Fluorescence lifetime imaging microscopy: fundamentals and advances in instrumentation, analysis, and applications

Leaf microscopy applications in photosynthesis research: identifying the gaps

Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Multiphoton imaging of melanoma 3D models with plasmonic nanocapsules

We report the synthesis of plasmonic nanocapsules and the cellular responses they induce in 3D melanoma models for their perspective use as a photothermal therapeutic agent. The wall of the nanocapsules is composed of polyelectrolytes. The inner part is functionalized with discrete gold nanoislands. The cavity of the nanocapsules contains a fluorescent payload to show their ability for loading a cargo. The nanocapsules exhibit simultaneous two-photon luminescent, fluorescent properties and X-ray contrasting ability. The average fluorescence lifetime (τ) of the nanocapsules measured with FLIM (0.3 ns) is maintained regardless of the intracellular environment, thus proving their abilities for bioimaging of models such as 3D spheroids with a complex architecture. Their multimodal imaging properties are exploited for the first time to study tumorspheres cellular responses exposed to the nanocapsules. Specifically, we studied cellular uptake, toxicity, intracellular fate, generation of reactive oxygen species, and effect on the levels of hypoxia by using multi-photon and confocal laser scanning microscopy. Because of the high X-ray attenuation and atomic number of the gold nanostructure, we imaged the nanocapsule-cell interactions without processing the sample. We confirmed maintenance of the nanocapsules' geometry in the intracellular milieu with no impairment of the cellular ultrastructure. Furthermore, we observed the lack of cellular toxicity and no alteration in oxygen or reactive oxygen species levels. These results in 3D melanoma models contribute to the development of these nanocapsules for their exploitation in future applications as agents for imaging-guided photothermal therapy. STATEMENT OF SIGNIFICANCE: The novelty of the work is that our plasmonic nanocapsules are multimodal. They are responsive to X-ray and to multiphoton and single-photon excitation. This allowed us to study their interaction with 2D and 3D cellular structures and specifically to obtain information on tumor cell parameters such as hypoxia, reactive oxygen species, and toxicity. These nanocapsules will be further validated as imaging-guided photothermal probes.

Label-Free Imaging to Track Reprogramming of Human Somatic Cells

The process of reprogramming patient samples to human-induced pluripotent stem cells (iPSCs) is stochastic, asynchronous, and inefficient, leading to a heterogeneous population of cells. In this study, we track the reprogramming status of patient-derived erythroid progenitor cells (EPCs) at the single-cell level during reprogramming with label-free live-cell imaging of cellular metabolism and nuclear morphometry to identify high-quality iPSCs. EPCs isolated from human peripheral blood of three donors were used for our proof-of-principle study. We found distinct patterns of autofluorescence lifetime for the reduced form of nicotinamide adenine dinucleotide (phosphate) and flavin adenine dinucleotide during reprogramming. Random forest models classified iPSCs with ∼95% accuracy, which enabled the successful isolation of iPSC lines from reprogramming cultures. Reprogramming trajectories resolved at the single-cell level indicated significant reprogramming heterogeneity along different branches of cell states. This combination of micropatterning, autofluorescence imaging, and machine learning provides a unique, real-time, and nondestructive method to assess the quality of iPSCs in a biomanufacturing process, which could have downstream impacts in regenerative medicine, cell/gene therapy, and disease modeling.

Spatial resolution improved fluorescence lifetime imaging via deep learning

We present a deep learning approach to obtain high-resolution (HR) fluorescence lifetime images from low-resolution (LR) images acquired from fluorescence lifetime imaging (FLIM) systems. We first proposed a theoretical method for training neural networks to generate massive semi-synthetic FLIM data with various cellular morphologies, a sizeable dynamic lifetime range, and complex decay components. We then developed a degrading model to obtain LR-HR pairs and created a hybrid neural network, the spatial resolution improved FLIM net (SRI-FLIMnet) to simultaneously estimate fluorescence lifetimes and realize the nonlinear transformation from LR to HR images. The evaluative results demonstrate SRI-FLIMnet's superior performance in reconstructing spatial information from limited pixel resolution. We also verified SRI-FLIMnet using experimental images of bacterial infected mouse raw macrophage cells. Results show that the proposed data generation method and SRI-FLIMnet efficiently achieve superior spatial resolution for FLIM applications. Our study provides a solution for fast obtaining HR FLIM images.

Near-infrared excitation/emission microscopy with lanthanide-based nanoparticles

Near-infrared optical imaging offers some advantages over conventional imaging, such as deeper tissue penetration, low or no autofluorescence, and reduced tissue scattering. Lanthanide-doped nanoparticles (LnNPs) have become a trend in the field of photoactive nanomaterials for optical imaging due to their unique optical features and because they can use NIR light as excitation and/or emission light. This review is focused on NaREF₄ NPs and offers an overview of the state-of-the-art investigation in their use as luminophores in optical microscopy, time-resolved imaging, and super-resolution nanoscopy based on, or applied to, LnNPs. Secondly, whenever LnNPs are combined with other nanomaterial or nanoparticle to afford nanohybrids, the characterization of their physical and chemical properties is of current interest. In this context, the latest trends in optical microscopy and their future perspectives are discussed.

High Resolution Fluorescence Lifetime Maps from Minimal Photon Counts

Fluorescence lifetime imaging microscopy (FLIM) may reveal subcellular spatial lifetime maps of key molecular species. Yet, such a quantitative picture of life necessarily demands high photon budgets at every pixel under the current analysis paradigm, thereby increasing acquisition time and photodamage to the sample. Motivated by recent developments in computational statistics, we provide a direct means to update our knowledge of the lifetime maps of species of different lifetimes from direct photon arrivals, while accounting for experimental features such as arbitrary forms of the instrument response function (IRF) and exploiting information from empty laser pulses not resulting in photon detection. Our ability to construct lifetime maps holds for arbitrary lifetimes, from short lifetimes (comparable to the IRF) to lifetimes exceeding interpulse times. As our method is highly data efficient, for the same amount of data normally used to determine lifetimes and photon ratios, working within the Bayesian paradigm, we report direct blind unmixing of lifetimes with subnanosecond resolution and subpixel spatial resolution using standard raster scan FLIM images. We demonstrate our method using a wide range of simulated and experimental data.

