Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges

Exploring GPCR conformational dynamics using single-molecule fluorescence

G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.

Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy

The introduction of super-resolution microscopy (SRM) has significantly advanced our understanding of cellular and molecular dynamics, offering a detailed view previously beyond our reach. Implementing SRM in biophysical research, however, presents numerous challenges. This review addresses the crucial aspects of utilizing SRM effectively, from selecting appropriate fluorophores and preparing samples to analyzing complex data sets. We explore recent technological advancements and methodological improvements that enhance the capabilities of SRM. Emphasizing the integration of SRM with other analytical methods, we aim to overcome inherent limitations and expand the scope of biological insights achievable. By providing a comprehensive guide for choosing the most suitable SRM methods based on specific research objectives, we aim to empower researchers to explore complex biological processes with enhanced precision and clarity, thereby advancing the frontiers of biophysical research.

STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii

Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ∼20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.

Multimodal illumination platform for 3D single-molecule super-resolution imaging throughout mammalian cells

Single-molecule super-resolution imaging is instrumental in investigating cellular architecture and organization at the nanoscale. Achieving precise 3D nanometric localization when imaging structures throughout mammalian cells, which can be multiple microns thick, requires careful selection of the illumination scheme in order to optimize the fluorescence signal to background ratio (SBR). Thus, an optical platform that combines different wide-field illumination schemes for target-specific SBR optimization would facilitate more precise 3D nanoscale studies of a wide range of cellular structures. Here, we demonstrate a versatile multimodal illumination platform that integrates the sectioning and background reduction capabilities of light sheet illumination with homogeneous, flat-field epi- and TIRF illumination. Using primarily commercially available parts, we combine the fast and convenient switching between illumination modalities with point spread function engineering to enable 3D single-molecule super-resolution imaging throughout mammalian cells. For targets directly at the coverslip, the homogenous intensity profile and excellent sectioning of our flat-field TIRF illumination scheme improves single-molecule data quality by providing low fluorescence background and uniform fluorophore blinking kinetics, fluorescence signal, and localization precision across the entire field of view. The increased contrast achieved with LS illumination, when compared with epi-illumination, makes this illumination modality an excellent alternative when imaging targets that extend throughout the cell. We validate our microscopy platform for improved 3D super-resolution imaging by two-color imaging of paxillin - a protein located in the focal adhesion complex - and actin in human osteosarcoma cells.

Exploring transient states of PAmKate to enable improved cryogenic single-molecule imaging

Super-resolved cryogenic correlative light and electron microscopy is a powerful approach which combines the single-molecule specificity and sensitivity of fluorescence imaging with the nano-scale resolution of cryogenic electron tomography. Key to this method is active control over the emissive state of fluorescent labels to ensure sufficient sparsity to localize individual emitters. Recent work has identified fluorescent proteins (FPs) which photoactivate or photoswitch efficiently at cryogenic temperatures, but long on-times due to reduced quantum yield of photobleaching remains a challenge for imaging structures with a high density of localizations. In this work, we explore the photophysical properties of the red photoactivatable FP PAmKate and identify a 2-color process leading to enhanced turn-off of active emitters, improving localization rate. Specifically, after excitation of ground state molecules, we find a transient state forms with a lifetime of ~2 ms which can be bleached by exposure to a second wavelength. We measure the response of the transient state to different wavelengths, demonstrate how this mechanism can be used to improve imaging, and provide a blueprint for study of other FPs at cryogenic temperatures.

Traceable localization enables accurate integration of quantum emitters and photonic structures with high yield

In a popular integration process for quantum information technologies, localization microscopy of quantum emitters guides lithographic placement of photonic structures. However, a complex coupling of microscopy and lithography errors degrades registration accuracy, severely limiting device performance and process yield. We introduce a methodology to solve this widespread but poorly understood problem. A new foundation of traceable localization enables rapid characterization of lithographic standards and comprehensive calibration of cryogenic microscopes, revealing and correcting latent systematic effects. Of particular concern, we discover that scale factor deviation and complex optical distortion couple to dominate registration errors. These novel results parameterize a process model for integrating quantum dots and bullseye resonators, predicting higher yield by orders of magnitude, depending on the Purcell factor threshold as a quantum performance metric. Our foundational methodology is a key enabler of the lab-to-fab transition of quantum information technologies and has broader implications to cryogenic and correlative microscopy.

