Phototoxicity in live fluorescence microscopy, and how to avoid it

Accessible and accurate cytometry analysis of adherent cells using fluorescence microscopes

We have developed a method along with a Python-based analysis tool to capture images and produce flow-cytometry-like data for adherent cell culture utilizing simple accessible microscopes. Leveraging the recently developed generalist algorithms for cell segmentation, our approach efficiently quantifies single-cell fluorescence signals. We demonstrated the utility of this method by screening a set of 88 prime editing conditions using the integration of mNeonGreen211 as a reporter.

Gentle Label-Free Nonlinear Optical Imaging Relaxes Linear-Absorption-Mediated Triplet

Sample health is critical for live-cell fluorescence microscopy and has promoted light-sheet microscopy that restricts its ultraviolet-visible excitation to one plane inside a 3D sample. It is thus intriguing that laser-scanning nonlinear optical microscopy, which similarly restricts its near-infrared excitation, has not broadly enabled gentle label-free molecular imaging. It is hypothesized that intense near-infrared excitation induces phototoxicity via linear absorption of intrinsic biomolecules with subsequent triplet buildup, rather than the commonly assumed mechanism of nonlinear absorption. Using a reproducible phototoxicity assay based on the time-lapse elevation of autofluorescence (hyper-fluorescence) from a homogeneous tissue model (chicken breast), strong evidence is provided supporting this hypothesis. The study justifies a simple imaging technique, e.g., rapidly scanned sub-80-fs excitation with full triplet-relaxation, to mitigate this ubiquitous linear-absorption-mediated phototoxicity independent of sample types. The corresponding label-free imaging can track freely moving C. elegans in real-time at an irradiance up to one-half of water optical breakdown.

Near-zero photon bioimaging by fusing deep learning and ultralow-light microscopy

Enhancing the reliability and reproducibility of optical microscopy by reducing specimen irradiance continues to be an important biotechnology target. As irradiance levels are reduced, however, the particle nature of light is heightened, giving rise to Poisson noise, or photon sparsity that restricts only a few (0.5%) image pixels to comprise a photon. Photon sparsity can be addressed by collecting approximately 200 photons per pixel; this, however, requires long acquisitions and, as such, suboptimal imaging rates. Here, we introduce near-zero photon bioimaging, a method that operates at kHz rates and 10,000-fold lower irradiance than standard microscopy. To achieve this level of performance, we uniquely combined a judiciously designed epifluorescence microscope enabling ultralow background levels and AI that learns to reconstruct biological images from as low as 0.01 photons per pixel. We demonstrate that near-zero photon bioimaging captures the structure of multicellular and subcellular features with high fidelity, including features represented by nearly zero photons. Beyond optical microscopy, the near-zero photon bioimaging paradigm can be applied in remote sensing, covert applications, and biomedical imaging that utilize damaging or quantum light.

The Heterogeneity in the Response of A549 Cells to Toyocamycin Observed Using Hopping Scanning Ion Conductance Microscopy

Scanning ion conductance microscopy (SICM) is a noninvasive topographic mapping technique used in imaging live cells, unlike electron microscopy and certain applications of fluorescence microscopy, which can disrupt cell integrity. In this study, we used SICM to track the morphological changes of the same A549 cells to uncover the cell-to-cell heterogeneity in their response to the drug. We found that toyocamycin (TOY) induced rapid reorganization of the actin cytoskeleton in A549 cells, causing them to become circular, irregular, or ellipsoidal in shape. Mapping of the dynamic changes in morphology revealed membrane blebbing and a significant decrease in volume over time. Using high-throughput SICM, we mapped the morphology of multiple single cells treated with TOY, which revealed that A549 showed characteristics of apoptosis and necrosis. The drug treatment does not significantly change the average root-mean-square (RMS) roughness of the cells. However, the drug leads to an increase in membrane height, possibly indicating early apoptotic changes. Plotting the individual RMS roughness of the cells showed a cell with an increase in roughness and the presence of pores, which is also an indication of necrosis behavior. Our results demonstrate that SICM is an effective technique for revealing the evolution of heterogeneity in single cells in their responses to anticancer drugs over time.

Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout

Genetically encoded biosensors with changes in fluorescence lifetime (as opposed to fluorescence intensity) can quantify small molecules in complex contexts, even in vivo. However, lifetime-readout sensors are poorly understood at a molecular level, complicating their development. Although there are many sensors that have fluorescence-intensity changes, there are currently only a few with fluorescence-lifetime changes. Here, we optimized two biosensors for thiol-disulfide redox (RoTq-Off and RoTq-On) with opposite changes in fluorescence lifetime in response to oxidation. Using biophysical approaches, we showed that the high-lifetime states of these sensors lock the chromophore more firmly in place than their low-lifetime states do. Two-photon fluorescence lifetime imaging of RoTq-On fused to a glutaredoxin (Grx1) enabled robust, straightforward monitoring of cytosolic glutathione redox state in acute mouse brain slices. The motional mechanism described here is probably common and may inform the design of other lifetime-readout sensors; the Grx1-RoTq-On fusion sensor will be useful for studying glutathione redox in physiology.

Protocol for real-time glycolytic monitoring in mammalian cells using confocal microscopy and HYlight, a biosensor for fructose 1,6-bisphosphate

Here, we present a protocol for a glycolytic stress test using HYlight, a fluorescent protein-based biosensor that specifically binds fructose 1,6-bisphosphate (FBP), a product of the rate-limiting step of glycolysis. We describe steps for HYlight delivery into cells, real-time imaging by confocal microscopy, and data analysis. Compared with other techniques, HYlight allows glycolytic activity assessment in intact cells with single-cell resolution. This protocol can be applied to studies in which glycolysis might play a role, such as cancer or diabetes research. For complete details on the use and execution of this protocol, please refer to Pérez-Chávez et al.1.

Statistical analysis of fluorescence intensity transients with Bayesian methods

Molecular movement and interactions at the single-molecule level, particularly in live cells, are often studied using fluorescence correlation spectroscopy (FCS). While powerful, FCS has notable drawbacks: It requires high laser intensities and long acquisition times, increasing phototoxicity, and often relies on problematic statistical assumptions in data fitting. We introduce fluorescence intensity trace statistical analysis (FITSA), a Bayesian method that directly analyzes fluorescence intensity traces. FITSA offers faster, more stable convergence than previous approaches and provides robust parameter estimation from far shorter measurements than conventional FCS. Our results demonstrate that FITSA achieves comparable precision to FCS while requiring substantially fewer photons. This advantage becomes even more pronounced when accounting for statistical dependencies in FCS analysis, which are often overlooked but necessary for accurate error estimation. By reducing laser exposure, FITSA minimizes phototoxicity effects, representing a major advancement in the quantitative analysis of molecular processes across fields.

