Microscopy Imaging Techniques Research Articles

Phase imaging through a single multimode fiber.

Phase imaging techniques are pivotal for achieving high-contrast visualization of unstained biological specimens in vitro, which is typically not applicable in narrow spaces. Recently, multimode fiber (MMF) has shown promise in enabling high-resolution in vivo endoscopy in biological research. Herein, we introduce a novel, to the best of our knowledge, phase imaging microscopy technique employing a single multimode fiber, showcasing remarkable capabilities in high-contrast imaging and quantitative shape reconstruction through frequency-domain modulation. Our method, validated through comparisons with reflection and phase-contrast results, demonstrates exceptional ability in imaging diverse samples, including microspheres, semiconductor chips, and oral epithelial cells. Notably, the quantitative reconstruction of surface shape achieves a sensitivity of less than 100 nm, enabling the extraction of three-dimensional information from single focal plane images. Moreover, our technique excels in contrast enhancement and defocused background suppression, presenting a promising avenue for minimally invasive, high-contrast, label-free in vivo phase imaging.

Laser engineered architectures for magnetic flux manipulation on superconducting Nb thin films

Custom shaped magnetic flux guiding channels have been fabricated on superconducting Nb thin films by laser nanopatterning of their surface. Preferential pathways are defined by suitable combination of imprinted anisotropic pinning domains through laser-induced periodic surface structures (LIPSS). Generated by the selective energy deposition of femtosecond UV laser pulses, quasi-parallel ripple structures are formed under optimized irradiation conditions. On average, each domain is formed by grooves with a lateral period of 260–270 nm and a depth about 80 nm. By combination of scanning and transmission electron microscopy, magneto-optical imaging, and conductive atomic force microscopy techniques, we conclude that the boundaries of the LIPSS-covered domains play a prominent role in the magnetic flux diversion process within the film. This is confirmed by dedicated modeling of the flux dynamics, combined with the inversion of the magneto-optical signal. The created metasurfaces enable control of the flux penetration process at the microscale.

PH-Sensitive blue and red N-CDs for L-asparaginase quantification in complex biological matrices

A novel fluorometric method for the determination of L-asparaginase, an enzyme crucial in cancer therapy and food industry applications, is presented. This sensitive and selective approach utilizes L-asparagine and two pH-sensitive carbon dots (blue-N-CDs and red-N-CDs) as probes. The interaction between L-asparagine and L-asparaginase liberates ammonia, causing an increase in pH. This pH change simultaneously decreases the fluorescence of blue-N-CDs while enhancing the emission of red-N-CDs, enabling ratiometric detection of L-asparaginase. Comprehensive characterization of both carbon dots and investigation of their response mechanism towards L-asparaginase were conducted using ultraviolet–visible spectrophotometry, fluorescence spectroscopy, and transmission electron microscopy (TEM) imaging techniques. The designed approach demonstrates outstanding linearity (20 to 2000 U L-1) and a low detection limit (6.95 U L-1) for L-asparaginase quantification. Moreover, when tested to human serum samples, the detection system exhibits outstanding selectivity and high recovery rates (96.15% to 99.75%) with low standard deviation, underscoring its suitability for practical implementation in clinical diagnostics.

Green biosynthesis of selenium and zinc oxide nanoparticles using whole plant extract of Rheum ribes: Characterization, anticancer, and antimicrobial activity