Quantifying Förster Resonance Energy Transfer from Single Perovskite Quantum Dots to Organic Dyes

Colloidal quantum dots (QDs) are promising regenerable photoredox catalysts offering broadly tunable redox potentials along with high absorption coefficients. QDs have thus far been examined for various organic transformations, water splitting, and CO2 reduction. Vast opportunities emerge from coupling QDs with other homogeneous catalysts, such as transition metal complexes or organic dyes, into hybrid nanoassemblies exploiting energy transfer (ET), leveraging a large absorption cross-section of QDs and long-lived triplet states of cocatalysts. However, a thorough understanding and further engineering of the complex operational mechanisms of hybrid nanoassemblies require simultaneously controlling the surface chemistry of the QDs and probing dynamics at sufficient spatiotemporal resolution. Here, we probe the ET from single lead halide perovskite QDs, capped by alkylphospholipid ligands, to organic dye molecules employing single-particle photoluminescence spectroscopy with single-photon resolution. We identify a Förster-type ET by spatial, temporal, and photon-photon correlations in the QD and dye emission. Discrete quenching steps in the acceptor emission reveal stochastic photobleaching events of individual organic dyes, allowing a precise quantification of the transfer efficiency, which is >70% for QD-dye complexes with strong donor-acceptor spectral overlap. Our work explores the processes occurring at the QD/molecule interface and demonstrates the feasibility of sensitizing organic photocatalysts with QDs.

Squaraine Dyes Exhibit Spontaneous Fluorescence Blinking That Enables Live-Cell Nanoscopy

Hampered by their susceptibility to nucleophilic attack and chemical bleaching, electron-deficient squaraine dyes have long been considered unsuitable for biological imaging. This study unveils a surprising twist: in aqueous environments, bleaching is not irreversible but rather a reversible spontaneous quenching process. Leveraging this new discovery, we introduce a novel deep-red squaraine probe tailored for live-cell super-resolution imaging. This probe enables single-molecule localization microscopy (SMLM) under physiological conditions without harmful additives or intense lasers and exhibits spontaneous blinking orchestrated by biological nucleophiles, such as glutathione or hydroxide anion. With a low duty cycle (∼0.1%) and high-emission rate (∼6 × 104 photons/s under 400 W/cm2), the squaraine probe surpasses the benchmark Cy5 dye by 4-fold and Si-rhodamine by a factor of 1.7 times. Live-cell SMLM with the probe reveals intricate structural details of cell membranes, which demonstrates the high potential of squaraine dyes for next-generation super-resolution imaging.

Ultrabright Xanthene Fluorescence Probe for Mitochondrial Super-Resolution Imaging

Mitochondria are important organelles that provide energy for cellular physiological activities. Changes in their structures may indicate the occurrence of diseases, and the super-resolution imaging of mitochondria is of great significance. However, developing fluorescent probes for mitochondrial super-resolution visualization still remains challenging due to insufficient fluorescence brightness and poor stability. Herein, we rationally synthesized an ultrabright xanthene fluorescence probe Me-hNR for mitochondria-specific super-resolution imaging using structured illumination microscopy (SIM). The rigid structure of Me-hNR provided its ultrahigh fluorescence quantum yield of up to 0.92 and ultrahigh brightness of up to 16,000. Occupying the para-position of the O atom in the xanthene skeleton by utilizing the smallest methyl group ensured its excellent stability. The study of the photophysical process indicated that Me-hNR mainly emitted fluorescence via radiative decay, and nonradiative decay and inter-system crossing were rare due to the slow nonradiative decay rate and large energy gap (ΔEst = 0.55 eV). Owing to these excellent merits, Me-hNR can specifically light up mitochondria at ultralow concentrations down to 5 nM. The unprecedented spatial resolution for mitochondria with an fwhm of 174 nm was also achieved. Therefore, this ultrabright xanthene fluorescence probe has great potential in visualizing the structural changes of mitochondria and revealing the pathogenesis of related diseases using SIM.

A practical guide to time-resolved fluorescence microscopy and spectroscopy

Time-correlated single photon counting (TCSPC) coupled with confocal microscopy is a versatile biophysical tool that enables real-time monitoring of biomolecular dynamics across many timescales. With TCSPC, Fluorescence correlation spectroscopy (FCS) and pulsed interleaved excitation-Förster resonance energy transfer (PIE-FRET) are collected simultaneously on diffusing molecules to extract diffusion characteristics and proximity information. This article is a guide to calibrating FCS and PIE-FRET measurements with several biological samples including liposomes, streptavidin-coated quantum dots, proteins, and nucleic acids for reliable determination of diffusion coefficients and FRET efficiency. The FRET efficiency results are also compared to surface-attached single molecules using fluorescence lifetime imaging microscopy (FLIM-FRET). Combining the methods is a powerful approach to revealing mechanistic details of biological processes and pathways.

Exploiting the Photo-Physical Properties of Metal Halide Perovskite Nanocrystals for Bioimaging

Perovskite nanomaterials have recently been exploited for bioimaging applications due to their unique photo-physical properties, including high absorbance, good photostability, narrow emissions, and nonlinear optical properties. These attributes outperform conventional fluorescent materials such as organic dyes and metal chalcogenide quantum dots and endow them with the potential to reshape a wide array of bioimaging modalities. Yet, their full potential necessitates a deep grasp of their structure-attribute relationship and strategies for enhancing water stability through surface engineering for meeting the stringent and unique requirements of each individual imaging modality. This review delves into this evolving frontier, highlighting how their distinctive photo-physical properties can be leveraged and optimized for various bioimaging modalities, including visible light imaging, near-infrared imaging, and super-resolution imaging.