When light meets biology - how the specimen affects quantitative microscopy

Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.

Label-free metabolic and structural profiling of dynamic biological samples using multimodal optical microscopy with sensorless adaptive optics

Label-free optical microscopy has matured as a noninvasive tool for biological imaging; yet, it is criticized for its lack of specificity, slow acquisition and processing times, and weak and noisy optical signals that lead to inaccuracies in quantification. We introduce FOCALS (Fast Optical Coherence, Autofluorescence Lifetime imaging, and Second harmonic generation) microscopy capable of generating NAD(P)H fluorescence lifetime, second harmonic generation (SHG), and polarization-sensitive optical coherence microscopy (OCM) images simultaneously. Multimodal imaging generates quantitative metabolic and morphological profiles of biological samples in vitro, ex vivo, and in vivo. Fast analog detection of fluorescence lifetime and real-time processing on a graphical processing unit enables longitudinal imaging of biological dynamics. We detail the effect of optical aberrations on the accuracy of FLIM beyond the context of undistorting image features. To compensate for the sample-induced aberrations, we implemented a closed-loop single-shot sensorless adaptive optics solution, which uses computational adaptive optics of OCM for wavefront estimation within 2 s and improves the quality of quantitative fluorescence imaging in thick tissues. Multimodal imaging with complementary contrasts improves the specificity and enables multidimensional quantification of the optical signatures in vitro, ex vivo, and in vivo, fast acquisition and real-time processing improve imaging speed by 4-40 × while maintaining enough signal for quantitative nonlinear microscopy, and adaptive optics improves the overall versatility, which enable FOCALS microscopy to overcome the limits of traditional label-free imaging techniques.

Microphysiological model of the renal cell carcinoma to inform anti-angiogenic therapy

Renal cell carcinomas are common genitourinary tumors characterized by high vascularization and strong reliance on glycolysis. Despite the many available therapies for renal cell carcinomas, first-line targeted therapies, such as cabozantinib, and durable reaponses are seen in only a small percentage of patients. Yet, little is known about the mechanisms that drive response (or lack thereof). This dearth of knowledge can be explained by the dynamic and complex microenvironment of renal carcinoma, which remains challenging to recapitulate in vitro. Here, we present a microphysiological model of renal cell carcinoma, including a tubular blood vessel model of induced pluripotent stem cell-derived endothelial cells and an adjacent 3D carcinoma model. Our model recapitulated hypoxia, glycolic metabolism, and sprouting angiogenesis. Using our model, we showed that cabozantinib altered cancer cell metabolism and decreased sprouting angiogenesis but did not restore barrier function. This microphysiological model could be helpful to elucidate, through multiple endpoints, the contributions of the relevant environmental components in eliciting a functional response or resistance to therapy in renal cell carcinoma.

Adaptive optics fluorescence lifetime imaging ophthalmoscopy of in vivo human retinal pigment epithelium

The intrinsic fluorescence properties of lipofuscin - naturally occurring granules that accumulate in the retinal pigment epithelium - are a potential biomarker for the health of the eye. A new modality is described here which combines adaptive optics technology with fluorescence lifetime detection, allowing for the investigation of functional and compositional differences within the eye and between subjects. This new adaptive optics fluorescence lifetime imaging ophthalmoscope was demonstrated in 6 subjects. Repeated measurements between visits had a minimum intraclass correlation coefficient of 0.59 Although the light levels were well below maximum permissible exposures, the safety of the imaging paradigm was tested using clinical measures; no concerns were raised. This new technology allows for in vivo adaptive optics fluorescence lifetime imaging of the human RPE mosaic.

Classification of fluorescent anisotropy decay based on the distance approach in the frequency domain

Frequency-domain (FD) fluorometry is a widely utilized tool to probe unique features of complex biological structures, which may serve medical diagnostic purposes. The conventional data analysis approaches used today to extract the fluorescence intensity or fluorescence anisotropy (FA) decay data suffer from several drawbacks and are inherently limited by the characteristics and complexity of the decay models. This paper presents the squared distance (D²) technique, which categorized samples based on the direct frequency response data (FRD) of the FA decay. As such, it improves the classification ability of the FD measurements of the FA decay as it avoids any distortion that results from the challenged translation into time domain data. This paper discusses the potential use of the D² approach to classify biological systems. Mathematical formulation of D² technique adjusted to the FRD of the FA decay is described. In addition, it validates the D² approach using 2 simulated data sets of 6 groups with similar widely and closely spaced FA decay data as well as in experimental data of 4 samples of a fluorophore-solvent (fluorescein-glycerol) system. In the simulations, the classification accuracy was above 95% for all 6 groups. In the experimental data, the classification accuracy was 100%. The D² approach can help classify samples whose FA decay data are difficult to extract making FA in the FD a realistic diagnostic tool. The D² approach offers an advanced method for sorting biological samples with differences beyond the practical temporal resolution limit in a reliable and efficient manner based on the FRD of their time-resolved fluorescence measurements thereby achieving better diagnostic quality in a shorter time.

John MA, Stafsudd O. Ex vivo hypercellular parathyroid gland differentiation using dynamic optical contrast imaging (DOCI)

Primary hyperparathyroidism, often caused by a single adenoma (80-85%) or four-gland hyperplasia (10-15%), can lead to elevated parathyroid hormone (PTH) levels and resultant hypercalcemia. Surgical excision of offending lesions is the standard of care, as the removal of pathologic adenomas reduces PTH and calcium values to baseline. The small size, variable location, and indistinct external features of parathyroid glands can make their identification quite challenging intraoperatively. Our group has developed the dynamic optical contrast imaging (DOCI) technique, a novel realization of dynamic temporally dependent measurements of tissue autofluorescence. In this study, we evaluated the efficacy of using the DOCI technique and normalized steady-state fluorescence intensity data for differentiating types of human parathyroid and thyroid tissues. We demonstrate that the DOCI technique has the capability to distinguish normal parathyroid tissue from diseased parathyroid glands as well as from adjacent healthy thyroid and adipose tissue across 8 different spectral channels between 405nm-600nm (p<0.05). Patient tissue DOCI data was further analyzed with a logistic regression classifier trained across the 8 spectral channels. After computer training, the computer-aided identification was able to accurately locate hypercellular parathyroid tissue with 100% sensitivity and 98.8% specificity within the captured DOCI image.