Scientists are becoming interested in nanomedicine as a potential new approach to cancer detection and therapy in the twenty-first century. This paper presents the first investigation of the anticancer and antibacterial properties of selenium (Se) and zinc oxide (ZnO) nanoparticles obtained from Rheum ribes plant extract by a green synthesis method. Morphological and spectroscopic characterization of the synthesized nanoparticles was performed using transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), ultraviolet–visible (UV–Vis), which is a useful and straightforward technique for the preliminary characterisation of nanoparticles, dynamic light scattering (DLS) and X-ray diffraction (XRD) analysis. The size of the nanoparticles was determined to be 33 nm for Se-Nps and 32.8 nm for ZnO-Nps. The anticancer activity was assessed by the use of MTT, annexin V, caspase 3/7, and confocal microscopy imaging techniques. ZnO-Nps and Se-Nps were found to have significant antibacterial activity with MIC values for Escherichia coli (0.7 μg/mL, 0.63 μg/mL), and Staphylococcus aureus (1.56 μg/mL and 1.1 μg/mL). Furthermore, the antibacterial activity and the mechanism of action of the nanoparticles on E. coli and S. aureus bacteria were evaluated using microdilution and disc diffusion methods. In addition, the antiproliferative properties of ZnO-Np and Se-Np significantly suppressed the growth of A549 cells during a 24-hour incubation period (IC50 18.89 μg/mL ve 23.88 μg/mL). The results of the anti-cancer and anti-bacterial activity of the present study suggest that certain concentrations of Se-Np and ZnO-Np could be useful for pharmacological applications in cancer treatment and for coating surfaces for sterilization of medical equipment in healthcare settings, particularly in intensive care units.

Preparation of an environment-friendly microbial limestone dust suppressant and its dust suppression mechanism.

The development of an efficient and environmentally friendly dust suppressant is crucial to address the issue of dust pollution in limestone mines. Leveraging the synergistic microbial-induced calcium carbonate precipitation (MICP) technology involving NaHCO3 and dodecyl glucoside (APG), the optimal ratio of the dust suppressant was determined through single-factor and response surface tests. The dust suppression efficacy and mechanisms were analyzed through performance testing and microscopic imaging techniques, indicating that the optimal ratio of the new microbial dust suppressant was 20% mineralized bacteria cultured for 72h, 0.647molL-1 cementing solution, 3.142% NaHCO3, and 0.149% APG. Under these conditions, the yield of calcium carbonate increased by 24.89% as compared to when no NaHCO3 was added. The dust suppressant demonstrated excellent wind, moisture, and rain resistance, as well as curing ability. More calcite was formed in the dust samples after treatment, and the stable form of the dust suppressant contributed to consolidating the limestone dust into a cohesive mass. These findings indicate that the synergistic effect of NaHCO3 and APG significantly enhanced the dust suppression capabilities of the designed microbial dust suppressant.

New insights into the relationship between optical response and physicochemical properties in apple flesh: Hyperspectral microscope imaging technology

Hyperspectral microscope imaging (HMI) technique was employed to assess the changes in physicochemical parameters and microstructure of ‘Golden Delicious’ apples flesh during storage. Four regions of interest (ROIs), including whole-cell ROI, intercellular space ROI, cytoplasm ROI, and cell wall ROI were investigated to assess their relationships with physicochemical parameters. Different ROIs presented similar vibrational profiles, but with slight differences in spectral intensity, especially in the range of 800–1000 nm. Spectral angle mapper (SAM) was applied to the HMI of apple tissues at different storage stages to clearly show the structural changes of parenchyma cells, while principal component analysis (PCA) could highlight the distribution of sugars, water and pigments in apple flesh at the cellular scale. Simultaneously with the degradation of acid-soluble pectin (ASP), middle lamella dissolution and increased intercellular space were observed using SEM and TEM. Single feature variables were used to construct linear models based on pearson correlation analysis, with R2 of 0.96 for moisture at 982 nm, 0.85 for water-soluble pectin (WSP) at 420 nm, 0.82 for L* at 946 nm, 0.77 for soluble solids content (SSC) at 484 nm, and 0.66 for firmness at 490 nm. This work demonstrated the great potential of HMI technology as a fast, accurate and efficient solution for assessing the quality of ‘Golden Delicious’ apples.