Visualizing the intracellular aggregation behavior of gold nanoclusters via structured illumination microscopy and scanning transmission electron microscopy

Given the growing concerns about nanotoxicity, numerous studies have focused on providing mechanistic insights into nanotoxicity by imaging the intracellular fate of nanoparticles. A suitable imaging strategy is necessary to uncover the intracellular behavior of nanoparticles. Although each conventional technique has its own limitations, scanning transmission electron microscopy (STEM) and three-dimensional structured illumination microscopy (3D-SIM) combine the advantages of chemical element mapping, ultrastructural analysis, and cell dynamic tracking. Gold nanoclusters (AuNCs), synthesized using 6-aza-2 thiothymine (ATT) and L-arginine (Arg) as reducing and protecting ligands, referred to as Arg@ATT-AuNCs, have been widely used in biological sensing and imaging, medicine, and catalyst yield. Based on their intrinsic fluorescence and high electron density, Arg@ATT-AuNCs were selected as a model. STEM imaging showed that both the single-particle and aggregated states of Arg@ATT-AuNCs were compartmentally distributed within a single cell. Real-time 3D-SIM imaging showed that the fluorescent Arg@ATT-AuNCs gradually aggregated after being located in the lysosomes of living cells, causing lysosomal damage. The aggregate formation of Arg@ATT-AuNCs was triggered by the low-pH medium, particularly in the lysosomal acidic environment. The proposed dual imaging strategy was verified using other types of AuNCs, which is valuable for studying nano-cell interactions and any associated cytotoxicity, and has the potential to be a useful approach for exploring the interaction of cells with various nanoparticles.

Multimodal illumination platform for 3D single-molecule super-resolution imaging throughout mammalian cells

Single-molecule super-resolution imaging is instrumental for investigating cellular architecture and organization at the nanoscale. Achieving precise 3D nanometric localization when imaging structures throughout mammalian cells, which can be multiple microns thick, requires careful selection of the illumination scheme in order to optimize the fluorescence signal to background ratio (SBR). Thus, an optical platform that combines different wide-field illumination schemes for target-specific SBR optimization would facilitate more precise, 3D nanoscale studies of a wide range of cellular structures. Here we demonstrate a versatile multimodal illumination platform that integrates the sectioning and background reduction capabilities of light sheet illumination with homogeneous, flat-field epi-and TIRF illumination. Using primarily commercially available parts, we combine the fast and convenient switching between illumination modalities with point spread function engineering to enable 3D single-molecule super-resolution imaging throughout mammalian cells. For targets directly at the coverslip, the homogenous intensity profile and excellent sectioning of our flat-field TIRF illumination scheme improves single-molecule data quality by providing low fluorescence background and uniform fluorophore blinking kinetics, fluorescence signal, and localization precision across the entire field of view. The increased contrast achieved with LS illumination, when compared with epi-illumination, makes this illumination modality an excellent alternative when imaging targets that extend throughout the cell. We validate our microscopy platform for improved 3D super-resolution imaging by two-color imaging of paxillin - a protein located in the focal adhesion complex - and actin in human osteosarcoma cells.

Methodological Pitfalls of Investigating Lipid Rafts in the Brain: What Are We Still Missing?

The purpose of this review is to succinctly examine the methodologies used in lipid raft research in the brain and to highlight the drawbacks of some investigative approaches. Lipid rafts are biochemically and biophysically different from the bulk membrane. A specific lipid environment within membrane domains provides a harbor for distinct raftophilic proteins, all of which in concert create a specialized platform orchestrating various cellular processes. Studying lipid rafts has proved to be arduous due to their elusive nature, mobility, and constant dynamic reorganization to meet the cellular needs. Studying neuronal lipid rafts is particularly cumbersome due to the immensely complex regional molecular architecture of the central nervous system. Biochemical fractionation, performed with or without detergents, is still the most widely used method to isolate lipid rafts. However, the differences in solubilization when various detergents are used has exposed a dire need to find more reliable methods to study particular rafts. Biochemical methods need to be complemented with other approaches such as live-cell microscopy, imaging mass spectrometry, and the development of specific non-invasive fluorescent probes to obtain a more complete image of raft dynamics and to study the spatio-temporal expression of rafts in live cells.

Blinking characteristics of organic fluorophores for blink-based multiplexing

Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.

