Conventional Microscopy Research Articles

Femtosecond electron microscopy of relativistic electron bunches

The development of plasma-based accelerators has enabled the generation of very high brightness electron bunches of femtosecond duration, micrometer size and ultralow emittance, crucial for emerging applications including ultrafast detection in material science, laboratory-scale free-electron lasers and compact colliders for high-energy physics. The precise characterization of the initial bunch parameters is critical to the ability to manipulate the beam properties for downstream applications. Proper diagnostic of such ultra-short and high charge density laser-plasma accelerated bunches, however, remains very challenging. Here we address this challenge with a novel technique we name as femtosecond ultrarelativistic electron microscopy, which utilizes an electron bunch from another laser-plasma accelerator as a probe. In contrast to conventional microscopy of using very low-energy electrons, the femtosecond duration and high electron energy of such a probe beam enable it to capture the ultra-intense space-charge fields of the investigated bunch and to reconstruct the charge distribution with very high spatiotemporal resolution, all in a single shot. In the experiment presented here we have used this technique to study the shape of a laser-plasma accelerated electron beam, its asymmetry due to the drive laser polarization, and its beam evolution as it exits the plasma. We anticipate that this method will significantly advance the understanding of complex beam-plasma dynamics and will also provide a powerful new tool for real-time optimization of plasma accelerators.

Clinical observation of tear film breakup time with a novel smartphone-attachable technology

PurposeTo demonstrate the practicability of a portable instrument in assessing tear film breakup time (TFBUT): a lens attachment for smartphones (LAS).MethodsBy applying LAS in combination with the iPhone 12 pro, and a recordable slit-lamp microscope, we obtained TFBUT videos from 58 volunteers. The comparison between the conventional slit-lamp microscope and LAS by an experienced ophthalmologist. Moreover, we also invited an ophthalmic postgraduate student and an undergraduate student with no clinical experience to assess TFBUT in those videos. The inter-observer reliability was assessed using intraclass correlation coefficients (ICC).ResultsThe TFBUT of 116 eyes in total was recorded. Reliability indexes were adequate. The Spearman’s correlation analysis and the intraclass correlation coefficient suggested a strong correlation between the 2 modalities (Right eye: Spearman’s r = 0.929, 95% confidence interval (CI) = 0.847–0.963, ICC = 0.978, p < 0.001; Left eye: Spearman’s r = 0.931, 95% CI = 0.866–0.964, ICC = 0.985, p < 0.001;). Between instruments, the majority of TFBUT measurements showed good agreement on Bland Altman plot. A high concordance was observed in TFBUT, when assessed by an ophthalmologist and an ophthalmic postgraduate student (Left eye: LAS ICC = 0.951, p < 0.001; Left eye: slit-lamp microscope ICC = 0.944, p < 0.001).ConclusionsCompared with the conventional slit-lamp microscope, the LAS has sufficient validity for evaluating TFBUT in clinics or at home.

Maternal antibiotic administration during gestation can affect the memory and brain structure in mouse offspring.

Maternal antibiotics administration (MAA) is among the widely used therapeutic approaches in pregnancy. Although published evidence demonstrates that infants exposed to antibiotics immediately after birth have altered recognition memory responses at one month of age, very little is known about in utero effects of antibiotics on the neuronal function and behavior of children after birth. Therefore, this study aimed to evaluate the impact of MAA at different periods of pregnancy on memory decline and brain structural alterations in young mouse offspring after their first month of life. To study the effects of MAA on 4-week-old offspring, pregnant C57BL/6J mouse dams (2-3-month-old; n = 4/group) were exposed to a cocktail of amoxicillin (205 mg/kg/day) and azithromycin (51 mg/kg/day) in sterile drinking water (daily/1 week) during either the 2nd or 3rd week of pregnancy and stopped after delivery. A control group of pregnant dams was exposed to sterile drinking water alone during all three weeks of pregnancy. Then, the 4-week-old offspring mice were first evaluated for behavioral changes. Using the Morris water maze assay, we revealed that exposure of pregnant mice to antibiotics at the 2nd and 3rd weeks of pregnancy significantly altered spatial reference memory and learning skills in their offspring compared to those delivered from the control group of dams. In contrast, no significant difference in long-term associative memory was detected between offspring groups using the novel object recognition test. Then, we histologically evaluated brain samples from the same offspring individuals using conventional immunofluorescence and electron microscopy assays. To our knowledge, we observed a reduction in the density of the hippocampal CA1 pyramidal neurons and hypomyelination in the corpus callosum in groups of mice in utero exposed to antibiotics at the 2nd and 3rd weeks of gestation. In addition, offspring exposed to antibiotics at the 2nd or 3rd week of gestation demonstrated a decreased astrocyte cell surface area and astrocyte territories or depletion of neurogenesis in the dentate gyrus and hippocampal synaptic loss, respectively. Altogether, this study shows that MAA at different times of pregnancy can pathologically alter cognitive behavior and brain development in offspring at an early age after weaning.

