neutrophils, which either phagocytose the inhaled pathogens or kill them by releasing cytotoxic chemicals. A recent addition to the arsenal of neutrophils is their explosive release of extracellular DNA-NETs by which bacteria or fungi can be caught or inactivated even after the NET releasing cells have died. We present here a method that allows one to directly observe neutrophils, migrating within a recently infected lung, phagocytosing fungal pathogens as well as visualize the extensive NETs that they have produced throughout the infected tissue. The method describes the preparation of thick viable lung slices 7 hours after intratracheal infection of mice with conidia of the mold Aspergillus fumigatus and their examination by multicolor time-lapse 2-photon microscopy. This approach allows one to directly investigate antifungal defense in native lung tissue and thus opens a new avenue for the detailed investigation of pulmonary immunity.

Spatially-chirped modulation imaging of absorbtion and fluorescent objects on single-element optical detector

Line imaging of fluorescent and absorptive objects with a single-pixel imaging technique that acquires one-dimensional cross-sections through a sample by imposing a spatially-varying amplitude modulation on the probing beam is demonstrated. The fluorophore concentration or absorber distribution of the sample is directly mapped to modulation frequency components of the spatially-integrated temporal signal. Time-domain signals are obtained from a single photodiode, with object spatial frequency correlation encoded in time-domain bursts in the electronic signal from the photodiode.

Intravital microscopy as a tool to study drug delivery in preclinical studies

The technical developments in the field of non-linear microscopy have made intravital microscopy one of the most successful techniques for studying physiological and pathological processes in live animals. Intravital microscopy has been utilized to address many biological questions in basic research and is now a fundamental tool for preclinical studies, with an enormous potential for clinical applications. The ability to dynamically image cellular and subcellular structures combined with the possibility to perform longitudinal studies have empowered investigators to use this discipline to study the mechanisms of action of therapeutic agents and assess the efficacy on their targets in vivo. The goal of this review is to provide a general overview of the recent advances in intravital microscopy and to discuss some of its applications in preclinical studies.

Intravital microscopy: a novel tool to study cell biology in living animals

Intravital microscopy encompasses various optical microscopy techniques aimed at visualizing biological processes in live animals. In the last decade, the development of non-linear optical microscopy resulted in an enormous increase of in vivo studies, which have addressed key biological questions in fields such as neurobiology, immunology and tumor biology. Recently, few studies have shown that subcellular processes can be imaged dynamically in the live animal at a resolution comparable to that achieved in cell cultures, providing new opportunities to study cell biology under physiological conditions. The overall aim of this review is to give the reader a general idea of the potential applications of intravital microscopy with a particular emphasis on subcellular imaging. An overview of some of the most exciting studies in this field will be presented using resolution as a main organizing criterion. Indeed, first we will focus on those studies in which organs were imaged at the tissue level, then on those focusing on single cells imaging, and finally on those imaging subcellular organelles and structures.

Extending the knowledge in histochemistry and cell biology

Central to modern Histochemistry and Cell Biology stands the need for visualization of cellular and molecular processes. In the past several years, a variety of techniques has been achieved bridging traditional light microscopy, fluorescence microscopy and electron microscopy with powerful software-based post-processing and computer modeling. Researchers now have various tools available to investigate problems of interest from bird's- up to worm's-eye of view, focusing on tissues, cells, proteins or finally single molecules. Applications of new approaches in combination with well-established traditional techniques of mRNA, DNA or protein analysis have led to enlightening and prudent studies which have paved the way toward a better understanding of not only physiological but also pathological processes in the field of cell biology. This review is intended to summarize articles standing for the progress made in "histo-biochemical" techniques and their manifold applications.

State-of-the-art technologies, current opinions and developments, and novel findings: news from the field of histochemistry and cell biology

Investigations of cell and tissue structure and function using innovative methods and approaches have again yielded numerous exciting findings in recent months and have added important data to current knowledge, inspiring new ideas and hypotheses in various fields of modern life sciences. Topics and contents of comprehensive expert reviews covering different aspects in methodological advances, cell biology, tissue function and morphology, and novel findings reported in original papers are summarized in the present review.