Thiolation for Enhancing Photostability of Fluorophores at the Single-Molecule Level

Fluorescent probes are essential for single-molecule imaging. However, their application in biological systems is often limited by the short photobleaching lifetime. To overcome this, we developed a novel thiolation strategy for squaraine dyes. By introducing thiolation of the central cyclobutene of squaraine (thio-squaraine), we observed a ≈5-fold increase in photobleaching lifetime. Our single-molecule data analysis attributes this improvement to improved photostability resulting from thiolation. Interestingly, bulk measurements show rapid oxidation of thio-squaraine to its oxo-analogue under irradiation, giving the perception of inferior photostability. This discrepancy between bulk and single-molecule environments can be ascribed to the factors in the latter, including larger intermolecular distances and restricted mobility, which reduce the interactions between a fluorophore and reactive oxygen species produced by other fluorophores, ultimately impacting photobleaching and photoconversion rate. We demonstrate the remarkable performance of thio-squaraine probes in various imaging buffers, such as glucose oxidase with catalase (GLOX) and GLOX+trolox. We successfully employed these photostable probes for single-molecule tracking of CD56 membrane protein and monitoring mitochondria movements in live neurons. CD56 tracking revealed distinct motion states and the corresponding protein fractions. This investigation is expected to propel the development of single-molecule imaging probes, particularly in scenarios where bulk measurements show suboptimal performance.

Towards multimodal cellular imaging: optical and X-ray fluorescence

Imaging techniques permit the study of the molecular interactions that underlie health and disease. Each imaging technique collects unique chemical information about the cellular environment. Multimodal imaging, using a single probe that can be detected by multiple imaging modalities, can maximise the information extracted from a single cellular sample by combining the results of different imaging techniques. Of particular interest in biological imaging is the combination of the specificity and sensitivity of optical fluorescence microscopy (OFM) with the quantitative and element-specific nature of X-ray fluorescence microscopy (XFM). Together, these techniques give a greater understanding of how native elements or therapeutics affect the cellular environment. This review focuses on recent studies where both techniques were used in conjunction to study cellular systems, demonstrating the breadth of biological models to which this combination of techniques can be applied and the potential for these techniques to unlock untapped knowledge of disease states.

Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates

The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.

Super-resolution Fluorescence Imaging of Recycled Polymer Blends via Hydrogen Bond-Assisted Adsorption of a Nile Red Derivative

A key challenge in the recycling of multilayer plastic films of polyethylene and polyamide, as typically used for food packaging, is to assess and control the phase separation of the two types of polymers in the recycled material, the specifics of which determine the mechanical strength of the recycled material. However, visualizing the polyamide-in-polyethylene domains with conventional fluorescence methods or electron microscopy is challenging. We present a new approach that combines the point accumulation in nanoscale topography (PAINT) super-resolution method with a newly synthesized Nile Red probe (diOHNR) as the fluorescent label. The molecule was modified to undergo a hydrogen bond-assisted interaction with the polyamide phase in the blend due to its two additional hydroxyl groups but preserves the spectral properties of Nile Red. As a result, the localization density of the probe in the PAINT image is 13 times larger at the polyamide phase than at the polyethylene phase, enabling quantitative evaluation of the spatial polyamide/polyethylene distribution down to the nanoscale. The method achieved a spatial resolution of 18.8 nm, and we found that over half of the polyamide particles in a recycled sample were smaller than the optical diffraction limit. Being able to image the blends with nanoscopic resolution can help to optimize the composition and mechanical properties of recycled materials and thus contribute to an increased reuse of plastics.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

Characteristics of genetic tags for correlative light and electron microscopy

Fluorescence microscopy is indispensable in live cell studies of fluorescently-labeled proteins, but has limited resolution and context. Electron microscopy offers high-resolution imaging of cellular ultrastructure, including membranes, organelles, and other nanoscale features. However, identifying proteins by EM remains a substantial challenge. There is potential to combine the strengths of both FM and EM through correlative light and EM (CLEM), and bridging the two modalities enables new discoveries and biological insights. CLEM enables cellular proteins to be observed dynamically, across size scales, and in relationship to sub-cellular structures. A central limitation to using CLEM is the scarcity of methods for labeling proteins with CLEM reporters. This review will describe the characteristics of genetic tags for CLEM that are available today, including fixation-resistant fluorescent proteins, 3,3'-diaminobenzidine (DAB)-based tags, metal-chelating tags, DNA origami tags, and VIP tags.

Bond-selective fluorescence imaging with single-molecule sensitivity

Bioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared (mid-IR) excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here, we report bond selective fluorescence-detected infrared-excited (BonFIRE) spectral microscopy. BonFIRE employs two-photon excitation in the mid-IR and near-IR to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tuneable narrowband picosecond pulses to ensure high sensitivity, biocompatibility, and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons, and tissues, with promises for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations.