Mineral Assemblage of Olivine-Hosted Melt Inclusions in a Mantle Xenolith from the V. Grib Kimberlite Pipe: Direct Evidence for the Presence of an Alkali-Rich Carbonate Melt in the Mantle Beneath the Baltic Super-Craton

This report deals with the first mineralogical examination of secondary crystallized melt inclusions (CMIs) in healed cracks within olivine in a mantle peridotite xenolith from the V. Grib kimberlite pipe (Arkhangelsk diamondiferous province). In contrast to micro/nano-inclusions in diamonds, the studied CMIs are quite large (up to 50 µm), so that the mineral composition of the CMIs can be determined via conventional analytical approaches, e.g., Raman spectroscopy and scanning electron microscopy. Garnet peridotite is a coarse-grained mantle rock that equilibrates at 3.3 GPa and 750 °C (corresponding to a depth of ~100 km). The CMIs are therefore tiny snapshots of melt that existed in the shallow lithospheric mantle and were entrapped in olivine. In total, nineteen mineral species were identified among the daughter magmatic minerals of the CMIs. Various Na-K-Ca-, Na-Ca-, Na-Mg-, Ca-Mg-, Mg- and Ca-carbonates; Na-Mg-carbonates with the additional anions Cl−, SO42− and PO43−; alkali sulfates; chlorides; phosphates; sulfides; oxides; and silicates were established. Within the mineral assemblage, carbonates were predominant, with their abundance being more than 62 vol.%. The CMIs contained twelve alkali-rich minerals; nine of them were Na-bearing and showed bulk molar (Na + K)/Ca ≥ 1. The CMIs’ parental melt was an alkali-rich carbonate liquid that contained low amounts of SiO2 (≤9.6 wt%) and H2O (≤2.6 wt%). According to our estimates, the time of complete equilibration between olivine within the healed cracks and host olivine in the mantle at the calculated P-T parameters for the studied xenolith should be no more than several years. Based on this geologically short time span, a genetic link between the studied CMIs and the magmatism that formed the V. Grib kimberlite pipe is suggested.

Temporal coherence envelope function of field emission in electron microscopy

Imaging in electron microscopy is adversely affected by partial electron spatial and temporal coherence. Temporal coherence has been treated theoretically in the past using the method pioneered fifty years ago by Hanßen and Trepte, who assumed a Gaussian energy distribution. However, state-of-the-art instruments employ field emission (FE) sources that emit electrons with a non-Gaussian energy distribution. We have updated the treatment of temporal coherence to describe the effects of an arbitrary energy distribution on image formation. The updated approach is implemented in Fourier optics simulations to explore the effect of FE on image formation in conventional, non-aberration-corrected (NAC) and aberration-corrected (AC) low energy electron microscopy. It is found that the resolution that can be achieved for the FE distribution is only slightly degraded compared to a Gaussian distribution with the same energy spread. FE also produces a focus offset. These two effects are weaker for AC than for NAC microscopy. These and other insights may be relevant to the selection of the aperture size that optimizes resolution and to analyses that make use of focal image series. The approach developed here is also applicable to transmission electron microscopy.

Pressure induced changes in endothelial cell morphology and Ca2+ signaling in ex vivo pressurized resistance arteries revealed using 4D diSPIM myography and AI deep-learning