Single crystals of purely organic free-standing two-dimensional woven polymer networks

The aesthetic and practicality of macroscopic fabrics continue to encourage chemists to weave molecules into interlaced patterns with the aim of providing emergent physical and chemical properties when compared with their starting materials. Weaving purely organic molecular threads into flawless two-dimensional patterns remains a formidable challenge, even though its feasibility has been proposed on several occasions. Herein we describe the synthesis of a flawless, purely organic, free-standing two-dimensional woven polymer network driven by dative B−N bonds. Single crystals of this woven polymer network were obtained and its well-defined woven topology was revealed by X-ray diffraction analysis. Free-standing two-dimensional monolayer nanosheets of the woven polymer network were exfoliated from the layered crystals using Scotch Magic Tape. The surface features of the nanosheets were investigated by integrated low-dose and cryogenic electron microscopy imaging techniques. These findings demonstrate the precise construction of purely organic woven polymer networks and highlight the unique opportunities for the application of woven topologies in two-dimensional organic materials.

Fourier Ptychographic Microscopy Reconstruction Method Based on Residual Local Mixture Network.

Fourier Ptychographic Microscopy (FPM) is a microscopy imaging technique based on optical principles. It employs Fourier optics to separate and combine different optical information from a sample. However, noise introduced during the imaging process often results in poor resolution of the reconstructed image. This article has designed an approach based on a residual local mixture network to improve the quality of Fourier ptychographic reconstruction images. By incorporating channel attention and spatial attention into the FPM reconstruction process, the network enhances the efficiency of the network reconstruction and reduces the reconstruction time. Additionally, the introduction of the Gaussian diffusion model further reduces coherent artifacts and improves image reconstruction quality. Comparative experimental results indicate that this network achieves better reconstruction quality, and outperforming existing methods in both subjective observation and objective quantitative evaluation.

Highly sensitive and specific detection of human papillomavirus type 16 using CRISPR/Cas12a assay coupled with an enhanced single nanoparticle dark-field microscopy imaging technique

Human papillomavirus (HPV) is a prevalent sexually transmitted pathogen associated with cervical cancer. Detecting high-risk HPV (hr-HPV) infections is crucial for cervical cancer prevention, particularly in resource-limited settings. Here, we present a highly sensitive and specific sensor for HPV-16 detection based on CRISPR/Cas12a coupled with enhanced single nanoparticle dark-field microscopy (DFM) imaging techniques. Ag–Au satellites were assembled through the hybridization of AgNPs-based spherical nucleic acid (Ag-SNA) and AuNPs-based spherical nucleic acid (Au-SNA), and their disassembly upon target-mediated cleavage by the Cas12a protein was monitored using DFM for HPV-16 quantification. To enhance the cleavage efficiency and detection sensitivity, the composition of the ssDNA sequences on Ag-SNA and Au-SNA was optimized. Additionally, we explored using the SynSed technique (synergistic sedimentation of Brownian motion suppression and dehydration transfer) as an alternative particle transfer method in DFM imaging to traditional electrostatic deposition. This addresses the issue of inconsistent deposition efficiency of Ag–Au satellites and their disassembly due to their size and charge differences. The sensor achieved a remarkable limit of detection (LOD) of 10 fM, lowered by 9-fold compared to traditional electrostatic deposition methods. Clinical testing in DNA extractions from 10 human cervical swabs demonstrated significant response differences between the positive and negative samples. Our sensor offers a promising solution for sensitive and specific HPV-16 detection, with implications for cancer screening and management.