Simultaneous spectral differentiation of multiple fluorophores in super-resolution imaging using a glass phase plate

By engineering the point-spread function (PSF) of single molecules, different fluorophore species can be imaged simultaneously and distinguished by their unique PSF patterns. Here, we insert a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to produce distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrate that the resulting PSFs can be localized spatially and spectrally using a maximum-likelihood estimation algorithm and can be utilized for hyper-spectral super-resolution microscopy of biological samples. We produced superresolution images of fixed U2OS cells using X-PSFs for dSTORM imaging with simultaneous illumination of up to three fluorophore species. The species were distinguished only by the PSF pattern. We achieved ∼21-nm lateral localization precision (FWHM) and ∼17-nm axial precision (FWHM) with an average of 1,800 - 3,500 photons per PSF and a background as high as 130 - 400 photons per pixel. The modified PSF distinguished fluorescent probes with ∼80 nm separation between spectral peaks.

Trends in Single-Molecule Total Internal Reflection Fluorescence Imaging and Their Biological Applications with Lab-on-a-Chip Technology

Single-molecule imaging technologies, especially those based on fluorescence, have been developed to probe both the equilibrium and dynamic properties of biomolecules at the single-molecular and quantitative levels. In this review, we provide an overview of the state-of-the-art advancements in single-molecule fluorescence imaging techniques. We systematically explore the advanced implementations of in vitro single-molecule imaging techniques using total internal reflection fluorescence (TIRF) microscopy, which is widely accessible. This includes discussions on sample preparation, passivation techniques, data collection and analysis, and biological applications. Furthermore, we delve into the compatibility of microfluidic technology for single-molecule fluorescence imaging, highlighting its potential benefits and challenges. Finally, we summarize the current challenges and prospects of fluorescence-based single-molecule imaging techniques, paving the way for further advancements in this rapidly evolving field.

Novel Förster Resonance Energy Transfer probe with quantum dot for a long-time imaging of active caspases inside individual cells

With the goal to investigate biological phenomena at a single-cell level, we designed, synthesized and tested a molecular probe based on Förster resonance energy transfer (FRET) between a highly luminescent quantum dot (QD) as a donor and a fluorophore or fluorescence quencher as an acceptor linked by a specific peptide. In principle, QD luminescence, effectively dissipated in the probe, is switched on after the cleavage of the peptide by a protease and the release of the quencher. We proposed a novel synthesis strategy of a probe. A two-step synthesis consists of: (i) Conjugation of CdTe QDs functionalized by -COOH groups of succinic acid on the nanoparticle surface with the designed specific peptide (GTADVEDTSC) using a ligand-exchange approach; (ii) A fast, high-yield reaction of amine-reactive succinimidyl group on the BHQ-2 quencher with N-terminal of the peptide. This way, any crosslinking between individual nanoparticles and any nonspecific conjugation bonds are excluded. The analysis of the product after the first step proved a high reaction yield and nearly no occurrence of unreacted QDs, a prerequisite of the specificity of our luminescent probe. Its parameters evaluated as Michaelis-Menten description of enzymatic kinetics are similar to products published by other groups. Our research is focused on the fluorescence microscopy analyses of biologically active molecules, such as proteolytic active caspases, playing important roles in cell signaling regulations in normal and diseased states. Consequently, they are attractive targets for clinical diagnosis and medical therapy. The ultimate goal of our work was to synthesize a new QD luminescent probe for a long-time quantitative monitoring of active caspase-3/7 distribution in apoptotic osteoblastic MC3T3-E1 cells treated with camptothecin. As a result of comparison, our synthetized luminescent probe provides longer imaging times of caspases than commercial products. The probe proved the stability of the luminescence signal inside cells for more than 14 days.

Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates

The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SM d M), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.

Plasmon-Enhanced Expansion Microscopy

Expansion microscopy (ExM) is a rapidly emerging super-resolution microscopy technique that involves isotropic expansion of biological samples to improve spatial resolution. However, fluorescence signal dilution due to volumetric expansion is a hindrance to the widespread application of ExM. Here, we introduce plasmon-enhanced expansion microscopy (p-ExM) by harnessing an ultrabright fluorescent nanoconstruct, called plasmonic-fluor (PF), as a nanolabel. The unique structure of PFs renders nearly 15000-fold brighter fluorescence signal intensity and higher fluorescence retention following the ExM protocol (nearly 76%) compared to their conventional counterparts (<16% for IR-650). Individual PFs can be easily imaged using conventional fluorescence microscopes, making them excellent "digital" labels for ExM. We demonstrate that p-ExM enables improved tracing and decrypting of neural networks labeled with PFs, as evidenced by improved quantification of morphological markers (nearly a 2.5-fold increase in number of neurite terminal points). Overall, p-ExM complements the existing ExM techniques for probing structure-function relationships of various biological systems.