The vascular endothelium is critical in promoting vasodilation of resistance-size arteries through Ca 2+ dependent pathways. Vascular endothelial cells (ECs) are exposed to mechanical stimulation through changing intravascular pressure and flow, yet it is unclear how these forces impact EC morphology and Ca 2+ signaling in pressurized arteries. Visualizing how the endothelium of an intact resistance-size vessel responds to changing physical forces requires isometric, sub-micron, resolution. Conventional confocal fluorescent microscope systems are limited by poor axial resolution. 4D dual inverted selective plane of illumination microscopy (diSPIM; 3i) uniquely provides isometric resolution at ~330 nm with high temporal resolution and minimal photobleaching or phototoxicity. We designed custom pressure myography chambers to allow simultaneous 4D diSPIM fluorescent imaging and vessel diameter tracking measurements via transmitted IR light (diSPIM Myography). We captured fluorescent images of ex vivo pressurized resistance-size mouse mesenteric arteries at 80, 60, 40, and 20 mm Hg before and after the generation of myogenic tone and in the absence of extracellular Ca 2+ . Representative images were annotated for ECs, nuclei, myoendothelial projections (MEPS), and Ca 2+ signals. Annotations were used as ground truth for CNN AI model generation and validation using Apeer (Zeiss). Arivis Vision4D (Zeiss) was used to run the AI model and quantify data. As static intravascular pressure is increased in arteries without tone (with or without Ca 2+ ), ECs increase in width as the vessel dilates. Myogenic tone minimizes pressure dilation and changes in EC width, however, ECs compress by up to 1 micron as pressure increases from 20 to 80 mm Hg. Additionally, increasing intravascular pressure in arteries with tone decreases local EC Ca 2+ signaling. The data demonstrate a relationship between intravascular pressure and EC shape and Ca 2+ signaling in intact resistance arteries under conditions of physiologic temperature, pressure, pH, and tone. diSPIM myography provides a method of studying the effects of physiologically relevant mechanical stimuli and the roles of various mechanosensitive mechanisms on vascular function. AI image annotation reduces analysis bias and increases the breadth of quantifiable microscopy data. DMC is supported by NIH R00HL133451 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Using Expansion Microscopy to Physically Enlarge Whole-Mount Drosophila Embryos for Super-Resolution Imaging.

The workhorse of developmental biology is the confocal microscope, which allows researchers to determine the three-dimensional localization of tagged molecules within complex biological samples. While traditional confocal microscopes allow one to resolve two adjacent fluorescent point sources located a few hundred nanometers apart, observing the finer details of subcellular biology requires the ability to resolve signals in the order of tens of nanometers. Numerous hardware-based methods for super-resolution microscopy have been developed to allow researchers to sidestep such resolution limits, although these methods require specialized microscopes that are not available to all researchers. An alternative method for increasing resolving power is to isotropically enlarge the sample itself through a process known as expansion microscopy (ExM), which was first described by the Boyden group in 2015. ExM is not a type of microscopy per se but is rather a method for swelling a sample while preserving the relative spatial organization of its constituent molecules. The expanded sample can then be observed at an effectively increased resolution using a traditional confocal microscope. Here, we describe a protocol for implementing ExM in whole-mount Drosophila embryos, which is used to examine the localization of Par-3, myosin II, and mitochondria within the surface epithelial cells. This protocol yields an approximately four-fold increase in sample size, allowing for the detection of subcellular details that are not visible with conventional confocal microscopy. As proof of principle, an anti-GFP antibody is used to distinguish distinct pools of myosin-GFP between adjacent cell cortices, and fluorescently labeled streptavidin is used to detect endogenous biotinylated molecules to reveal the fine details of the mitochondrial network architecture. This protocol utilizes common antibodies and reagents for fluorescence labeling, and it should be compatible with many existing immunofluorescence protocols.

3D full-wave multi-scattering forward solver for coherent microscopes.

A rigorous forward model solver for conventional coherent microscope is presented. The forward model is derived from Maxwell's equations and models the wave behaviour of light matter interaction. Vectorial waves and multiple-scattering effect are considered in this model. Scattered field can be calculated with given distribution of the refractive index of the biological sample. Bright field images can be obtained by combining the scattered field and reflected illumination, and experimental validation is included. Insights into the utility of the full-wave multi-scattering (FWMS) solver and comparison with the conventional Born approximation based solver are presented. The model is also generalizable to the other forms of label-free coherent microscopes, such as quantitative phase microscope and dark-field microscope.

Tunable reflective Fourier ptychographic microscopy using a digital micromirror device and an LED source

We propose a tunable reflective Fourier ptychographic microscopy approach in which the resolution and field of view are variable with different objective lenses and a digital micromirror device. Several objective lenses are applied to tunable reflective Fourier ptychographic microscopy without additional optical alignment while also enhancing the resolution. To demonstrate the feasibility of the new technique, tunable reflective Fourier ptychographic microscopy with 10 × and 50 × objective lenses is demonstrated. Moreover, we compare the resolution of the new technique and conventional Fourier ptychographic microscopy to verify the improved resolution of the new technique.