Fluorescence lifetime needle optical biopsy discriminates hepatocellular carcinoma

This work presents results of in vivo and in situ measurements of hepatocellular carcinoma by a developed optical biopsy system. Here, we describe the technical details of the implementation of fluorescence lifetime and diffuse reflectance measurements by the system, equipped with an original needle optical probe, compatible with the 17.5G biopsy needle standard. The fluorescence lifetime measurements observed by the setup were verified in fresh solutions of NADH and FAD⁺⁺, and then applied in a murine model for the characterisation of inoculated hepatocellular carcinoma (HCC) and adjacent liver tissue. The technique, applied in vivo and in situ and supplemented by measurements of blood oxygen saturation, made it possible to reveal statistically significant transformation in the set of measured parameters linked with the cellular pools of NADH and NADPH. In the animal model, we demonstrate that the characteristic changes in registered fluorescent parameters can be used to reliably distinguish the HCC tissue, liver tissue in the control, and the metabolically changed liver tissues of animals with the developed HCC tumour. For further transition to clinical applications, the optical biopsy system was tested during the routing procedure of the PNB in humans with suspected HCC. The comparison of the data from murine and human HCC tissues suggests that the tested animal model is generally representative in the sense of the registered fluorescence lifetime parameters, while statistically significant differences between their absolute values can still be observed.

Assessing hypoxic damage to placental trophoblasts by measuring membrane viscosity of extracellular vesicles

INTRODUCTION

As highly sophisticated intercellular communication vehicles in biological systems, extracellular vesicles (EVs) have been investigated as both promising liquid biopsy-based disease biomarkers and drug delivery carriers. Despite tremendous progress in understanding their biological and physiological functions, mechanical characterization of these nanoscale entities remains challenging due to the limited availability of proper techniques. Especially, whether damage to parental cells can be reflected by the mechanical properties of their EVs remains unknown.

METHODS

In this study, we characterized membrane viscosities of different types of EVs collected from primary human trophoblasts (PHTs), including apoptotic bodies, microvesicles and small extracellular vesicles, using fluorescence lifetime imaging microscopy (FLIM). The biochemical origin of EV membrane viscosity was examined by analyzing their phospholipid composition, using mass spectrometry.

RESULTS

We found that different EV types derived from the same cell type exhibit different membrane viscosities. The measured membrane viscosity values are well supported by the lipidomic analysis of the phospholipid compositions. We further demonstrate that the membrane viscosity of microvesicles can faithfully reveal hypoxic injury of the human trophoblasts. More specifically, the membrane of PHT microvesicles released under hypoxic condition is less viscous than its counterpart under standard culture condition, which is supported by the reduction in the phosphatidylethanolamine-to-phosphatidylcholine ratio in PHT microvesicles.

DISCUSSION

Our study suggests that biophysical properties of released trophoblastic microvesicles can reflect cell health. Characterizing EV's membrane viscosity may pave the way for the development of new EV-based clinical applications.

The Multifarious Applications of Copper Nanoclusters in Biosensing and Bioimaging and Their Translational Role in Early Disease Detection

Nanoclusters possess an ultrasmall size, amongst other favorable attributes, such as a high fluorescence and long-term colloidal stability, and consequently, they carry several advantages when applied in biological systems for use in diagnosis and therapy. Particularly, the early diagnosis of diseases may be facilitated by the right combination of bioimaging modalities and suitable probes. Amongst several metallic nanoclusters, copper nanoclusters (Cu NCs) present advantages over gold or silver NCs, owing to their several advantages, such as high yield, raw abundance, low cost, and presence as an important trace element in biological systems. Additionally, their usage in diagnostics and therapeutic modalities is emerging. As a result, the fluorescent properties of Cu NCs are exploited for use in optical imaging technology, which is the most commonly used research tool in the field of biomedicine. Optical imaging technology presents a myriad of advantages over other bioimaging technologies, which are discussed in this review, and has a promising future, particularly in early cancer diagnosis and imaging-guided treatment. Furthermore, we have consolidated, to the best of our knowledge, the recent trends and applications of copper nanoclusters (Cu NCs), a class of metal nanoclusters that have been gaining much traction as ideal bioimaging probes, in this review. The potential modes in which the Cu NCs are used for bioimaging purposes (e.g., as a fluorescence, magnetic resonance imaging (MRI), two-photon imaging probe) are firstly delineated, followed by their applications as biosensors and bioimaging probes, with a focus on disease detection.

Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters

Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of "watching metabolism in real time."

Computational Methods for Single-Cell Imaging and Omics Data Integration

Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.

Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to quantify molecular compositions and study molecular states in complex cellular environment as the lifetime readings are not biased by fluorophore concentration or excitation power. However, the current methods to generate FLIM images are either computationally intensive or unreliable when the number of photons acquired at each pixel is low. Here we introduce a new deep learning-based method termed flimGANE (fluorescence lifetime imaging based on Generative Adversarial Network Estimation) that can rapidly generate accurate and high-quality FLIM images even in the photon-starved conditions. We demonstrated our model is up to 2,800 times faster than the gold standard time-domain maximum likelihood estimation (TD_MLE) and that flimGANE provides a more accurate analysis of low-photon-count histograms in barcode identification, cellular structure visualization, Förster resonance energy transfer characterization, and metabolic state analysis in live cells. With its advantages in speed and reliability, flimGANE is particularly useful in fundamental biological research and clinical applications, where high-speed analysis is critical.