Template bacteria-free fabrication of surface imprinted polymer-based biosensor for E. coli detection using photolithographic mimics: Hacking bacterial adhesion

As one class of molecular imprinted polymers (MIPs), surface imprinted polymer (SIP)-based biosensors show great potential in direct whole-bacteria detection. Micro-contact imprinting, that involves stamping the template bacteria immobilized on a substrate into a pre-polymerized polymer matrix, is the most straightforward and prominent method to obtain SIP-based biosensors. However, the major drawbacks of the method arise from the requirement for fresh template bacteria and often non-reproducible bacteria distribution on the stamp substrate. Herein, we developed a positive master stamp containing photolithographic mimics of the template bacteria (E. coli) enabling reproducible fabrication of biomimetic SIP-based biosensors without the need for the “real” bacteria cells. By using atomic force and scanning electron microscopy imaging techniques, respectively, the E. coli-capturing ability of the SIP samples was tested, and compared with non-imprinted polymer (NIP)-based samples and control SIP samples, in which the cavity geometry does not match with E. coli cells. It was revealed that the presence of the biomimetic E. coli imprints with a specifically designed geometry increases the sensor E. coli-capturing ability by an “imprinting factor” of about 3. These findings show the importance of geometry-guided physical recognition in bacterial detection using SIP-based biosensors. In addition, this imprinting strategy was employed to interdigitated electrodes and QCM (quartz crystal microbalance) chips. E. coli detection performance of the sensors was demonstrated with electrochemical impedance spectroscopy (EIS) and QCM measurements with dissipation monitoring technique (QCM-D).

Surfactant-Dependent Partitioning of Organics in Aqueous-Organic Reaction Systems.

A fluorescence lifetime imaging microscopy (FLIM) technique characterizes surfactant-dependent partitioning of organics in a system that mimics a Negishi-like cross-coupling reaction in water, under synthetic concentrations, with emulsion droplets. Experimental partitioning data were not predictable from simple hydrophilic-lipophilic balances. The ionic surfactant cetrimonium chloride suppressed the reactivity of the metallic zinc surface, presumably through competitive chloride binding and concurrent cetrimonium coating, a finding that may contribute to the reduced performance of ionic surfactants in the bench-scale coupling reaction.

The AMSlide for noninvasive time-lapse imaging of arbuscular mycorrhizal symbiosis.

Arbuscular mycorrhizal (AM) symbiosis, the nutritional partnership between AM fungi and most plant species, is globally ubiquitous and of great ecological and agricultural importance. Studying the processes of AM symbiosis is confounded by its highly spatiotemporally dynamic nature. While microscopy methods exist to probe the spatial side of this plant-fungal interaction, the temporal side remains more challenging, as reliable deep-tissue time-lapse imaging requires both symbiotic partners to remain undisturbed over prolonged time periods. Here, we introduce the AMSlide: a noninvasive, high-resolution, live-imaging system optimised for AM symbiosis research. We demonstrate the AMSlide's applications in confocal microscopy of mycorrhizal roots, from whole colonisation zones to subcellular structures, over timeframes from minutes to weeks. The AMSlide's versatility for different microscope set-ups, imaging techniques, and plant and fungal species is also outlined. It is hoped that the AMSlide will be applied in future research to fill in the temporal blanks in our understanding of AM symbiosis, as well as broader root and rhizosphere processes.

Ultrastructural features of primary cancer and its metastases

Mortality from metastatic lesions accounts for a significant proportion of oncological practice, and the issues of tumor chemoresistance and micrometastasis formation with the development of early recurrence are also important, which requires research and solution of these problems. Methods: The study used sectional material from the Pathology Department for ultrastructural examination of primary tumors and metastases, employing fixation, embedding, sectioning, staining, and electron microscopy imaging techniques.

Assessment of the effects of 2,4-D-dichlorophenoxyacetic acid-based herbicide exposure in eggs and embryos of golden apple snails using OCT