Hybrid Iterating-Averaging Low Photon Budget Gabor Holographic Microscopy

Achieving high-contrast, label-free imaging with minimal impact on live cell culture behavior remains a primary challenge in quantitative phase imaging (QPI). By enabling imaging under low illumination intensities (low photon budget, LPB), it is possible to minimize cell photostimulation, phototoxicity, and photodamage while supporting long-term and high-speed observations. However, LPB imaging introduces significant difficulties in QPI due to high levels of camera shot noise and quantification noise. Digital in-line holographic microscopy (DIHM) is a QPI technique known for its robustness against LPB data. However, simultaneous minimization of shot noise and inherent in DIHM twin image perturbation remains a critical challenge. In this study, we present the iterative Gabor averaging (IGA) algorithm, a novel approach that integrates iterative phase retrieval with frame averaging to effectively suppress both twin image disturbance and shot noise in multiframe DIHM. The IGA algorithm achieves this by leveraging an iterative process that reconstructs high-fidelity phase images while selectively averaging camera shot noise across frames. Our simulations demonstrate that IGA consistently outperforms conventional methods, achieving superior reconstruction accuracy, particularly under high-noise conditions. Experimental validations involving high-speed imaging of dynamic sperm cells and a static phase test target measurement under low illumination further confirmed IGA's efficacy. The algorithm also proved successful for optically thin samples, which often yield low signal-to-noise holograms even at high photon budgets. These advancements make IGA a powerful tool for photostimulation-free, high-speed imaging of dynamic biological samples and enhance the ability to image samples with extremely low optical thickness, potentially transforming biomedical and environmental applications in low-light settings.

Bright and photostable yellow fluorescent proteins for extended imaging

Fluorescent proteins are indispensable molecular tools for visualizing biological structures and processes, but their limited photostability restricts the duration of dynamic imaging experiments. Yellow fluorescent proteins (YFPs), in particular, photobleach rapidly. Here, we introduce mGold2s and mGold2t, YFPs with up to 25-fold greater photostability than mVenus and mCitrine, two commonly used YFPs, while maintaining comparable brightness. These variants were identified using a high-throughput pooled single-cell platform, simultaneously screening for high brightness and photostability. Compared with our previous benchmark, mGold, the mGold2 variants display a ~4-fold increase in photostability without sacrificing brightness. mGold2s and mGold2t extend imaging durations across diverse modalities, including widefield, total internal reflection fluorescence (TIRF), super-resolution, single-molecule, and laser-scanning confocal microscopy. When incorporated into fluorescence resonance energy transfer (FRET)-based biosensors, the proposed YFPs enable more reliable, prolonged imaging of dynamic cellular processes. Overall, the enhanced photostability of mGold2s and mGold2t enables high-sensitivity imaging of subcellular structures and cellular activity over extended periods, broadening the scope and precision of biological imaging.

Making sense of blobs, whorls, and shades: methods for label-free, inverse imaging in bright-field optical microscopy

Despite its long history and widespread use, conventional bright-field optical microscopy has received recent attention as an excellent option to perform accurate, label-free, imaging of biological objects. As with any imaging system, bright-field produces an ill-defined representation of the specimen, in this case characterized by intertwined phase and amplitude in image formation, invisibility of phase objects at exact focus, and both positive and negative contrast present in images. These drawbacks have prevented the application of bright-field to the accurate imaging of unlabeled specimens. To address these challenges, a variety of methods using hardware, software or both have been developed, with the goal of providing solutions to the inverse imaging problem set in bright-field. We revise the main operating principles and characteristics of bright-field microscopy, followed by a discussion of the solutions (and potential limitations) to reconstruction in two dimensions (2D). We focus on methods based on conventional optics, including defocusing microscopy, transport of intensity, ptychography and deconvolution. Advances to achieving three-dimensional (3D) bright-field imaging are presented, including methods that exploit multi-view reconstruction, physical modeling, deep learning and conventional digital image processing. Among these techniques, optical sectioning in bright-field microscopy (OSBM) constitutes a direct approach that captures z-image stacks using a standard microscope and applies digital filters in the spatial domain, yielding inverse-imaging solutions in 3D. Finally, additional techniques that expand the capabilities of bright-field are discussed. Label-free, inverse imaging in conventional optical microscopy thus emerges as a powerful biophysical tool for accurate 2D and 3D imaging of biological samples.

Development of label-free cell tracking for discrimination of the heterogeneous mesenchymal migration

Image-based cell phenotyping is fundamental in both cell biology and medicine. As cells are dynamic systems, phenotyping based on static data is complemented by dynamic data extracted from time-dependent cell characteristics. We developed a label-free automatic tracking method for phase contrast images. We examined the possibility of using cell motility-based discrimination to identify different types of mesenchymal migration in invasive malignant cancer and non-cancer cells. These cells were cultured in plastic tissue culture vessels, using motility parameters from cell trajectories extracted with label-free tracking. Correlation analysis with these motility parameters identified characteristic parameters for cancer HT1080 fibrosarcoma and non-cancer 3T3-Swiss fibroblast cell lines. The parameter "sum of turn angles," combined with the "frequency of turns" at shallow angles and "migration speed," proved effective in highlighting the migration characteristics of these cells. It revealed differences in their mechanisms for generating effective propulsive forces. The requirements to characterize these differences included the spatiotemporal resolution of segmentation and tracking, capable of detecting polarity changes associated with cell morphological alterations and cell body displacement. With the segmentation and tracking method proposed here, a discrimination curve computed using quadratic discrimination analysis from the "sum of turn angles" and "frequency of turns below 30°" gave the best performance with a 94% sensitivity. Cell migration is a process related not only to cancer but also to tissue healing and growth. The proposed methodology is easy to use, enabling anyone without professional skills in image analysis, large training datasets, or special devices. It has the potential for application not only in cancer cell discrimination but also in a broad range of applications and basic research. Validating the expandability of this method to characterize cell migration, including the scheme of propulsive force generation, is an important consideration for future study.

The Astrocytic Zinc Transporter ZIP12 Is a Synaptic Protein That Contributes to Synaptic Zinc Levels in the Mouse Auditory Cortex

Synaptically released zinc is a neuronal signaling system that arises from the actions of the presynaptic vesicular zinc transporter protein zinc transporter 3 (ZnT3). Mechanisms that regulate the actions of zinc at synapses are of great importance for many aspects of synaptic signaling in the brain. Here, we identify the astrocytic zinc transporter protein ZIP12 as a candidate mechanism that contributes to zinc clearance at cortical synapses. We identify small-molecule compounds that antagonize the function of ZIP12 in heterologous expression systems, and we use one of these compounds, ZIP12 modulator 8, to increase the concentration of ZnT3-dependent zinc at synapses in the brain of male and female mice to inhibit the activity of neuronal AMPA and NMDA glutamate receptors. These results identify a cellular mechanism and provide a pharmacological toolbox to target the molecular machinery that supports the actions of synaptic zinc in the brain.