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

Multiplexed mRNA profiling in the spatial context provides new information enabling basic research and clinical applications. Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity. Here, we introduce a spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based decoding. We demonstrate MOSAICA's multiplexing scalability in detecting 10-plex targets in fixed colorectal cancer cells using combinatorial labeling of five fluorophores with facile error-detection and removal of autofluorescence. MOSAICA's analysis is strongly correlated with sequencing data (Pearson's r = 0.96) and was further benchmarked using RNAscopeTM and LGC StellarisTM. We further apply MOSAICA for multiplexed analysis of clinical melanoma Formalin-Fixed Paraffin-Embedded (FFPE) tissues. We finally demonstrate simultaneous co-detection of protein and mRNA in cancer cells.

Building and Using a Two-Photon Fluorescence Cross-Correlation Spectroscopy Setup Including Fluorescence Lifetime Analysis

Fluorescence Cross-Correlation Spectroscopy (FCCS) is a well-established and useful tool in physics and chemistry. Furthermore, due to its hybrid character of being a bulk assay at a single molecular level, it found many applications in biophysics and molecular biochemistry. Examples may be investigating kinetics and dynamics of chemical and biochemical reactions such as protein-ligand-, protein-protein-binding, fast conformational changes, and intracellular transportation. Also, it was utilized to characterize larger structures such as lipid vesicles and multi-protein complexes. A two-photon excitation source makes FCCS relatively easy-to-use and easy-to-maintain. Combining this technique with fluorescence lifetime analysis results in a versatile biophysical tool that can be used to solve many biological problems, as even small changes in the local environment, like pH or salt concentration, can be monitored if appropriate fluorophores are used. An example of its use for membrane docking and fusion assays is described in Chap. 13 . In this chapter, we want to give the reader a simple, detailed step-by-step guide of how to set up such a tool.

Above pile-up fluorescence microscopy with a 32 Mc/s single-channel time-resolved SPAD system

One of the major drawbacks of time-correlated single-photon counting (TCSPC) is generally represented by pile-up distortion, which strongly bounds the maximum acquisition speed to a few percent of the laser excitation rate. Based on a previous theoretical analysis, recently we presented the first, to the best of our knowledge, low-distortion and high-speed TCSPC system capable of overcoming the pile-up limitation by perfectly matching the single-photon avalanche diode (SPAD) dead time to the laser period. In this work, we validate the proposed system in a standard fluorescence measurement by comparing experimental data with the reference theoretical framework. As a result, a count rate of 32 Mc/s was achieved with a single-channel system still observing a negligible lifetime distortion.

Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances

The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...

Near-infrared probes for luminescence lifetime imaging

Biomedical luminescence imaging in the near-infrared (NIR, 700-1700 nm) region has shown great potential in visualizing biological processes and pathological conditions at cellular and animal levels, owing to the reduced tissue absorption and scattering compared to light in the visible (400-700 nm) region. To overcome the background interference and signal attenuation during intensity-based luminescence imaging, lifetime imaging has demonstrated a reliable imaging modality complementary to intensity measurement. Several selective or environment-responsive probes have been successfully developed for luminescence lifetime imaging and multiplex detection. This review summarizes recent advances in the application of luminescence lifetime imaging at cellular and animal levels in NIR-I and NIR-II regions. Finally, the challenges and further directions of luminescence lifetime imaging are also discussed.

Seeing is believing: tools to study the role of Rho GTPases during cytokinesis

Cytokinesis is required to cleave the daughter cells at the end of mitosis and relies on the spatiotemporal control of RhoA GTPase. Cytokinesis failure can lead to changes in cell fate or aneuploidy, which can be detrimental during development and/or can lead to cancer. However, our knowledge of the pathways that regulate RhoA during cytokinesis is limited, and the role of other Rho family GTPases is not clear. This is largely because the study of Rho GTPases presents unique challenges using traditional cell biological and biochemical methods, and they have pleiotropic functions making genetic studies difficult to interpret. The recent generation of optogenetic tools and biosensors that control and detect active Rho has overcome some of these challenges and is helping to elucidate the role of RhoA in cytokinesis. However, improvements are needed to reveal the role of other Rho GTPases in cytokinesis, and to identify the molecular mechanisms that control Rho activity. This review examines some of the outstanding questions in cytokinesis, and explores tools for the imaging and control of Rho GTPases.

In vivo fluorescence lifetime imaging of macrophage intracellular metabolism during wound responses in zebrafish

The function of macrophages in vitro is linked to their metabolic rewiring. However, macrophage metabolism remains poorly characterized in situ. Here, we used two-photon intensity and lifetime imaging of autofluorescent metabolic coenzymes, nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD), to assess the metabolism of macrophages in the wound microenvironment. Inhibiting glycolysis reduced NAD(P)H mean lifetime and made the intracellular redox state of macrophages more oxidized, as indicated by reduced optical redox ratio. We found that TNFα+ macrophages had lower NAD(P)H mean lifetime and were more oxidized compared to TNFα- macrophages. Both infection and thermal injury induced a macrophage population with a more oxidized redox state in wounded tissues. Kinetic analysis detected temporal changes in the optical redox ratio during tissue repair, revealing a shift toward a more reduced redox state over time. Metformin reduced TNFα+ wound macrophages, made intracellular redox state more reduced and improved tissue repair. By contrast, depletion of STAT6 increased TNFα+ wound macrophages, made redox state more oxidized and impaired regeneration. Our findings suggest that autofluorescence of NAD(P)H and FAD is sensitive to dynamic changes in intracellular metabolism in tissues and can be used to probe the temporal and spatial regulation of macrophage metabolism during tissue damage and repair.

Mapping the Time Dependent DNA Fragmentation caused by doxorubicin Loaded on PEGylated Carbogenic Nanodots using Fluorescence Lifetime Imaging and Super-resolution microscopy

Doxorubicin is an anthracycline drug most commonly used in cancer therapy. It intercalates with the nuclear DNA and induces toxicity by causing DNA breaks and histone evictions. However, the kinetics...