This study aimed to evaluate the effects of herbicide 2, 4-D-dichlorophenoxy acetic acid on golden apple snail eggs and embryos. Additionally, the study assessed the applicability of optical coherence tomography (OCT), a non-invasive depth cross-sectional microscopic imaging technique, as a novel method, to the best of our knowledge, for studying morphological changes in golden apple snail eggs and embryos, in comparison to the conventional approach of using white light microscopy. The study revealed that the herbicide 2,4-D-dichlorophenoxy acetic acid affected the hatchery rate and morphological changes of the eggs and embryos. The lethal concentration (LC50), representing the concentration of a substance that is expected to cause death in half of the population being studied, of the golden apple eggs and embryos increased with longer exposure time and higher concentrations. The estimated median effective concentration (EC50), which denotes the concentration producing the desired effect in 50% of the exposed golden apple embryos, exhibited a similar trend of change as the LC50. When compared to the microscopic study, it was observed that OCT could be employed to investigate morphological changes of golden apple snail eggs and embryos, enabling evaluation of alterations in both 2D and 3D structures.

A Perspective Review: Analyzing Collagen Alterations in Ovarian Cancer by High-Resolution Optical Microscopy.

High-grade serous ovarian cancer (HGSOC) is the predominant subtype of ovarian cancer (OC), occurring in more than 80% of patients diagnosed with this malignancy. Histological and genetic analysis have confirmed the secretory epithelial of the fallopian tube (FT) as a major site of origin of HGSOC. Although there have been significant strides in our understanding of this disease, early stage detection and diagnosis are still rare. Current clinical imaging modalities lack the ability to detect early stage pathogenesis in the fallopian tubes and the ovaries. However, there are several microscopic imaging techniques used to analyze the structural modifications in the extracellular matrix (ECM) protein collagen in ex vivo FT and ovarian tissues that potentially can be modified to fit the clinical setting. In this perspective, we evaluate and compare the myriad of optical tools available to visualize these alterations and the invaluable insights these data provide on HGSOC initiation. We also discuss the clinical implications of these findings and how these data may help novel tools for early diagnosis of HGSOC.

Polymorphism Dependent Cytotoxicity, Cellular Uptake, and Live Cell Imaging Studies on Napthalimide-Vinyl-Phenothiazine Conjugate.

Polymorphism-dependent cytotoxicity and cellular uptake of drug molecules have been studied for the past two decades. However, the visualization of polymorph-dependent cellular uptake and cytotoxicity using microscopy imaging techniques has not yet been reported. The luminescent polymorph is an ideal candidate to validate the above hypothesis. Herein, we report the polymorph-dependent cellular uptake, cytotoxicity, and bio-imaging functions of polymorphs 1Y and 1R of a naphthalimide-phenothiazine dyad. These polymorphs show different luminescence colors in the solid state and exhibit aggregation-induced enhanced emission (AIEE) in the DMSO-Water mixture. Bioimaging, cytotoxicity assay, and fluorescence-activated cell sorting (FACS) studies revealed that these polymorphs show different levels of cytotoxicity, cellular uptake, localization, and imaging potential. Detailed photophysical, morphological, and biological studies revealed that the difference in molecular conformation in these polymorphs enables them to form aggregates of different sizes and morphology, which leads to the differential uptake of these into the cells and consequently shows different cytotoxicity and imaging potentials.

Imaging the Iodine Sorption-Induced Synchronous Skeleton-Pore Interactions of Single Covalent Organic Framework Particles.

Covalent organic frameworks (COFs) are promising iodine adsorbents. For improved performances, it is critical and essential to fundamentally understand the underlying mechanism. Here, using the operando dark-field optical microscopy (DFM) imaging technique, the observation of an extraordinary structure shrinkage of 2D triphenylbenzene (TPB)-dimethoxyterephthaldehyde (DMTP)-COF upon the adsorption of I2 vapor at the single-particle resolution is reported. Combining single-particle DFM imaging with other experimental and theoretical methods, it is revealed that the shrinkage mechanism of the TPB-DMTP-COF is attributed to the I2 sorption-induced synchronous skeleton-pore interactions. The redox reaction of I2 and TPB-DMTP-COF yields some cationic skeletons and I3 - species, which triggers the multi-directional halogen-bonding interactions of I2 and I3 - as well as strong cation-π interactions between neutral and cationic skeletons, accompanying the synchronous in-plane skeleton shrinking in the xy plane and compact out-of-plane layer packing in the z-direction. This understanding of the synchronous action between the skeleton and pore breaks the perspective on the structure robustness of 2D COFs with excellent stability during the I2 uptake, which offers pivotal guidance for the rational design and creation of advanced microporous adsorbents.

Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts

Historical paper documents are susceptible to complex degradation processes, including biodeterioration, which can progressively compromise their aesthetic and structural integrity. This study analyses seventeenth century handwritten historical letters stored at the Correr Museum Library in Venice, Italy, exhibiting pronounced signs of biodeterioration. The techniques used encompassed traditional colony isolation on agar plates and proteomics analyses, employing nanoscale liquid chromatography coupled with high-resolution mass spectrometry (nano-LC–MS). Fluorescence microscopy was used for the first time in the historical paper biodeterioration context to supplement the conventional stereoscopic, optical, and scanning electron microscopic imaging techniques. This method enables the visualisation of microorganisms beyond and beneath the paper’s surface through their natural intrinsic autofluorescence in a non-invasive and non-destructive way. The results demonstrate a diverse, complex, and abundant microbiota composed of coexisting fungal and bacterial species (Ascomycota, Mucoromycota, Basidiomycota, Proteobacteria, and Actinobacteria), along with mite carcasses, insects, parasites, and possibly protists. Furthermore, this study reveals certain species that were not previously documented in the biodeterioration of historical paper, including human pathogens, such as Histoplasma capsulatum, Brucella, Candida albicans, and species of Aspergillus (A. flavus, A. fumigatus, A. oryzae, A. terreus, A. niger) known to cause infections or produce mycotoxins, posing substantial risk to both artefacts and humans.

YOLO2U-Net: Detection-guided 3D instance segmentation for microscopy

Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and low resolution in the z-axis may pose challenges (even for human experts) to detect individual cells in 3D volumes as these non-overlapping cells may appear as overlapping. A comprehensive method for accurate 3D instance segmentation of cells in the brain tissue is introduced here. The proposed method combines the 2D YOLO detection method with a multi-view fusion algorithm to construct a 3D localization of the cells. Next, the 3D bounding boxes along with the data volume are input to a 3D U-Net network that is designed to segment the primary cell in each 3D bounding box, and in turn, to carry out instance segmentation of cells in the entire volume. The promising performance of the proposed method is shown in comparison with current deep learning-based 3D instance segmentation methods.

Joint Learning Neuronal Skeleton and Brain Circuit Topology with Permutation Invariant Encoders for Neuron Classification

Determining the types of neurons within a nervous system plays a significant role in the analysis of brain connectomics and the investigation of neurological diseases. However, the efficiency of utilizing anatomical, physiological, or molecular characteristics of neurons is relatively low and costly. With the advancements in electron microscopy imaging and analysis techniques for brain tissue, we are able to obtain whole-brain connectome consisting neuronal high-resolution morphology and connectivity information. However, few models are built based on such data for automated neuron classification. In this paper, we propose NeuNet, a framework that combines morphological information of neurons obtained from skeleton and topological information between neurons obtained from neural circuit. Specifically, NeuNet consists of three components, namely Skeleton Encoder, Connectome Encoder, and Readout Layer. Skeleton Encoder integrates the local information of neurons in a bottom-up manner, with a one-dimensional convolution in neural skeleton's point data; Connectome Encoder uses a graph neural network to capture the topological information of neural circuit; finally, Readout Layer fuses the above two information and outputs classification results. We reprocess and release two new datasets for neuron classification task from volume electron microscopy(VEM) images of human brain cortex and Drosophila brain. Experiments on these two datasets demonstrated the effectiveness of our model with accuracies of 0.9169 and 0.9363, respectively. Code and data are available at: https://github.com/WHUminghui/NeuNet.