Deep learning image analysis for continuous single-cell imaging of dynamic processes in Plasmodium falciparum-infected erythrocytes

Continuous high-resolution imaging of the disease-mediating blood stages of the human malaria parasite Plasmodium falciparum faces challenges due to photosensitivity, small parasite size, and the anisotropy and large refractive index of host erythrocytes. Previous studies often relied on snapshot galleries from multiple cells, limiting the investigation of dynamic cellular processes. We present a workflow enabling continuous, single-cell monitoring of live parasites throughout the 48-hour intraerythrocytic life cycle with high spatial and temporal resolution. This approach integrates label-free, three-dimensional differential interference contrast and fluorescence imaging using an Airyscan microscope, automated cell segmentation through pre-trained deep-learning algorithms, and 3D rendering for visualization and time-resolved analyses. As a proof of concept, we applied this workflow to study knob-associated histidine-rich protein (KAHRP) export into the erythrocyte compartment and its clustering beneath the plasma membrane. Our methodology opens avenues for in-depth exploration of dynamic cellular processes in malaria parasites, providing a valuable tool for further investigations.

Mapping cellular processes that determine delivery of plasmid DNA to the nucleus: application in Chinese hamster ovary and human embryonic kidney cells to enhance protein production

Delivery of DNA into nucleated eukaryotic cells is known as transfection and has been essential in establishing technologies such as recombinant protein production and gene therapy. Considerable research efforts have led to development of a variety of transfection methods for a multitude of applications and cell types. Many methods are efficient in delivering DNA across the plasma membrane but few focus on subsequent delivery into the nucleus, a necessary step in expression of a recombinant transgene, and the cellular processes governing nuclear import of DNA during transfection have proved elusive. Herein, live confocal microscopy was used to track plasmid DNA during transfection of Chinese hamster ovary (CHO) and human embryonic kidney (HEK) cells to map key cellular processes central to nuclear import of DNA showing that there is a strong relationship between events of cell division, promotion of DNA dispersal from endosomes and subsequent nuclear import leading to gene expression. Furthermore, cationic lipid-mediated transfection is more dependent on events of the cell cycle than electroporation to deliver DNA into the nucleus. These findings have informed the design of a method where both CHO and HEK cells are synchronised at G2 phase of the cell cycle followed by timely release enabling cell cycle progression to maximise the frequency of division events immediately after transfection. This led to a 1.2-1.5 fold increase in transfection efficiency for polyethylenimine (PEI) mediated and electroporation transfection respectively. This process enhanced production yields of a monoclonal antibody 4.5 fold in HEK and 18 fold in CHO cells in the first 24 h post transfection. Overall, this study elucidated key cellular processes fundamental to transfection of CHO and HEK cells providing knowledge which can be applied to DNA delivery technologies in a plethora of fields.

Time-resolved tracking of cellulose biosynthesis and assembly during cell wall regeneration in live Arabidopsis protoplasts

Cellulose, the most abundant polysaccharide on earth composing plant cell walls, is synthesized by coordinated action of multiple enzymes in cellulose synthase complexes embedded within the plasma membrane. Multiple chains of cellulose fibrils form intertwined extracellular matrix networks. It remains largely unknown how newly synthesized cellulose is assembled into an intricate fibril network on cell surfaces. Here, we have established an in vivo time-resolved imaging platform to continuously visualize cellulose biosynthesis and fibril network assembly on Arabidopsis thaliana protoplast surfaces as the primary cell wall regenerates. Our observations provide the basis for a model of cellulose fibril network development in protoplasts driven by an interplay of multiscale dynamics that includes rapid diffusion and coalescence of nascent cellulose fibrils, processive elongation of single fibrils, and cellulose fibrillar network rearrangement during maturation. This study provides fresh insights into the dynamic and mechanistic aspects of cell wall synthesis at the single-cell level.

3D printing cytoskeletal networks: ROS-induced filament severing leads to surge in actin polymerization

The cytoskeletal protein actin forms a spatially organized biopolymer network that plays a central role in many cellular processes. Actin filaments continuously assemble and disassemble, enabling cells to rapidly reorganize their cytoskeleton. Filament severing accelerates actin turnover, as both polymerization and depolymerization rates depend on the number of free filament ends - which severing increases. Here, we use light to control actin severing in vitro by locally generating reactive oxygen species (ROS) with photosensitive molecules such as fluorophores. We see that ROS sever actin filaments, which increases actin polymerization in our experiments. However, beyond a certain threshold, excessive severing leads to the disassembly of actin networks. Our experimental data is supported by simulations using a kinetic model of actin polymerization, which helps us understand the underlying dynamics. In cells, ROS are known to regulate the actin cytoskeleton, but the molecular mechanisms are poorly understood. Here we show that, in vitro, ROS directly affect actin reorganization.

Visualizing Epigenetics: A Review of Microscopy Techniques for Investigating DNA Methylation Patterns, Chromatin Structure, and Gene Expression

Microscopy approaches are frequently used to decipher the localization and quantify the abundance of biologically relevant molecular targets within single cells. Recent research has applied many optical imaging techniques to specifically visualize epigenetic modifications, the mechanisms by which organisms control gene expression in response to environmental factors. While many molecular and omics-based approaches are used to understand epigenetic mechanisms, imaging approaches provide spatial information that supplies greater context for discerning function. Thus, labeling approaches have been developed to quantify and visualize epigenetic targets using various fluorescence microscopy, electron microscopy, and super-resolution microscopy techniques. Here, we synthesize information about microscopy methods that enable visualization of epigenetic marks including DNA methylation, histone modifications, and localization of RNAs, which provide insights into mechanisms involved in chromatin remodeling and gene expression. The ability to determine how and where specific epigenetic marks manifest structurally and functionally in cells demonstrates the power of microscopy in aiding our understanding of epigenetic processes.

Standardized measurements for monitoring and comparing multiphoton microscope systems

The goal of this protocol is to improve the characterization and performance standardization of multiphoton microscopy hardware across a large user base. We purposefully focus on hardware and only briefly touch on software and data analysis routines where relevant. Here we cover the measurement and quantification of laser power, pulse width optimization, field of view, resolution and photomultiplier tube performance. The intended audience is scientists with little expertise in optics who either build or use multiphoton microscopes in their laboratories. They can use our procedures to test whether their multiphoton microscope performs well and produces consistent data over the lifetime of their system. Individual procedures are designed to take 1-2 h to complete without the use of expensive equipment. The procedures listed here help standardize the microscopes and facilitate the reproducibility of data across setups.

Fluorescent labeling strategies for molecular bioimaging

Super-resolution microscopy (SRM) has transformed biological imaging by circumventing the diffraction limit of light and enabling the visualization of cellular structures and processes at the molecular level. Central to the capabilities of SRM is fluorescent labeling, which ensures the precise attachment of fluorophores to biomolecules and has direct impact on the accuracy and resolution of imaging. Continuous innovation and optimization in fluorescent labeling are essential for the successful application of SRM in cutting-edge biological research. In this review, we discuss recent advances in fluorescent labeling strategies for molecular bioimaging, with a special focus on protein labeling. We compare different approaches, highlight technological breakthroughs, and address challenges such as linkage error and labeling density. By evaluating both established and emerging methods, we aim to guide researchers through all aspects that should be considered before opting for any labeling technique.