NAD(P)H autofluorescence lifetime imaging enables single cell analyses of cellular metabolism of osteoblasts in vitro and in vivo via two-photon microscopy

Two-photon fluorescence lifetime microscopy (2P-FLIM) is a non-invasive optical technique that can obtain cellular metabolism information based on the intrinsic autofluorescence lifetimes of free and enzyme-bound NAD(P)H, which reflect the metabolic state of single cells within the native microenvironment of the living tissue. NAD(P)H 2P-FLIM was initially performed in bone marrow stromal cell (BMSC) cultures established from Col (I) 2.3GFP or OSX-mCherry mouse models, in which osteoblastic lineage cells were labelled with green or red fluorescence protein, respectively. Measurement of the mean NAD(P)H lifetime, τ_M, demonstrated that osteoblasts in osteogenic media had a progressively increased τ_M compared to cells in regular media, suggesting that osteoblasts undergoing mineralization had higher NAD⁺/NAD(P)H ratio and may utilize more oxidative phosphorylation (OxPhos). In vivo NAD(P)H 2P-FLIM was conducted in conjunction with two-photon phosphorescence lifetime microscopy (2P-PLIM) to evaluate cellular metabolism of GFP⁺ osteoblasts as well as bone tissue oxygen at different locations of the native cranial bone in Col (I) 2.3GFP mice. Our data showed that osteocytes dwelling within lacunae had higher τ_M than osteoblasts at the bone edge of suture and marrow space. Measurement of pO₂ showed poor correlation of pO₂ and τ_M in native bone. However, when NAD(P)H 2P-FLIM was used to examine osteoblast cellular metabolism at the leading edge of the cranial defects during repair in Col (I) 2.3GFP mouse model, a significantly lower τ_M was recorded, which was associated with lower pO₂ at an early stage of healing, indicating an impact of hypoxia on energy metabolism during bone tissue repair. Taken together, our current study demonstrates the feasibility of using non-invasive optical NAD(P)H 2P-FLIM technique to examine cellular energy metabolism at single cell resolution in living animals. Our data further support that both glycolysis and OxPhos are being used in the osteoblasts, with more mature osteoblasts exhibiting higher ratio of NAD⁺/NAD(P)H, indicating a potential change of energy mode during differentiation. Further experiments utilizing animals with genetic modification of cellular metabolism could enhance our understanding of energy metabolism in various cell types in living bone microenvironment.

Compressed sensing in fluorescence microscopy

Compressed sensing (CS) is a signal processing approach that solves ill-posed inverse problems, from under-sampled data with respect to the Nyquist criterium. CS exploits sparsity constraints based on the knowledge of prior information, relative to the structure of the object in the spatial or other domains. It is commonly used in image and video compression as well as in scientific and medical applications, including computed tomography and magnetic resonance imaging. In the field of fluorescence microscopy, it has been demonstrated to be valuable for fast and high-resolution imaging, from single-molecule localization, super-resolution to light-sheet microscopy. Furthermore, CS has found remarkable applications in the field of mesoscopic imaging, facilitating the study of small animals' organs and entire organisms. This review article illustrates the working principles of CS, its implementations in optical imaging and discusses several relevant uses of CS in the field of fluorescence imaging from super-resolution microscopy to mesoscopy.

Retinal Organoids Long-Term Functional Characterization Using Two-Photon Fluorescence Lifetime and Hyperspectral Microscopy

Pluripotent stem cell-derived organoid technologies have opened avenues to preclinical basic science research, drug discovery, and transplantation therapy in organ systems. Stem cell-derived organoids follow a time course similar to species-specific organ gestation in vivo. However, heterogeneous tissue yields, and subjective tissue selection reduce the repeatability of organoid-based scientific experiments and clinical studies. To improve the quality control of organoids, we introduced a live imaging technique based on two-photon microscopy to non-invasively monitor and characterize retinal organoids’ (RtOgs’) long-term development. Fluorescence lifetime imaging microscopy (FLIM) was used to monitor the metabolic trajectory, and hyperspectral imaging was applied to characterize structural and molecular changes. We further validated the live imaging experimental results with endpoint biological tests, including quantitative polymerase chain reaction (qPCR), single-cell RNA sequencing, and immunohistochemistry. With FLIM results, we analyzed the free/bound nicotinamide adenine dinucleotide (f/b NADH) ratio of the imaged regions and found that there was a metabolic shift from glycolysis to oxidative phosphorylation. This shift occurred between the second and third months of differentiation. The total metabolic activity shifted slightly back toward glycolysis between the third and fourth months and stayed relatively stable between the fourth and sixth months. Consistency in organoid development among cell lines and production lots was examined. Molecular analysis showed that retinal progenitor genes were expressed in all groups between days 51 and 159. Photoreceptor gene expression emerged around the second month of differentiation, which corresponded to the shift in the f/b NADH ratio. RtOgs between 3 and 6 months of differentiation exhibited photoreceptor gene expression levels that were between the native human fetal and adult retina gene expression levels. The occurrence of cone opsin expression (OPN1 SW and OPN1 LW) indicated the maturation of photoreceptors in the fourth month of differentiation, which was consistent with the stabilized level of f/b NADH ratio starting from 4 months. Endpoint single-cell RNA and immunohistology data showed that the cellular compositions and lamination of RtOgs at different developmental stages followed those in vivo.