Aptamer-based expansion microscopy platform enables signal-amplified imaging of dendritic spines

Super-resolution imaging of dendritic spines (DS) can provide valuable information for mechanistic studies related to synaptic physiology and neural plasticity, but challenged by their small dimension (50–200 nm) below the spatial resolution of conventional optical microscopes. In this work, by combining the molecular recognition specificity of aptamer with high programmability of DNA nanotechnology, we developed an expansion microscopy (ExM) platform for imaging DS with enhanced spatial resolution and amplified signal output. Our results demonstrated that the aptamer probe could specifically bind to DS of primary hippocampal neurons. With physical expansion, the DS structure could be effectively enlarged by 4–5 folds, leading to the generation of more structural information. Meantime, the aptamer binding signal could be readily amplified by the introduction of DNA signal amplification strategy, overcoming the drawback of fluorescence dilution during the ExM treatment. This platform enabled evaluation of ischemia-induced early stroke based on the morphological change of DS, highlighting a promising avenue for studying nanoscale structures in biological systems.

Rabies virus-based labeling of layer 6 corticothalamic neurons for two-photon imaging in vivo

Neocortical layer 6 (L6) is less understood than other more superficial layers, largely owing to limitations of performing high-resolution investigations invivo. Here, we show that labeling with the Challenge Virus Standard (CVS) rabies virus strain enables high-quality imaging of L6 neurons by conventional two-photon microscopes. CVS virus injection into the medial geniculate body can selectively label L6 neurons in the auditory cortex. Only three days after injection, dendrites and cell bodies of L6 neurons could be imaged across all cortical layers. Ca2+ imaging in awake mice showed that sound stimulation evokes neuronal responses from cell bodies with minimal contamination from neuropil signals. In addition, dendritic Ca2+ imaging revealed significant responses from spines and trunks across all layers. These results demonstrate a reliable method capable of rapid, high-quality labeling of L6 neurons that can be readily extended to other brain regions.

Achieving High Temporal Resolution in Single‐Molecule Fluorescence Techniques Using Plasmonic Nanoantennas

AbstractSingle‐molecule fluorescence techniques are essential for investigating the molecular mechanisms in biological processes. However, achieving sub‐millisecond temporal resolution to monitor fast molecular dynamics remains a significant challenge. The fluorescence brightness is the key parameter that generally defines the temporal resolution for these techniques. Conventional microscopes and standard fluorescent emitters fall short in achieving the high brightness required for sub‐millisecond monitoring. Plasmonic nanoantennas are proposed as a solution, but despite huge fluorescence enhancement having been obtained with these structures, the brightness generally remains below 1 million photons/s/molecule. Therefore, the improvement of temporal resolution is overlooked. This article presents a method for achieving high temporal resolution in single‐molecule fluorescence techniques using plasmonic nanoantennas, specifically optical horn antennas. This work demonstrates about 90% collection efficiency of the total emitted light, reaching a high fluorescence brightness of 2 million photons/s/molecule in the saturation regime. This enables observations of single molecules with microsecond binning time and fast fluorescence correlation spectroscopy measurements. This work expands the applications of plasmonic antennas and zero‐mode waveguides in the fluorescence saturation regime toward brighter single‐molecule signal, faster temporal resolutions, and improved detection rates to advance fluorescence sensing, DNA sequencing, and dynamic studies of molecular interactions.

Synchrotron X-ray Studies of the Structural and Functional Hierarchies in Mineralised Human Dental Enamel: A State-of-the-Art Review.

Hard dental tissues possess a complex hierarchical structure that is particularly evident in enamel, the most mineralised substance in the human body. Its complex and interlinked organisation at the Ångstrom (crystal lattice), nano-, micro-, and macro-scales is the result of evolutionary optimisation for mechanical and functional performance: hardness and stiffness, fracture toughness, thermal, and chemical resistance. Understanding the physical-chemical-structural relationships at each scale requires the application of appropriately sensitive and resolving probes. Synchrotron X-ray techniques offer the possibility to progress significantly beyond the capabilities of conventional laboratory instruments, i.e., X-ray diffractometers, and electron and atomic force microscopes. The last few decades have witnessed the accumulation of results obtained from X-ray scattering (diffraction), spectroscopy (including polarisation analysis), and imaging (including ptychography and tomography). The current article presents a multi-disciplinary review of nearly 40 years of discoveries and advancements, primarily pertaining to the study of enamel and its demineralisation (caries), but also linked to the investigations of other mineralised tissues such as dentine, bone, etc. The modelling approaches informed by these observations are also overviewed. The strategic aim of the present review was to identify and evaluate prospective avenues for analysing dental tissues and developing treatments and prophylaxis for improved dental health.