New Fluorescent Chemodosimetric Mechanism for Selective Recognition of Selenocysteine by Dansyl-Appended Ruthenium Nitrosyl Complexes

Selenocysteine (Sec) is a biologically essential amino acid that serves as a crucial component in selenoproteins that play a key role in various cellular functions. Thus, developing a reliable and rapid method for detecting Sec in physiological media is of paramount importance. This report introduces for the first time a novel fluorescent chemodosimetric mechanism for the selective recognition of Sec using dansyl-appended ruthenium nitrosyl complexes. These complexes consist of a tetradentate ligand featuring a π-extended system (L = N,N'-bis(2-hydroxy-1-naphthylidene)-1,2-phenylenediamine) and a monodentate ligand derived from the conjugated dansyl group, which acts as a strong fluorescent signaling unit (ID = dansyl-imidazole, BD = dansyl-benzimidazole). The reaction between Sec and the complexes {RuNO}6 = [RuL(NO)(ID)]Cl or [RuL(NO)(BD)]Cl in an aqueous phase enhances fluorescence; as a result, it releases NO• that has been demonstrated through fluorimetric titrations, UV-vis titrations, 77Se NMR, EPR, IR, MS, and electronic density calculations. [RuL(NO)(ID)]Cl and [RuL(NO)(BD)]Cl quantitatively detect Sec within a micromolar concentration range, achieving the limit of detection as low as 0.31 and 0.12 μM, respectively, within just 5 min. Remarkably, these chemodosimeters can also be conveniently employed to detect Sec in living Saccharomyces cerevisiae cells.

Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy

Most biological processes, from development to pathogenesis, span multiple time and length scales. While light-sheet fluorescence microscopy has become a fast and efficient method for imaging organisms, cells and subcellular dynamics, simultaneous observations across all these scales have remained challenging. Moreover, continuous high-resolution imaging inside living organisms has mostly been limited to a few hours, as regions of interest quickly move out of view due to sample movement and growth. Here, we present a self-driving, multiresolution light-sheet microscope platform controlled by custom Python-based software, to simultaneously observe and quantify subcellular dynamics in the context of entire organisms in vitro and in vivo over hours of imaging. We apply the platform to the study of developmental processes, cancer invasion and metastasis, and we provide quantitative multiscale analysis of immune-cancer cell interactions in zebrafish xenografts.

Cellpose3: one-click image restoration for improved cellular segmentation

Generalist methods for cellular segmentation have good out-of-the-box performance on a variety of image types; however, existing methods struggle for images that are degraded by noise, blurring or undersampling, all of which are common in microscopy. We focused the development of Cellpose3 on addressing these cases and here we demonstrate substantial out-of-the-box gains in segmentation and image quality for noisy, blurry and undersampled images. Unlike previous approaches that train models to restore pixel values, we trained Cellpose3 to output images that are well segmented by a generalist segmentation model, while maintaining perceptual similarity to the target images. Furthermore, we trained the restoration models on a large, varied collection of datasets, thus ensuring good generalization to user images. We provide these tools as 'one-click' buttons inside the graphical interface of Cellpose as well as in the Cellpose API.

Advanced strategies for single embryo selection in assisted human reproduction: A review of clinical practice and research methods

Among the primary objectives of contemporary assisted reproductive technology research are achieving the births of healthy singletons and improving overall fertility outcomes. Substantial advances have been made in refining the selection of single embryos for transfer, with the aim of maximizing the likelihood of successful implantation. The principal criterion for this selection is embryo morphology. Morphological evaluation systems are based on traditional parameters, including cell count and fragmentation, pronuclear morphology, cleavage rate, blastocyst formation, and various sequential embryonic assessments. To reduce the incidence of multiple pregnancies and to identify the single embryo with the highest potential for growth, invasive techniques such as preimplantation genetic screening are employed in in vitro fertilization clinics. However, new approaches have been suggested for clinical application that do not harm the embryo and that provide consistent, accurate results. Noninvasive technologies, such as time-lapse imaging and omics, leverage morphokinetic parameters and the byproducts of embryo metabolism, respectively, to identify noninvasive prognostic markers for competent single embryo selection. While these technologies have garnered considerable interest in the research community, they are not incorporated into routine clinical practice and still have substantial room for improvement. Currently, the most promising strategies involve integrating multiple methodologies, which together are anticipated to increase the likelihood of successful pregnancy.

Trans-scale live-imaging of an E5.5 mouse embryo using incubator-type biaxial light-sheet microscopy

During mouse embryonic development, the embryonic day (E) 5.5 stage represents a crucial period for the formation of the primitive body axis, where the symmetry breaking of cellular states influences the multicellular system. Elucidating the detailed mechanisms of this process necessitates a trans-layered dynamic observation of the embryo and all internal cells. In this report, we present our success in achieving in-toto single-cell observation in a whole hemisphere of an E5.5 embryo for 12 h, using a newly developed incubator-type biaxial light-sheet microscope. To achieve the success, we optimized our microscope system, including an incubator for culture stability, and refining the observation protocol to reduce phototoxicity. Our key discovery is that the scan speed during light-sheet formation plays a critical role in reducing phototoxicity, rather than the irradiation intensity or the interval time between frames. This innovative system not only enabled in-toto single-cell tracking but also led to the discovery of the abrupt shrinking of embryos whose contractile center was located at the extraembryonic ectoderm during monotonous growth up to the E6.5 stage.

Quantitative analysis of human umbilical vein endothelial cell morphology and tubulogenesis

Primary human umbilical vein endothelial cells can grow as both a monolayer in culture and also as a capillary-like network making them an ideal model system in order to study vascular remodelling. Image-based analysis can allow assessment of cell morphology and motility but is dependent on accurate cell segmentation which requires high-contrast images not normally achievable without fluorescent markers. Here, ptychography is employed as a label-free image-based modality in order to extract quantitative metrics of morphology and tubulogenesis from cultured HUVECs over time in an automated multiwell assay. Phase-specific parameters of dry mass, optical thickness and sphericity were extracted and assessed alongside other metrics of cell number and shape. Tubulogenesis could be captured dynamically without any imaging artefacts from use of a basement membrane matrix and metrics of tube number, growth and branching exported alongside morphology metrics at early time-points. Utilising ptychography-based image analysis, all VEGF165a isoforms studied, elicited a concentration-dependent effect on cell elongation and survival within a HUVEC monolayer. Pharmacologically relevant parameters of potency (EC50) and efficacy were derived, exemplifying this label-free approach for the multiparameter and multiwell quantitative study of vascular remodelling in physiologically relevant cells at 37°C.