PLEKHA7 signaling is necessary for the growth of mutant KRAS driven colorectal cancer

Plekha7 (Pleckstrin homology [PH] domain containing, family A member 7) regulates the assembly of proteins of the cytoplasmic apical zonula adherens junction (AJ), thus ensuring cell-cell adhesion and tight-junction barrier integrity. Little is known of Plekha7 function in cancer. In colorectal cancer (CRC) Plekha7 expression is elevated compared to adjacent normal tissue levels, increasing with clinical stage. Plekha7 was present at plasma membrane AJ with wild-type KRas (wt-KRas) but was dispersed in cells expressing mutant KRas (mut-KRas). Fluorescence lifetime imaging microscopy (FLIM) indicated a direct Plekha7 interaction with wt-KRas but scantily with mut-KRas. Inhibiting Plekha7 specifically decreased mut-KRas cell signaling, proliferation, attachment, migration, and retarded mut-KRAS CRC tumor growth. Binding of diC8-phosphoinositides (PI) to the PH domain of Plekha7 was relatively low affinity. This may be because a D175 amino acid residue plays a "sentry" role preventing PI(3,4)P₂ and PI(3,4,5)P₃ binding. Molecular or pharmacological inhibition of the Plekha7 PH domain prevented the growth of mut-KRas but not wt-KRas cells. Taken together the studies suggest that Plekha7, in addition to maintaining AJ structure plays a role in mut-KRas signaling and phenotype through interaction of its PH domain with membrane mut-KRas, but not wt-KRas, to increase the efficiency of mut-KRas downstream signaling.

Intravital and high-content multiplex imaging of the immune system

Highly motile and functionally diverse immune cells orchestrate effective immune responses through complex and dynamic cooperative behavior. Multiphoton intravital microscopy (MP-IVM) presents a unique and powerful tool to study the coordinated action of immune cell interactions in situ. Here, we review the current state of intravital microscopy in deepening our understanding of the immune system and discuss its fundamental limitations. In addition, we draw insights from recent technical advances in multiplex static tissue-imaging methods and propose an approach that could enable simultaneous visualization of cellular dynamics, deep phenotyping, and transcriptional states through a new type of correlative microscopy that combines these imaging technologies with advances in complex data analysis.

Luminescence Ratiometric Nanothermometry Regulated by Tailoring Annihilators of Triplet-Triplet Annihilation Upconversion Nanomicelles

Triplet-triplet annihilation (TTA) upconversion is a special non-linear photophysical process that converts low-energy photons into high-energy photons based on sensitizer/annihilator pairs. Here, we constructed a novel luminescence ratiometric nanothermometer based on TTA upconversion nanomicelles by encapsulating sensitizer/annihilator molecules into a temperature-sensitive amphiphilic triblock polymer and obtained good linear relationships between the luminescence ratio (integrated intensity ratio of upconverted luminescence peak to the downshifted phosphorescence peak) and the temperature. We also found chemical modification of annihilators would rule out the interference of the polymer concentration and stereochemical engineering of annihilators would readily regulate the thermal sensitivity.

Nanosecond-resolution photothermal dynamic imaging via MHZ digitization and match filtering

Photothermal microscopy has enabled highly sensitive label-free imaging of absorbers, from metallic nanoparticles to chemical bonds. Photothermal signals are conventionally detected via modulation of excitation beam and demodulation of probe beam using lock-in amplifier. While convenient, the wealth of thermal dynamics is not revealed. Here, we present a lock-in free, mid-infrared photothermal dynamic imaging (PDI) system by MHz digitization and match filtering at harmonics of modulation frequency. Thermal-dynamic information is acquired at nanosecond resolution within single pulse excitation. Our method not only increases the imaging speed by two orders of magnitude but also obtains four-fold enhancement of signal-to-noise ratio over lock-in counterpart, enabling high-throughput metabolism analysis at single-cell level. Moreover, by harnessing the thermal decay difference between water and biomolecules, water background is effectively separated in mid-infrared PDI of living cells. This ability to nondestructively probe chemically specific photothermal dynamics offers a valuable tool to characterize biological and material specimens.

Photothermal microscopy is limited for imaging of thermal dynamics. Here, the authors introduce a lock-in free, mid-infrared photothermal dynamic imaging system, which significantly increases SNR and imaging speed, and demonstrate metabolism analysis at single-cell level and background removal.

Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell

Fluorescence-based sensors play a fundamental role in biological research. These sensors can be based on fluorescent proteins, fluorescent probes or they can be hybrid systems. The availability of a very large dataset of fluorescent molecules, both genetically encoded and synthetically produced, together with the structural insights on many sensing domains, allowed to rationally design a high variety of sensors, capable of monitoring both molecular and global changes in living cells or in in vitro systems. The advancements in the fluorescence-imaging field helped researchers to obtain a deeper understanding of how and where specific changes occur in a cell or in vitro by combining the readout of the fluorescent sensors with the spatial information provided by fluorescent microscopy techniques. In this review we give an overview of the state of the art in the field of fluorescent biosensors and fluorescence imaging techniques, and eventually guide the reader through the choice of the best combination of fluorescent tools and techniques to answer specific biological questions. We particularly focus on sensors for probing the bioenergetics and physicochemical status of the cell.

Nuclear envelope mechanobiology: linking the nuclear structure and function

The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to apply mechanical force and methods to measure nuclear mechanics in conjunction with DNA, RNA, and protein visualization in living cells. Ultimately, combining real-time nuclear deformations and chromatin dynamics can be a powerful tool to study mechanisms of how forces affect the dynamics of genome function.

Redox ratio in the left ventricle of the growth restricted fetus is positively correlated with cardiac output

Intrauterine growth restriction (IUGR) is a result of limited substrate supply to the developing fetus in utero, and can be caused by either placental, genetic or environmental factors. Babies born IUGR can have poor long-term health outcomes, including being at higher risk of developing cardiovascular disease. Limited substrate supply in the IUGR fetus not only changes the structure of the heart but may also affect metabolism and function of the developing heart. We have utilised two imaging modalities, two-photon microscopy and phase-contrast MRI (PC-MRI), to assess alterations in cardiac metabolism and function using a sheep model of IUGR. Two-photon imaging revealed that the left ventricle of IUGR fetuses (at 140-141 d GA) had a reduced optical redox ratio, suggesting a reliance on glycolysis for ATP production. Concurrently, the use of PC-MRI to measure foetal left ventricular cardiac output (LVCO) revealed a positive correlation between LVCO and redox ratio in IUGR, but not control fetuses. These data suggest that altered heart metabolism in IUGR fetuses is indicative of reduced cardiac output, which may contribute to poor cardiac outcomes in adulthood.