Simple, Economic, and Robust Rail-Based Setup for Super-Resolution Localization Microscopy

Research during the past 2 decades has showcased the power of single-molecule localization microscopy (SMLM) as a tool for exploring the nanoworld. However, SMLM systems are typically available in specialized laboratories and imaging facilities, owing to their expensiveness as well as complex assembly and alignment procedure. Here, we lay out the blueprint of a sturdy, rail-based, cost-efficient, multicolor SMLM setup that is easy to construct and align in service of simplifying the accessibility of SMLM. We characterize the optical properties of the design and assess its capabilities, robustness, and stability. The performance of the system is assayed using super-resolution imaging of biological samples. We believe that this design will make SMLM more affordable and broaden its availability.

Rapid, Accurate Classification of Single Emitters in Various Conditions and Environments for Blinking-Based Multiplexing

Although single-molecule imaging is widely applied in biology and materials science, most studies are limited by their reliance on spectrally distinct fluorescent probes. We recently introduced blinking-based multiplexing (BBM), a simple approach to differentiate spectrally overlapped single emitters based solely on their intrinsic blinking dynamics. The original proof-of-concept study implemented two methods for emitter classification: an empirically derived metric and a deep learning algorithm, both of which have significant drawbacks. Here, a multinomial logistic regression (LR) classification is applied to rhodamine 6G (R6G) and CdSe/ZnS quantum dots (QDs) in various experimental conditions (i.e., excitation power and bin time) and environments (i.e., glass versus polymer). We demonstrate that LR analysis is rapid and generalizable, and classification accuracies of 95% are routinely observed, even within a complex polymer environment where multiple factors contribute to blinking heterogeneity. In doing so, this study (1) reveals the experimental conditions (i.e., P_exc = 1.2 μW and t_bin = 10 ms) that optimize BBM for QD and R6G and (2) demonstrates that BBM via multinomial LR can accurately classify both emitter and environment, opening the door to new opportunities in single-molecule imaging.

Single-molecule localization microscopy goes quantitative

In the last few years, single-molecule localization (SMLM) techniques have been used to address biological questions in different research fields. More recently, super-resolution has also been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale level. In this scenario, quantitative approaches, mainly based on stepwise photobleaching and quantitative SMLM assisted by calibration standards, offer an exquisite tool for investigating protein complexes. This primer focuses on the basic concepts behind quantitative super-resolution microscopy, also providing strategies to overcome the technical hurdles that could limit their application.

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

Ultrasensitive Optical Fingerprinting of Biorelevant Molecules by Means of SERS-Mapping on Nanostructured Metasurfaces

The most relevant technique for portable (on-chip) sensors is Surface Enhanced Raman Scattering (SERS). This strategy crashes in the case of large (biorelevant) molecules and nano-objects, whose SERS spectra are irreproducible for "homeopathic" concentrations. We suggested solving this problem by SERS-mapping. We analyzed the distributions of SERS parameters for relatively "small" (malachite green (MG)) and "large" (phthalocyanine, H₂Pc*) molecules. While fluctuations of spectra for "small" MG were negligible, noticeable distribution of spectra was observed for "large" H₂Pc*. We show that the latter is due to a random arrangement of molecules with respect to "hot spot" areas, which have limited sizes, thus amplifying the lines corresponding to vibrations of different molecule parts. We have developed a method for engineering low-cost SERS substrates optimized for the best enhancement efficiency and a measurement protocol to obtain a reliable Raman spectrum, even for a countable number of large molecules randomly distributed over the substrate.

Nanoparticles for super-resolution microscopy: intracellular delivery and molecular targeting

Following an overview of the approaches and techniques used to acheive super-resolution microscopy, this review presents the advantages supplied by nanoparticle based probes for these applications. The various clases of nanoparticles that have been developed toward these goals are then critically described and these discussions are illustrated with a variety of examples from the recent literature.

Nanoscale regulation of Ca2+ dependent phase transitions and real-time dynamics of SAP97/hDLG

Synapse associated protein-97/Human Disk Large (SAP97/hDLG) is a conserved, alternatively spliced, modular, scaffolding protein critical in regulating the molecular organization of cell-cell junctions in vertebrates. We confirm that the molecular determinants of first order phase transition of SAP97/hDLG is controlled by morpho-functional changes in its nanoscale organization. Furthermore, the nanoscale molecular signatures of these signalling islands and phase transitions are altered in response to changes in cytosolic Ca²⁺. Additionally, exchange kinetics of alternatively spliced isoforms of the intrinsically disordered region in SAP97/hDLG C-terminus shows differential sensitivities to Ca²⁺ bound Calmodulin, affirming that the molecular signatures of local phase transitions of SAP97/hDLG depends on their nanoscale heterogeneity and compositionality of isoforms.