Cryo-EM tomography and automatic segmentation delineate modular structures in the postsynaptic density.

Postsynaptic densities (PSDs) are large protein complexes associated with the postsynaptic membrane of excitatory synapses important for synaptic function including plasticity. Conventional electron microscopy (EM) typically depicts PSDs as compact disk-like structures of hundreds of nanometers in size. Biochemically isolated PSDs were also similar in dimension revealing a predominance of proteins with the ability to polymerize into an extensive scaffold; several EM studies noted their irregular contours with often small granular structures (<30 nm) and holes. Super-resolution light microscopy studies observed clusters of PSD elements and their activity-induced lateral movement. Furthermore, our recent EM study on PSD fractions after sonication observed PSD fragments (40-90 nm in size) separate from intact PSDs; however, such structures within PSDs remained unidentified. Here we examined isolated PSDs by cryo-EM tomography with our new approach of automatic segmentation that enables delineation of substructures and their quantitative analysis. The delineated substructures broadly varied in size, falling behind 30 nm or exceeding 100 nm and showed that a considerable portion of the substructures (>38%) in isolated PSDs was in the same size range as those fragments. Furthermore, substructures spanning the entire thickness of the PSD were found, large enough to contain both membrane-associated and cytoplasmic proteins of the PSD; interestingly, they were similar to nanodomains in frequency. The structures detected here appear to constitute the isolated PSD as modules of various compositions, and this modular nature may facilitate remodeling of the PSD for proper synaptic function and plasticity.

PBMC derived extracellular vesicles in a smoking-related inflammatory disease model.

Extracellular vesicles (EVs) function as mediators of intercellular communication and as such influence the recipient cell function. EVs derived from immune cells can carry out many of the same functions as their parental cells, as they carry costimulatory molecules, antigens, and antigen-MHC complexes. As a result, there is a strong interest in understanding the composition and origin of immune cell derived EVs in order to understand their role in the pathogenesis of diseases. This study aimed to optimise methodologies to study immune cell derived EVs. Peripheral blood mononuclear cell-derived small EVs (sEVs) were isolated and observed using conventional transmission electron microscopy (TEM) and sized by nanoparticle tracking analysis (NTA). They were then enumerated and profiled using Imaging Flow Cytometry (IFC) and were further characterised using a flow cytometric multiplex bead assay. These techniques were then applied to our current research, namely smoking-related inflammatory disease. We present here a comprehensive approach to analyse PBMC-derived sEVs in smoking-related inflammatory disease following the Minimal Information for Studies of Extracellular Vesicle (MISEV) 2018 guidelines. This article is protected by copyright. All rights reserved.

Abstract 6613: Label-free multimodal multiphoton microscopy for predicting DNA damage response in patient derived non-small cell lung cancer organoids

Abstract Background: DNA damage response (DDR) is a fundamental mechanism for evaluating efficacy of cancer therapeutics, many of which target DNA or associated processes (e.g., etoposide: inhibits DNA synthesis, cisplatin: crosslinks DNA). Current techniques to evaluate DDR rely on immunostaining for gamma H2AX foci (γH2AX), which is an indicator of DNA double-strand break formation. While γH2AX immunostaining can provide a snapshot of DDR in fixed cellular and tissue samples, this method is technically cumbersome as: 1) temporal monitoring of DDR requires timepoint replicates; 2) extensive assay development efforts for 3D samples such as organoids, and 3) protocols for γH2AX immunostaining and its evaluation are time-consuming. The goal of this project is to reduce overall burden on assay duration and development in NSCLC organoids by leveraging label-free multiphoton imaging. Method: To predict DDR in 3D organoid samples, label-free multimodal multiphoton techniques such as simultaneous label-free autofluorescence multiharmonic (SLAM) imaging can provide intracellular information based on endogenous contrast mechanisms. SLAM makes use of a single laser to excite autofluorescence in multiple cellular components including FAD and NAD(P)H, enabling the calculation of the optical redox ratio, which estimates the equilibrium of electron donating versus accepting species in cells. Moreover, label-free, multiphoton systems enable imaging of live samples without the need to add labels or generate sacrificial samples and have improved image acquisition in 3D space over conventional confocal microscopy. Using SLAM, we propose to predict DDR in non-small cell lung cancer (NSCLC) organoids. NSCLC organoids recapitulate histological and genetic features of their derived patient tissue, retaining tumor variability. Results: Predictive modeling via gradient boost regressor between handcrafted SLAM image features and γH2AX immunostained images on weakly-paired images confirmed strong correlation between SLAM image features and γH2AX speckles/nuclei. Across multiple patient derived NSCLC organoid lines and multiple DNA targeting chemotherapeutics, the optical redox ratio was demonstrated to robustly predict DDR. Conclusion: Label-free imaging via SLAM can be used to predict DDR in live 3D NSCLC organoids with minimal sample handling and without the need to add labelled reporters, enabling quicker and less technically involved DDR assaying. Citation Format: Terrence T. Roh, Aneesh Alex, Janet E. Sorrells, Prasanna Chandramouleeswaran, Marina Marjanovic, Steve R. Hood, BanuPriya Sridharan, Stephen A. Boppart. Label-free multimodal multiphoton microscopy for predicting DNA damage response in patient derived non-small cell lung cancer organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6613.