Electrocatalytic Reaction Driven Flow: Role of pH in Flow Reversal

Immobilized bimetallic structures generate fluid flow during electrocatalytic reactions with hydrogen peroxide, which is typically driven from the anodic metal to the cathodic metal similar to an electroosmotic flow. However, under low reactive regimes, the generated flow becomes fully reversed, which cannot be explained by the classical electroosmotic theory. This work aims at unraveling the origin and dynamics of this flow hysteresis through a combined experimental and numerical approach. The key electrocatalytic parameters that contribute to flow reversal are analyzed experimentally and numerically under low reactive regimes induced by bulk pH variations. The proton gradient that initiates chemomechanical actuation is probed with the use of fluorescence lifetime imaging. The fluid flow dynamics under reactive regimes are visualized by the use of particle tracking. Our numerical simulations elucidate the role of pH variations and additional ionic species (counterions) toward flow reversal. The combination of these techniques highlights the interplay between electrocatalytic and electrokinetic phenomena on the occurrence of flow reversal.

Full spectrum fluorescence lifetime imaging with 0.5 nm spectral and 50 ps temporal resolution

The use of optical techniques to interrogate wide ranging samples from semiconductors to biological tissue for rapid analysis and diagnostics has gained wide adoption over the past decades. The desire to collect ever more spatially, spectrally and temporally detailed optical signatures for sample characterization has specifically driven a sharp rise in new optical microscopy technologies. Here we present a high-speed optical scanning microscope capable of capturing time resolved images across 512 spectral and 32 time channels in a single acquisition with the potential for ~0.2 frames per second (256 × 256 image pixels). Each pixel in the resulting images contains a detailed data cube for the study of diverse time resolved light driven phenomena. This is enabled by integration of system control electronics and on-chip processing which overcomes the challenges presented by high data volume and low imaging speed, often bottlenecks in previous systems.

High data volumes from multidimensional imaging techniques can lead to slow collection and processing times. Here, the authors implement multispectral fluorescence lifetime imaging microscopy (FLIM) that uses time-correlated photon counting technology to reach simultaneously high imaging rates combined with high spectral and temporal resolution.

Raman Imaging and Fluorescence Lifetime Imaging Microscopy for Diagnosis of Cancer State and Metabolic Monitoring

Hurdles for effective tumor therapy are delayed detection and limited effectiveness of systemic drug therapies by patient-specific multidrug resistance. Non-invasive bioimaging tools such as fluorescence lifetime imaging microscopy (FLIM) and Raman-microspectroscopy have evolved over the last decade, providing the potential to be translated into clinics for early-stage disease detection, in vitro drug screening, and drug efficacy studies in personalized medicine. Accessing tissue- and cell-specific spectral signatures, Raman microspectroscopy has emerged as a diagnostic tool to identify precancerous lesions, cancer stages, or cell malignancy. In vivo Raman measurements have been enabled by recent technological advances in Raman endoscopy and signal-enhancing setups such as coherent anti-stokes Raman spectroscopy or surface-enhanced Raman spectroscopy. FLIM enables in situ investigations of metabolic processes such as glycolysis, oxidative stress, or mitochondrial activity by using the autofluorescence of co-enzymes NADH and FAD, which are associated with intrinsic proteins as a direct measure of tumor metabolism, cell death stages and drug efficacy. The combination of non-invasive and molecular-sensitive in situ techniques and advanced 3D tumor models such as patient-derived organoids or microtumors allows the recapitulation of tumor physiology and metabolism in vitro and facilitates the screening for patient-individualized drug treatment options.

Single-photon peak event detection (SPEED): a computational method for fast photon counting in fluorescence lifetime imaging microscopy

Fluorescence lifetime imaging microscopy (FLIM) characterizes samples by examining the temporal properties of fluorescence emission, providing useful contrast within samples based on the local physical and biochemical environment of fluorophores. Despite this, FLIM applications have been limited in scope by either poor accuracy or long acquisition times. Here, we present a method for computational single-photon counting of directly sampled time-domain FLIM data that is capable of accurate fluorescence lifetime and intensity measurements while acquiring over 160 Mega-counts-per-second with sub-nanosecond time resolution between consecutive photon counts. We demonstrate that our novel method of Single-photon PEak Event Detection (SPEED) is more accurate than direct pulse sampling and faster than established photon counting FLIM methods. We further show that SPEED can be implemented for imaging and quantifying samples that benefit from higher -throughput and -dynamic range imaging with real-time GPU-accelerated processing and use this capability to examine the NAD(P)H-related metabolic dynamics of apoptosis in human breast cancer cells. Computational methods for photon counting such as SPEED open up more opportunities for fast and accurate FLIM imaging and additionally provide a basis for future innovation into alternative FLIM techniques.

Fast wide-field upconversion luminescence lifetime thermometry enabled by single-shot compressed ultrahigh-speed imaging

Photoluminescence lifetime imaging of upconverting nanoparticles is increasingly featured in recent progress in optical thermometry. Despite remarkable advances in photoluminescent temperature indicators, existing optical instruments lack the ability of wide-field photoluminescence lifetime imaging in real time, thus falling short in dynamic temperature mapping. Here, we report video-rate upconversion temperature sensing in wide field using single-shot photoluminescence lifetime imaging thermometry (SPLIT). Developed from a compressed-sensing ultrahigh-speed imaging paradigm, SPLIT first records wide-field luminescence intensity decay compressively in two views in a single exposure. Then, an algorithm, built upon the plug-and-play alternating direction method of multipliers, is used to reconstruct the video, from which the extracted lifetime distribution is converted to a temperature map. Using the core/shell NaGdF4:Er3+,Yb3+/NaGdF4 upconverting nanoparticles as the lifetime-based temperature indicators, we apply SPLIT in longitudinal wide-field temperature monitoring beneath a thin scattering medium. SPLIT also enables video-rate temperature mapping of a moving biological sample at single-cell resolution.