The Curse of the Red Pearl: A Fibroblast-Specific Pearl-Necklace Mitochondrial Phenotype Caused by Phototoxicity

The dynamic nature of mitochondria makes live cell imaging an important tool in mitochondrial research. Although imaging using fluorescent probes is the golden standard in studying mitochondrial morphology, these probes might introduce aspecific features. In this study, live cell fluorescent imaging was applied to investigate a pearl-necklace-shaped mitochondrial phenotype that arises when mitochondrial fission is restricted. In this fibroblast-specific pearl-necklace phenotype, constricted and expanded mitochondrial regions alternate. Imaging studies revealed that the formation time of this pearl-necklace phenotype differs between laser scanning confocal, widefield and spinning disk confocal microscopy. We found that the phenotype formation correlates with the excitation of the fluorescent probe and is the result of phototoxicity. Interestingly, the phenotype only arises in cells stained with red mitochondrial dyes. Serial section electron tomography of the pearl-necklace mitochondria revealed that the mitochondrial membranes remained intact, while the cristae structure was altered. Furthermore, filaments and ER were present at the constricted sites. This study illustrates the importance of considering experimental conditions for live cell imaging to prevent imaging artifacts that can have a major impact on the obtained results.

Self-Foldable Three-Dimensional Biointerfaces by Strain Engineering of Two-Dimensional Layered Materials on Polymers

Two-dimensional layered materials (2DLMs) have received increasing attention for their potential in bioelectronics due to their favorable electrical, optical, and mechanical properties. The transformation of the planar structures of 2DLMs into complex 3D shapes is a key strategic step toward creating conformal biointerfaces with cells and applying them as scaffolds to simultaneously guide their growth to tissues and enable integrated bioelectronic monitoring. Using a strain-engineered self-foldable bilayer, we demonstrate the facile formation of predetermined 3D microstructures of 2DLMs with controllable curvatures, called microrolls. Three types of 2DLM microrolls─graphene, hexagonal boron nitride, and molybdenum disulfide─provide scaffolds to encapsulate and organize human-induced pluripotent stem cell-derived cardiomyocytes into tubular aggregates. Encapsulating cardiomyocytes in porous 2DLMs-laden microrolls allows for real-time microscopic observation and construction of precisely shaped cardiac tissues interacting with their surroundings. The ability to combine 2DLMs of diverse properties in the same structure further demonstrates the potential of this self-folding strategy for creating flexible, ultrathin bioelectronic devices that integrate seamlessly with complex biological environments, offering real-time, noninvasive monitoring of engineered tissues and organoids.

Accessible and accurate cytometry analysis using fluorescence microscopes

We have developed a method along with a python-based analysis tool to capture images and produce flow cytometry like data utilizing simple accessible microscopes. Utilizing the recently developed generalist algorithms for cell segmentation, our approach easily segments semi-adherent or suspended cells facilitating quantification of fluorescent intensity similar to flow cytometry. We have shown that our approach exhibits similar speed and enhanced sensitivity when compared to typical flow cytometry. The utility of our approach is demonstrated by screening a set of 88 prime editing conditions utilizing the integration of mNeonGreen11 as a reporter.

Self-Driving Microscopes: AI Meets Super-Resolution Microscopy

The integration of Machine Learning (ML) with super-resolution microscopy represents a transformative advancement in biomedical research. Recent advances in ML, particularly deep learning (DL), have significantly enhanced image processing tasks, such as denoising and reconstruction. This review explores the growing potential of automation in super-resolution microscopy, focusing on how DL can enable autonomous imaging tasks. Overcoming the challenges of automation, particularly in adapting to dynamic biological processes and minimizing manual intervention, is crucial for the future of microscopy. Whilst still in its infancy, automation in super-resolution can revolutionize drug discovery and disease phenotyping leading to similar breakthroughs as have been recognized in this year's Nobel Prizes for Physics and Chemistry.

Imaging malaria parasites across scales and time

The idea that disease is caused at the cellular level is so fundamental to us that we might forget the critical role microscopy played in generating and developing this insight. Visually identifying diseased or infected cells lays the foundation for any effort to curb human pathology. Since the discovery of the Plasmodium-infected red blood cells, which cause malaria, microscopy has undergone an impressive development now literally resolving individual molecules. This review explores the expansive field of light microscopy, focusing on its application to malaria research. Imaging technologies have transformed our understanding of biological systems, yet navigating the complex and ever-growing landscape of techniques can be daunting. This review offers a guide for researchers, especially those working on malaria, by providing historical context as well as practical advice on selecting the right imaging approach. The review advocates an integrated methodology that prioritises the research question while considering key factors like sample preparation, fluorophore choice, imaging modality, and data analysis. In addition to presenting seminal studies and innovative applications of microscopy, the review highlights a broad range of topics, from traditional techniques like white light microscopy to advanced methods such as superresolution microscopy and time-lapse imaging. It addresses the emerging challenges of microscopy, including phototoxicity and trade-offs in resolution and speed, and offers insights into future technologies that might impact malaria research. This review offers a mix of historical perspective, technological progress, and practical guidance that appeal to novice and advanced microscopists alike. It aims to inspire malaria researchers to explore imaging techniques that could enrich their studies, thus advancing the field through enhanced visual exploration of the parasite across scales and time.

Long-Term Single-Molecule Tracking in Living Cells using Weak-Affinity Protein Labeling

Single-particle tracking (SPT) has become a powerful tool to monitor the dynamics of membrane proteins in living cells. However, permanent labeling strategies for SPT suffer from photobleaching as a major limitation, restricting observation times, and obstructing the study of long-term cellular processes within single living cells. Here, we use exchangeable HaloTag Ligands (xHTLs) as an easy-to-apply labeling approach for live-cell SPT and demonstrate extended observation times of individual living cells of up to 30 minutes. Using the xHTL/HaloTag7 labeling system, we measure the ligand-induced activation kinetics of the epidermal growth factor receptor (EGFR) in single living cells. We generate spatial maps of receptor diffusion in cells, report non-uniform distributions of receptor mobility, and the formation of spatially confined 'hot spots' of EGFR activation. Furthermore, we measured the mobility of an ER-luminal protein in living cells and found diffusion coefficients that correlated with the ER nano-structure. This approach represents a general strategy to monitor protein mobility in a functional context and for extended observation times in single living cells.

Genetically encoded bioluminescent glucose indicator for biological research

Glucose is an essential energy source in living cells and is involved in various phenomena. To understand the roles of glucose, measuring cellular glucose levels is important. Here, we developed a bioluminescent glucose indicator called LOTUS-Glc. Unlike fluorescence, bioluminescence doesn't require excitation light when imaging. Using LOTUS-Glc, we demonstrated drug effect evaluation, concurrent use with the optogenetic tool in HEK293T cells, and the measurement of light-dependent glucose fluctuations in plant-derived protoplasts. LOTUS-Glc would be a useful tool for understanding the roles of glucose in living organisms.

Live Cell Imaging of Bone Cell and Organ Cultures

Over the past two decades, there have been unprecedented advances in the capabilities for live cell imaging using light and confocal microscopy. Together with the discovery of green fluorescent protein and its derivatives and the development of a vast array of fluorescent imaging probes and conjugates, it is now possible to image virtually any intracellular or extracellular protein or structure. Traditional static imaging of fixed bone cells and tissues takes a snapshot view of events at a specific time point but can often miss the dynamic aspects of the events being investigated. This chapter provides an overview of the application of live cell imaging approaches for the study of bone cells and bone organ cultures. Rather than emphasizing technical aspects of the imaging equipment, which vary considerably in different laboratories, we have focused on what we consider to be the important principles that are of most practical use for an investigator setting up these techniques in their own laboratory. We also provide detailed protocols that our laboratory has used for live imaging of bone cell and organ cultures.