SAP97/hDLG is a ubiquitous, alternatively spliced, and conserved modular scaffolding protein involved in the organization cell junctions and excitatory synapses. Here, authors confirm that SAP97/hDLG condenses in to nanosized molecular domains in both heterologous cells and hippocampal pyramidal neurons. Authors demonstrate that in vivo and in vitro condensation, molecular signatures of nanoscale condensates and exchange kinetics of SAP97/hDLG is modulated by the local availability of alternatively spliced isoforms. Additionally, SAP97/hDLG isoforms exhibits a differential sensitivity to Ca²⁺ bound Calmodulin, resulting in altered properties of nanocondensates and their real-time regulation

Calcite-Assisted Localization and Kinetics (CLocK) Microscopy

Localization-based super-resolution imaging techniques have improved the spatial resolution of optical microscopy well below the diffraction limit, yet encoding additional information into super-resolved images, such as anisotropy and orientation, remains a challenge. Here we introduce calcite-assisted localization and kinetics (CLocK) microscopy, a multiparameter super-resolution imaging technique easily integrated into any existing optical microscope setup at low cost and with straightforward analysis. By placing a rotating calcite crystal in the infinity space of an optical microscope, CLocK microscopy provides immediate polarization and orientation information while maintaining the ability to localize an emitter/scatterer with <10 nm resolution. Further, kinetic information an order of magnitude shorter than the integration time of the camera is encoded in the unique point spread function of a CLocK image, allowing for new mechanistic insight into dynamic processes such as single-nanoparticle dissolution and single-molecule surface-enhanced Raman scattering.

Deep learning in single-molecule imaging and analysis: recent advances and prospects

Single-molecule microscopy is advantageous in characterizing heterogeneous dynamics at the molecular level. However, there are several challenges that currently hinder the wide application of single molecule imaging in bio-chemical studies, including how to perform single-molecule measurements efficiently with minimal run-to-run variations, how to analyze weak single-molecule signals efficiently and accurately without the influence of human bias, and how to extract complete information about dynamics of interest from single-molecule data. As a new class of computer algorithms that simulate the human brain to extract data features, deep learning networks excel in task parallelism and model generalization, and are well-suited for handling nonlinear functions and extracting weak features, which provide a promising approach for single-molecule experiment automation and data processing. In this perspective, we will highlight recent advances in the application of deep learning to single-molecule studies, discuss how deep learning has been used to address the challenges in the field as well as the pitfalls of existing applications, and outline the directions for future development.

Development of Deep-Learning-Based Single-Molecule Localization Image Analysis

Recent developments in super-resolution fluorescence microscopic techniques (SRM) have allowed for nanoscale imaging that greatly facilitates our understanding of nanostructures. However, the performance of single-molecule localization microscopy (SMLM) is significantly restricted by the image analysis method, as the final super-resolution image is reconstructed from identified localizations through computational analysis. With recent advancements in deep learning, many researchers have employed deep learning-based algorithms to analyze SMLM image data. This review discusses recent developments in deep-learning-based SMLM image analysis, including the limitations of existing fitting algorithms and how the quality of SMLM images can be improved through deep learning. Finally, we address possible future applications of deep learning methods for SMLM imaging.

Blinking-Based Multiplexing: A New Approach for Differentiating Spectrally Overlapped Emitters

Multicolor single-molecule imaging is widely applied to answer questions in biology and materials science. However, most studies rely on spectrally distinct fluorescent probes or time-intensive sequential imaging strategies to multiplex. Here, we introduce blinking-based multiplexing (BBM), a simple approach to differentiate spectrally overlapped emitters based solely on their intrinsic blinking dynamics. The blinking dynamics of hundreds of rhodamine 6G and CdSe/ZnS quantum dots on glass are obtained using the same acquisition settings and analyzed with a change point detection algorithm. Although substantial blinking heterogeneity is observed, the analysis yields a blinking metric with 93.5% classification accuracy. We further show that BBM with up to 96.6% accuracy is achieved by using a deep learning algorithm for classification. This proof-of-concept study demonstrates that a single emitter can be accurately classified based on its intrinsic blinking dynamics and without the need to probe its spectral color.

Blood Cell Analysis: From Traditional Methods to Super-Resolution Microscopy

Blood cell analysis is essential for the diagnosis and identification of hematological malignancies. The use of digital microscopy systems has been extended in clinical laboratories. Super-resolution microscopy (SRM) has attracted wide attention in the medical field due to its nanoscale spatial resolution and high sensitivity. It is considered to be a potential method of blood cell analysis that may have more advantages than traditional approaches such as conventional optical microscopy and hematology analyzers in certain examination projects. In this review, we firstly summarize several common blood cell analysis technologies in the clinic, and analyze the advantages and disadvantages of these technologies. Then, we focus on the basic principles and characteristics of three representative SRM techniques, as well as the latest advances in these techniques for blood cell analysis. Finally, we discuss the developmental trend and possible research directions of SRM, and provide some discussions on further development of technologies for blood cell analysis.