Compact Color Biofinder (CoCoBi): Fast, Standoff, Sensitive Detection of Biomolecules and Polyaromatic Hydrocarbons for the Detection of Life

We have developed a compact instrument called the "COmpact COlor BIofinder", or CoCoBi, for the standoff detection of biological materials and organics with polyaromatic hydrocarbons (PAHs) using a nondestructive approach in a wide area. The CoCoBi system uses a compact solid state, conductively cooled neodymium-doped yttrium aluminum garnet (Nd:YAG) nanosecond pulsed laser capable of simultaneously providing two excitation wavelengths, 355 and 532 nm, and a compact, sensitive-gated color complementary metal-oxide-semiconductor camera detector. The system is compact, portable, and determines the location of biological materials and organics with PAHs in an area 1590 cm2 wide, from a target distance of 3 m through live video using fast fluorescence signals. The CoCoBi system is highly sensitive and capable of detecting a PAH concentration below 1 part per billion from a distance of 1 m. The color images provide the simultaneous detection of various objects in the target area using shades of color and morphological features. We demonstrate that this unique feature successfully detected the biological remains present in a 150-million-year-old fossil buried in a fluorescent clay matrix. The CoCoBi was also successfully field-tested in Hawaiian ocean water during daylight hours for the detection of natural biological materials present in the ocean. The wide-area and video-speed imaging capabilities of CoCoBi for biodetection may be highly useful in future NASA rover-lander life detection missions.

Resonant Electro-Optic Imaging for Microscopy at Nanosecond Resolution

We demonstrate an electro-optic wide-field method to enable fluorescence lifetime microscopy (FLIM) with high throughput and single-molecule sensitivity. Resonantly driven Pockels cells are used to efficiently gate images at 39 MHz, allowing fluorescence lifetime to be captured on standard camera sensors. Lifetime imaging of single molecules is enabled in wide field with exposure times of less than 100 ms. This capability allows combination of wide-field FLIM with single-molecule super-resolution localization microscopy. Fast single-molecule dynamics such as FRET and molecular binding events are captured from wide-field images without prior spatial knowledge. A lifetime sensitivity of 1.9 times the photon shot-noise limit is achieved, and high throughput is shown by acquiring wide-field FLIM images with millisecond exposure and >10⁸ photons per frame. Resonant electro-optic FLIM allows lifetime contrast in any wide-field microscopy method.

Optimization of Advanced Live-Cell Imaging through Red/Near-Infrared Dye Labeling and Fluorescence Lifetime-Based Strategies

Fluorescence microscopy is essential for a detailed understanding of cellular processes; however, live-cell preservation during imaging is a matter of debate. In this study, we proposed a guide to optimize advanced light microscopy approaches by reducing light exposure through fluorescence lifetime (τ) exploitation of red/near-infrared dyes. Firstly, we characterized key instrumental elements which revealed that red/near-infrared laser lines with an 86x (Numerical Aperture (NA) = 1.2, water immersion) objective allowed high transmission of fluorescence signals, low irradiance and super-resolution. As a combination of two technologies, i.e., vacuum tubes (e.g., photomultiplier) and semiconductor microelectronics (e.g., avalanche photodiode), type S, X and R of hybrid detectors (HyD-S, HyD-X and HyD-R) were particularly adapted for red/near-infrared photon counting and τ separation. Secondly, we tested and compared lifetime-based imaging including coarse τ separation for confocal microscopy, fitting and phasor plot analysis for fluorescence lifetime microscopy (FLIM), and lifetimes weighting for enhanced stimulated emission depletion (STED) nanoscopy, in light of red/near-infrared multiplexing. Mainly, we showed that the choice of appropriate imaging approach may depend on fluorochrome number, together with their spectral/lifetime characteristics and STED compatibility. Photon-counting mode and sensitivity of HyDs together with phasor plot analysis of fluorescence lifetimes enabled the flexible and fast imaging of multi-labeled living H28 cells. Therefore, a combination of red/near-infrared dyes labeling with lifetime-based strategies offers new perspectives for live-cell imaging by enhancing sample preservation through acquisition time and light exposure reduction.

Designs, applications, and limitations of genetically encoded fluorescent sensors to explore plant biology

The understanding of signaling and metabolic processes in multicellular organisms requires knowledge of the spatial dynamics of small molecules and the activities of enzymes, transporters, and other proteins in vivo, as well as biophysical parameters inside cells and across tissues. The cellular distribution of receptors, ligands, and activation state must be integrated with information about the cellular distribution of metabolites in relation to metabolic fluxes and signaling dynamics in order to achieve the promise of in vivo biochemistry. Genetically encoded sensors are engineered fluorescent proteins that have been developed for a wide range of small molecules, such as ions and metabolites, or to report biophysical processes, such as transmembrane voltage or tension. First steps have been taken to monitor the activity of transporters in vivo. Advancements in imaging technologies and specimen handling and stimulation have enabled researchers in plant sciences to implement sensor technologies in intact plants. Here, we provide a brief history of the development of genetically encoded sensors and an overview of the types of sensors available for quantifying and visualizing ion and metabolite distribution and dynamics. We further discuss the pros and cons of specific sensor designs, imaging systems, and sample manipulations, provide advice on the choice of technology, and give an outlook into future developments.

Visualizing and quantifying antimicrobial drug distribution in tissue

The biodistribution and pharmacokinetics of drugs are vital to the mechanistic understanding of their efficacy. Measuring antimicrobial drug efficacy has been challenging as plasma drug concentration is used as a surrogate for tissue drug concentration, yet typically does not reflect that at the intended site(s) of action. Utilizing an image-guided approach, it is feasible to accurately quantify the biodistribution and pharmacokinetics within the desired site(s) of action. We outline imaging modalities used in visualizing drug distribution with examples ranging from in vitro cellular drug uptake to clinical treatment of microbial infections. The imaging modalities of interest are: radio-labeling, magnetic resonance, mass spectrometry imaging, computed tomography, fluorescence, and Raman spectroscopy. We outline the progress, limitations, and future outlook for each methodology. Further advances in these optical approaches would benefit patients and researchers alike, as non-invasive imaging could yield more profound insights with a lower clinical burden than invasive measurement approaches used today.