Novel application of metabolic imaging of early embryos using a light-sheet on-a-chip device: a proof-of-concept study

STUDY QUESTION

Is it feasible to safely determine metabolic imaging signatures of nicotinamide adenine dinucleotide [NAD(P)H] associated auto-fluorescence in early embryos using a light-sheet on-a-chip approach?

SUMMARY ANSWER

We developed an optofluidic device capable of obtaining high-resolution 3D images of the NAD(P)H autofluorescence of live mouse embryos using a light-sheet on-a-chip device as a proof-of-concept.

WHAT IS KNOWN ALREADY

Selecting the most suitable embryos for implantation and subsequent healthy live birth is crucial to the success rate of assisted reproduction and offspring health. Besides morphological evaluation using optical microscopy, a promising alternative is the non-invasive imaging of live embryos to establish metabolic activity performance. Indeed, in recent years, metabolic imaging has been investigated using highly advanced microscopy technologies such as fluorescence-lifetime imaging and hyperspectral microscopy.

STUDY DESIGN, SIZE, DURATION

The potential safety of the system was investigated by assessing the development and viability of live embryos after embryo culture for 67 h post metabolic imaging at the two-cell embryo stage (n = 115), including a control for culture conditions and sham controls (system non-illuminated). Embryo quality of developed blastocysts was assessed by immunocytochemistry to quantify trophectoderm and inner mass cells (n = 75). Furthermore, inhibition of metabolic activity (FK866 inhibitor) during embryo culture was also assessed (n = 18).

PARTICIPANTS/MATERIALS, SETTING, METHODS

The microstructures were fabricated following a standard UV-photolithography process integrating light-sheet fluorescence microscopy into a microfluidic system, including on-chip micro-lenses to generate a light-sheet at the centre of a microchannel. Super-ovulated F1 (CBA/C57Bl6) mice were used to produce two-cell embryos and embryo culture experiments. Blastocyst formation rates and embryo quality (immunocytochemistry) were compared between the study groups. A convolutional neural network (ResNet 34) model using metabolic images was also trained.

MAIN RESULTS AND THE ROLE OF CHANCE

The optofluidic device was capable of obtaining high-resolution 3D images of live mouse embryos that can be linked to their metabolic activity. The system's design allowed continuous tracking of the embryo location, including high control displacement through the light-sheet and fast imaging of the embryos (<2 s), while keeping a low dose of light exposure (16 J · cm-2 and 8 J · cm-2). Optimum settings for keeping sample viability showed that a modest light dosage was capable of obtaining 30 times higher signal-noise-ratio images than images obtained with a confocal system (P < 0.00001; t-test). The results showed no significant differences between the control, illuminated and non-illuminated embryos (sham control) for embryo development as well as embryo quality at the blastocyst stage (P > 0.05; Yate's chi-squared test). Additionally, embryos with inhibited metabolic activity showed a decreased blastocyst formation rate of 22.2% compared to controls, as well as a 47% reduction in metabolic activity measured by metabolic imaging (P < 0.0001; t-test). This indicates that the optofluidic device was capable of producing metabolic images of live embryos by measuring NAD(P)H autofluorescence, allowing a novel and affordable approach. The obtained metabolic images of two-cell embryos predicted blastocyst formation with an AUC of 0.974.

LARGE SCALE DATA

N/A.

LIMITATIONS, REASONS FOR CAUTION

The study was conducted using a mouse model focused on early embryo development assessing illumination at the two-cell stage. Further safety studies are required to assess the safety and use of 405 nm light at the blastocyst stage by investigating any potential negative impact on live birth rates, offspring health, aneuploidy rates, mutational load, changes in gene expression, and/or effects on epigenome stability in newborns.

WIDER IMPLICATIONS OF THE FINDINGS

This light-sheet on-a-chip approach is novel and after rigorous safety studies and a roadmap for technology development, potential future applications could be developed for ART. The overall cost-efficient fabrication of the device will facilitate scalability and integration into future devices if full-safety application is demonstrated.

STUDY FUNDING/COMPETING INTEREST(S)

This work was partially supported by an Ideas Grant (no 2004126) from the National Health and Medical Research Council (NHMRC), by the Education Program in Reproduction and Development (EPRD), Department Obstetrics and Gynaecology, Monash University, and by the Department of Mechanical and Aerospace Engineering, Faculty of Engineering, Monash University. The authors E.V-O, R.N., V.J.C., A.N., and F.H. have applied for a patent on the topic of this technology (PCT/AU2023/051132). The remaining authors have nothing to disclose.

Live Imaging Microscopy of Human Retina Organoids: Photoreceptor Pathology

Neurodegenerative diseases involve many different (sub)cellular pathologic processes like mitochondria damage, which are still incompletely understood and present future targets for therapy development. Live imaging microscopy of dynamic pathologic changes at single cell resolution might advance studies of pathomechanisms and biomarkers. Organoid technologies may complement and facilitate animal and patient studies: We recently reported a novel pathomechanism of photoreceptor degeneration via cell extrusion, identified and validated by live imaging in human retina organoids. Here, we describe the related workflow for live imaging organoid studies. As another use-case, we describe mitochondrial alterations in photoreceptors acutely damaged by the ionophore CCCP. Our data further support a CCCP-induced experimental model for photoreceptor pathology, which can be monitored by JC-1 live dye-assisted live imaging. Thus, we demonstrate that live imaging advances studies of early subcellular pathologic events in human organoids. Such approaches might facilitate future therapeutic target identification and development for early intervention.

Mapping Synaptic Activity at the Population and Cellular Levels with Genetically Encoded Voltage Indicators (GEVIs)

In this chapter, we provide examples of using genetically encoded voltage indicators (GEVIs) to monitor neuronal intercellular communications at the population level (hippocampus of CA1 region) and individual cell level (retinal ganglion cells). Providing an optical readout for voltage transients, GEVIs enable the reporting of synaptic activity, both activation and inhibition, from chemical and electrical synapses. With the added flexibility of restricting expression of the GEVI to distinct cell types, GEVIs are becoming a powerful tool for interrogating neuronal activity.

Protocol for live-cell imaging of immune synapse formation and activation of CAR T cells against cancer cells

Immune synapse (IS) formation determines T cell antitumor activity. Here, we present a protocol for characterizing the IS formation between chimeric antigen receptor (CAR) T cells and tumor cells by measuring the IS size and calcium flux by live-cell imaging. We describe steps for CAR T cell manufacturing, sample preparation, image acquisition, and data analysis. For complete details on the use and execution of this protocol, please refer to Chockley et al.,1 Ibanez et al.,2 and Zoine et al.3.