Displacement Statistics of Unhindered Single Molecules Show no Enhanced Diffusion in Enzymatic Reactions

Recent studies have sparked debate over whether catalytic reactions enhance the diffusion coefficients D of enzymes. Through high statistics of the transient (600 μs) displacements of unhindered single molecules freely diffusing in common buffers, we here quantify D for four enzymes under catalytic turnovers. We thus formulate how ∼ ±1% precisions may be achieved for D, and show no changes in diffusivity for catalase, urease, aldolase, and alkaline phosphatase under the application of wide concentration ranges of substrates. Our single-molecule approach thus overcomes potential limitations and artifacts underscored by recent studies to show no enhanced diffusion in enzymatic reactions.

Bleaching-Resistant Super-Resolution Fluorescence Microscopy

Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.

Evolving perspective on the origin and diversification of cellular life and the virosphere

The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.

Super-Resolution Microscopy for Structural Cell Biology

Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Imaging the endocannabinoid signaling system

The endocannabinoid (eCB) system is one of the most widespread neuromodulatory systems in the mammalian brain, with a multifaceted role in functions ranging from development to synaptic plasticity. Endocannabinoids are synthesized on demand from membrane lipid precursors, and act primarily on a single G-protein coupled receptor type, CB1, to carry out diverse functions. Despite the importance of the eCB system both in healthy brain function and in disease, critically important details of eCB signaling remained unknown. How eCBs are released from the membrane, how these lipid molecules are transported between cells, and how the distribution of their receptors is controlled, remained elusive. Recent advances in optical microscopy methods and biosensor engineering may open up new avenues for studying eCB signaling. We summarize applications of superresolution microscopy using single molecule localization to reveal distinct patterns of nanoscale CB1 distribution in neuronal axons and axon terminals. We review single particle tracking studies using quantum dots that allowed visualizing CB1 trajectories. We highlight the recent development of fluorescent eCB biosensors, that revealed spatiotemporally specific eCB release in live cells and live animals. Finally, we discuss future directions where method development may help to advance a precise understanding of eCB signaling.

Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm

Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.

Chemically Tuned, Reversible Fluorogenic Electrophile for Live Cell Nanoscopy

We report a chemically tuned fluorogenic electrophile designed to conduct live-cell super-resolution imaging by exploiting its stochastic reversible alkylation reaction with cellular nucleophiles. Consisting of a lipophilic BODIPY fluorophore tethered to an electrophilic cyanoacrylate warhead, the new probe cyanoAcroB remains nonemissive due to internal conversion along the cyanoacrylate moiety. Intermittent fluorescence occurs following thiolate Michael addition to the probe, followed by retro-Michael reaction, tuned by the cyano moiety in the acrylate warhead and BODIPY decoration. This design enables long-term super-resolved imaging of live cells by preventing fluorescent product accumulation and background increase, while preserving the pool of the probe. We demonstrate the imaging capabilities of cyanoAcroB via two methods: (i) single-molecule localization microscopy imaging with nanometer accuracy by stochastic chemical activation and (ii) super-resolution radial fluctuation. The latter tolerates higher probe concentrations and low imaging powers, as it exploits the stochastic adduct dissociation. Super-resolved imaging with cyanoAcroB reveals that electrophile alkylation is prevalent in mitochondria and endoplasmic reticulum. The 2D dynamics of these organelles within a single cell are unraveled with tens of nanometers spatial and sub-second temporal resolution through continuous imaging of cyanoAcroB extending for tens of minutes. Our work underscores the opportunities that reversible fluorogenic probes with bioinspired warheads bring toward illuminating chemical reactions with super-resolved features in live cells.

Extraction of Hidden Science from Nanoscale Images

Scanning probe microscopies and spectroscopies enable investigation of surfaces and even buried interfaces down to the scale of chemical-bonding interactions, and this capability has been enhanced with the support of computational algorithms for data acquisition and image processing to explore physical, chemical, and biological phenomena. Here, we describe how scanning probe techniques have been enhanced by some of these recent algorithmic improvements. One improvement to the data acquisition algorithm is to advance beyond a simple rastering framework by using spirals at constant angular velocity then switching to constant linear velocity, which limits the piezo creep and hysteresis issues seen in traditional acquisition methods. One can also use image-processing techniques to model the distortions that appear from tip motion effects and to make corrections to these images. Another image-processing algorithm we discuss enables researchers to segment images by domains and subdomains, thereby highlighting reactive and interesting disordered sites at domain boundaries. Lastly, we discuss algorithms used to examine the dipole direction of individual molecules and surface domains, hydrogen bonding interactions, and molecular tilt. The computational algorithms used for scanning probe techniques are still improving rapidly and are incorporating machine learning at the next level of iteration. That said, the algorithms are not yet able to perform live adjustments during data recording that could enhance the microscopy and spectroscopic imaging methods significantly.