Machine Learning Enhanced Optical Microscopy for the Rapid Morphology Characterization of Silver Nanoparticles.

The rapid characterization of nanoparticles for morphological information such as size and shape is essential for material synthesis as they are the determining factors for the optical, mechanical, and chemical properties and related applications. In this paper, we report a computational imaging platform to characterize nanoparticle size and morphology under conventional optical microscopy. We established a machine learning model based on a series of images acquired by through-focus scanning optical microscopy (TSOM) on a conventional optical microscope. This model predicts the size of silver nanocubes with an estimation error below 5% on individual particles. At the ensemble level, the estimation error is 1.6% for the averaged size and 0.4 nm for the standard deviation. The method can also identify the tip morphology of silver nanowires from the mix of sharp-tip and blunt-tip samples at an accuracy of 82%. Furthermore, we demonstrated online monitoring for the evolution of the size distribution of nanoparticles during synthesis. This method can be potentially extended to more complicated nanomaterials such as anisotropic and dielectric nanoparticles.

High-throughput single-molecule localization microscopy: Potential clinical applications.

High-throughput single-molecule localization microscopy: Potential clinical applications.

Rcell2: Microscopy‐Based Cytometry in R

This article describes a method for quantifying various cellular features (e.g., volume, curvature, total and sub-cellular fluorescence localization) of individual cells from sets of microscope images, and for tracking them over time-course microscopy experiments. One purposely defocused transmission image (sometimes referred to as bright-field or BF) is used to segment the image and locate each cell. Fluorescence images (one for each of the color channels or z-stacks to be analyzed) may be acquired by conventional wide-field epifluorescence or confocal microscopy. This method uses a set of R packages called rcell2. Relative to the original release of Rcell (Bush etal., 2012), the updated version bundles, into a single software suite, the image-processing capabilities of Cell-ID, offers new data analysis tools for cytometry, and relies on the widely used data analysis and visualization tools of the statistical programming framework R. © 2023 Wiley Periodicals LLC. Basic Protocol: Extracting quantitative information from single cells Support Protocol 1: Obtaining and installing Cell-ID and R Support Protocol 2: Preparing cells for imaging.

Measuring complex refractive index through deep-learning-enabled optical reflectometry

Optical spectroscopy is indispensable for research and development in nanoscience and nanotechnology, microelectronics, energy, and advanced manufacturing. Advanced optical spectroscopy tools often require both specifically designed high-end instrumentation and intricate data analysis techniques. Beyond the common analytical tools, deep learning methods are well suited for interpreting high-dimensional and complicated spectroscopy data. They offer great opportunities to extract subtle and deep information about optical properties of materials with simpler optical setups, which would otherwise require sophisticated instrumentation. In this work, we propose a computational approach based on a conventional tabletop optical microscope and a deep learning model called ReflectoNet. Without any prior knowledge about the multilayer substrates, ReflectoNet can predict the complex refractive indices of thin films and 2D materials on top of these nontrivial substrates from experimentally measured optical reflectance spectra with high accuracies. This task was not feasible previously with traditional reflectometry or ellipsometry methods. Fundamental physical principles, such as the Kramers–Kronig relations, are spontaneously learned by the model without any further training. This approach enables in-operando optical characterization of functional materials and 2D materials within complex photonic structures or optoelectronic devices.