Development and validation of the Normalized Organoid Growth Rate (NOGR) metric in brightfield imaging-based assays

This study focuses on refining growth-rate-based drug response metrics for patient-derived tumor organoid screening using brightfield live-cell imaging. Traditional metrics like Normalized Growth Rate Inhibition (GR) and Normalized Drug Response (NDR) have been used to assess organoid responses to anticancer treatments but face limitations in accurately quantifying cytostatic and cytotoxic effects across varying growth rates. Here, we introduce the Normalized Organoid Growth Rate (NOGR) metric, specifically developed for brightfield imaging-based assays. A label-free image analysis model was applied to segment organoids precisely, track their growth rates over time, and classify viable and dead organoids. Testing eleven phenotypically distinct pancreatic cancer organoid models with five chemotherapeutics demonstrates that the NOGR metric more effectively captures cytostatic and cytotoxic drug effects compared to existing methods. This approach enhances the biological relevance of drug sensitivity assessments on organoids and offers a valuable tool for advancing personalized cancer treatment strategies.

Nuclear deformability facilitates apical nuclear migration in the developing zebrafish retina

Nuclear positioning is a crucial aspect of cell and developmental biology. One example is the apical movement of nuclei in neuroepithelia before mitosis, which is essential for proper tissue formation. While the cytoskeletal mechanisms that drive nuclei to the apical side have been explored, the influence of nuclear properties on apical nuclear migration is less understood. Nuclear properties, such as deformability, can be linked to lamin A/C expression levels, as shown in various in vitro studies. Interestingly, many nuclei in early development, including neuroepithelial nuclei, express only low levels of lamin A/C. Therefore, we investigated whether increased lamin A expression in the densely packed zebrafish retinal neuroepithelium affects nuclear deformability and, consequently, migration phenomena. We found that overexpressing lamin A in retinal nuclei increases nuclear stiffness, which in turn indeed impairs apical nuclear migration. Interestingly, nuclei that do not overexpress lamin A but are embedded in a stiffer lamin A-overexpressing environment also exhibit impaired apical nuclear migration, indicating that these effects can be cell non-autonomous. Additionally, in the less crowded hindbrain neuroepithelium, only minor effects on apical nuclear migration are observed. Together, this suggests that the material properties of the nucleus influence nuclear movements in a tissue-dependent manner.

Imaging Brain Tissue with Quantum Light at Low Power

Light-induced tissue damage is a crucial limitation for traditional microscopy of the living brain, underscoring the need for new techniques that minimize exposure of samples to light. Here, we tested the hypothesis that quantum light, i.e., entangled photons, could detect brain structures at a lower excitation energy. In a proof of principle, we show microscopic images of fixed brain tissue in the hippocampus area created by fluorescence selective excitation in the process of entangled two-photon absorption in a scanning microscope. Quantum-enhanced entangled two-photon microscopy (TPM) had brain imaging capabilities at an unprecedented low excitation intensity of ∼3.6 × 107 photons/s, orders of magnitude lower than the excitation level for the classical two-photon fluorescence image obtained in the same microscope. The extremely low light probe intensity demonstrated in entangled TPM is of critical importance in the investigation of neural activity to minimize heating and photobleaching during repetitive imaging. It may have important functional implications in optogenetic technology, removing unintended heating and accumulated photodamage effects. This technology also opens avenues in spatially resolved brain tissue investigations with quantum light, providing new capabilities in local spectroscopy.

Potential consequences of phototoxicity on cell function during live imaging of intestinal organoids

Live imaging visualizes the structure, dynamics, and function of cells and tissues to reveal the molecular mechanisms, and has contributed to the advancement of life science. In live imaging, it has been well known that there is a trade-off between higher-resolution analysis and cell damage caused by light illumination, i.e., phototoxicity. However, despite the risk of unknowingly distorting experimental results, phototoxicity is an unresolved issue in live imaging because overall consequences occurring inside cells due to phototoxicity remains unknown. Here, we determined the molecular process of phototoxicity-induced cell damage systematically under low- and high-dose light illumination conditions by analyzing differential gene expression using RNA-sequencing in a three-dimensional organoid of small intestinal epithelial cells, enteroid. The low-dose light illumination already induced various abnormalities in functional molecules involved in the response to reactive oxygen species generated by the excitation of fluorescent dyes, intracellular metabolism, mitosis, immune responses, etc., at mRNA expression level. Together with the behavior toward apoptosis caused by high-dose light illumination, the light dose-dependent progression of intracellular damage was revealed. About visible impairment of intestinal epithelial function, failures in both the structure-forming ability of enteroids and Paneth cell granule secretion were observed under high-dose light illumination, while the drug efflux was not disturbed despite abnormal drug efflux transporter mRNA expression. Based on the gene expression profiles, we comprehensively clarified phenomena in the cells at mRNA level that cannot be recognized both morphologically and functionally during live imaging, further providing a new insight into the risk of phototoxicity. This study warns from the aspect of mRNA expression that awareness of phototoxic artifacts is needed when analyzing cellular function and the mechanism in live imaging.

Sensitive label free imaging of 3D cell models with minimal toxicity using confocal reflectance

Confocal reflectance imaging typically suffers from high background and poor sensitivity. We demonstrate sensitive and low-background reflectance imaging of cells encapsulated in transparent 3D hydrogels. Nanoscale cell morphology is visualized with sensitivity similar to confocal fluorescence, with low laser power, minimal specimen preparation, and reduced toxicity.

Intravital Microscopy With an Airy Beam Light Sheet Microscope Improves Temporal Resolution and Reduces Surgical Trauma

Intravital microscopy has emerged as a powerful imaging tool, which allows the visualization and precise understanding of rapid physiological processes at sites of inflammation in vivo, such as vascular permeability and leukocyte migration. Leukocyte interactions with the vascular endothelium can be characterized in the living organism in the murine cremaster muscle. Here, we present a microscopy technique using an Airy Beam Light Sheet microscope that has significant advantages over our previously used confocal microscopy systems. In comparison, the light sheet microscope offers near isotropic optical resolution and faster acquisition speed, while imaging a larger field of view. With less invasive surgery we can significantly reduce side effects such as bleeding, muscle twitching, and surgical inflammation. However, the increased acquisition speed requires exceptional tissue stability to avoid imaging artefacts. Since respiratory motion is transmitted to the tissue under investigation, we have developed a relocation algorithm that removes motion artefacts from our intravital microscopy images. Using these techniques, we are now able to obtain more detailed 3D time-lapse images of the cremaster vascular microcirculation, which allow us to observe the process of leukocyte emigration into the surrounding tissue with increased temporal resolution in comparison to our previous confocal approach.

Controlling the sound of light: photoswitching optoacoustic imaging

Optoacoustic (photoacoustic) imaging advances allow high-resolution optical imaging much deeper than optical microscopy. However, while label-free optoacoustics have already entered clinical application, biological imaging is in need of ubiquitous optoacoustic labels for use in ways that are similar to how fluorescent proteins propelled optical microscopy. We review photoswitching advances that shine a new light or, in analogy, 'bring a new sound' to biological optoacoustic imaging. Based on engineered labels and novel devices, switching uses light or other energy forms and enables signal modulation and synchronous detection for maximizing contrast and detection sensitivity over other optoacoustic labels. Herein, we explain contrast enhancement in the spectral versus temporal domains and review labels and key concepts of switching and their properties to modulate optoacoustic signals. We further outline systems and applications and discuss how switching can enable optoacoustic imaging of cellular or molecular contrast at depths and resolutions beyond those of other optical methods.

Accurate detection and instance segmentation of unstained living adherent cells in differential interference contrast images

Detecting and segmenting unstained living adherent cells in differential interference contrast (DIC) images is crucial in biomedical research, such as cell microinjection, cell tracking, cell activity characterization, and revealing cell phenotypic transition dynamics. We present a robust approach, starting with dataset transformation. We curated 520 pairs of DIC images, containing 12,198 HepG2 cells, with ground truth annotations. The original dataset was randomly split into training, validation, and test sets. Rotations were applied to images in the training set, creating an interim "α set." Similar transformations formed "β" and "γ sets" for validation and test data. The α set trained a Mask R-CNN, while the β set produced predictions, subsequently filtered and categorized. A residual network (ResNet) classifier determined mask retention. The γ set underwent iterative processing, yielding final segmentation. Our method achieved a weighted average of 0.567 in average precision (AP)0.75bbox and 0.673 in AP0.75segm, both outperforming major algorithms for cell detection and segmentation. Visualization also revealed that our method excels in practicality, accurately capturing nearly every cell, a marked improvement over alternatives.

Shades of phototoxicity in fluorescent imaging agents (that are not supposed to be phototoxic)

This article is a highlight of the paper by Huang et al. in this issue of Photochemistry and Photobiology. It describes shades of phototoxicity in fluorescent imaging agents that are not intended to be phototoxic. Phototoxicity was assessed using a modified neutral red uptake (NRU) in vitro assay with mean photo-effects (MPE) for the fluorescent agents IRdye800, indocyanine green (ICG), proflavine, and methylene blue (MB), with comparisons to known phototoxic agents benzoporphyrin derivative (BPD) and rose bengal (RB). The experimental conditions were aimed to mimic clinical settings, using not only visible light, but also near-infrared light for insight to photosafety and deep tissue damage. Molecular mechanisms underlying the phototoxicities were not sought, but IRdye800 and ICG were mainly deemed to be safe, whereas proflavine and MB would require precautions since phototoxicity can overshadow their utility as fluorescent imaging agents.

A bright cyan fluorescence calcium indicator for mitochondrial calcium with minimal interference from physiological pH fluctuations

Genetically Encoded Calcium (Ca2+) indicators (GECIs) are indispensable tools for dissecting intracellular Ca2+ signaling and monitoring cellular activities. Mitochondrion acts as a Ca2+ sink and a central player for maintaining Ca2+ homeostasis. Accurately monitoring Ca2+ transients within the mitochondrial matrix that undergo constant pH fluctuations is challenging, as signals of most currently available GECIs suffer from artifacts induced by physiological pH variations. Multiplexed monitoring of optophysiology is also hindered by the limited availability of GECIs with cyan fluorescence. Based on the bright variant of cyan fluorescence protein (CFP), mTurquoise2, we developed a GECI designated as TurCaMP. Results from molecular dynamics simulations and ab initio calculations revealed that the deprotonation of the chromophore may be responsible for the Ca2+-dependent changes in TurCaMP signals. TurCaMP sensors showed inverse response to Ca2+ transients, and their responses were not affected by pH changes within the range of pH 6-9. The high basal fluorescence and insensitivity to physiological pH fluctuations enabled TurCaMP to faithfully monitor mitochondrial Ca2+ responses with a high signal-to-noise ratio. TurCaMP sensors allow simultaneous multi-colored imaging of intracellular Ca2+ signals, expanding the possibility of multiplexed monitoring of Ca2+-dependent physiological events.

Machine learning in microscopy - insights, opportunities and challenges

Machine learning (ML) is transforming the field of image processing and analysis, from automation of laborious tasks to open-ended exploration of visual patterns. This has striking implications for image-driven life science research, particularly microscopy. In this Review, we focus on the opportunities and challenges associated with applying ML-based pipelines for microscopy datasets from a user point of view. We investigate the significance of different data characteristics - quantity, transferability and content - and how this determines which ML model(s) to use, as well as their output(s). Within the context of cell biological questions and applications, we further discuss ML utility range, namely data curation, exploration, prediction and explanation, and what they entail and translate to in the context of microscopy. Finally, we explore the challenges, common artefacts and risks associated with ML in microscopy. Building on insights from other fields, we propose how these pitfalls might be mitigated for in microscopy.

Quantification of cellular phototoxicity of organelle stains by the dynamics of microtubule polymerization

Being able to quantify the phototoxicity of dyes and drugs in live cells allows biologists to better understand cell responses to exogenous stimuli during imaging. This capability further helps to design fluorescent labels with lower phototoxicity and drugs with better efficacy. Conventional ways to evaluate cellular phototoxicity rely on late-stage measurements of individual or different populations of cells. Here, we developed a quantitative method using intracellular microtubule polymerization as a rapid and sensitive marker to quantify early-stage phototoxicity. Implementing this method, we assessed the photosensitization induced by organelle dyes illuminated with different excitation wavelengths. Notably, fluorescent markers targeting mitochondria, nuclei, and endoplasmic reticulum exhibited diverse levels of phototoxicity. Furthermore, leveraging a real-time precision opto-control technology allowed us to evaluate the synergistic effect of light and dyes on specific organelles. Studies in hypoxia revealed enhanced phototoxicity of Mito-Tracker Red CMXRos that is not correlated with the generation of reactive oxygen species but a different deleterious pathway in low oxygen conditions.

Induction of DNA single- and double-strand breaks by excited intra- or extracellular green fluorescent protein

Green fluorescent protein (GFP) has opened vast new avenues in studies of live cells and is generally perceived as a benign, nontoxic and harmless fluorescent tag. We demonstrat that excited GFP is capable of inducing substantial DNA damage in cells expressing fusion proteins. In the presence of GFP, even low doses of blue light (12 μJ) induce single strand breaks (SSBs). When the fluorescence of GFP located in the cell nucleus or in the cytoplasm is excited by a much higher dose (17 mJ), DNA double-strand breaks (DSBs) are also induced. Such breaks are induced even when GFP is placed and illuminated in culture medium outside of living cells. We demonstrate that DNA damage is induced by singlet oxygen, which is generated by excited GFP. Although short exposures of live cells to exciting light typically used in fluorescence microscopy induce SSBs but carry little risk of inducing DNA double-strand breaks, larger doses, which may be used in FRAP, FLIM, FCS and super-resolution fluorescence microscopy studies, are capable of inducing not only numerous SSBs but also DSBs.