Introduction to Confocal Microscopy

A modular framework for multi-scale tissue imaging and neuronal segmentation

The development of robust tools for segmenting cellular and sub-cellular neuronal structures lags behind the massive production of high-resolution 3D images of neurons in brain tissue. The challenges are principally related to high neuronal density and low signal-to-noise characteristics in thick samples, as well as the heterogeneity of data acquired with different imaging methods. To address this issue, we design a framework which includes sample preparation for high resolution imaging and image analysis. Specifically, we set up a method for labeling thick samples and develop SENPAI, a scalable algorithm for segmenting neurons at cellular and sub-cellular scales in conventional and super-resolution STimulated Emission Depletion (STED) microscopy images of brain tissues. Further, we propose a validation paradigm for testing segmentation performance when a manual ground-truth may not exhaustively describe neuronal arborization. We show that SENPAI provides accurate multi-scale segmentation, from entire neurons down to spines, outperforming state-of-the-art tools. The framework will empower image processing of complex neuronal circuitries.

Applications of Tissue Clearing in Central and Peripheral Nerves

The techniques of tissue clearing have been proposed and applied in anatomical and biomedical research since the 19th century. As we all know, the original study of the nervous system relied on serial ultrathin sections and stereoscopic techniques. The 3D visualization of the nervous system was established by software splicing and reconstruction. With the development of science and technology, microscope equipment had constantly been upgraded. Despite the great progress that has been made in this field, the workload is too complex, and it needs high technical requirements. Abundant mistakes due to manual sections were inescapable and structural integrity remained questionable. According to the classification of tissue transparency methods, we introduced the latest application of transparency methods in central and peripheral nerve research from optical imaging, molecular markers and data analysis. This review summarizes the application of transparent technology in neural pathways. We hope to provide some inspiration for the continuous optimization of tissue clearing methods.

Imaging Approach in the Diagnostics and Evaluation of the Psoriasis Plaque: A Preliminary Study and Literature Review

(1) Background: the aim of the study was to demonstrate its usefulness in the field of imaging evaluation of plaque morphology in psoriasis vulgaris, with an emphasis on the use of confocal microscopy and other advanced skin-imaging techniques. (2) Methods: we conducted a prospective study over two years (July 2022-April 2024), on patients diagnosed with moderate or severe psoriasis vulgaris, treated in the dermatology department of our institution. We selected 30 patients, of whom 15 became eligible according to the inclusion and the exclusion criteria. A total of 60 psoriasis plaques were analyzed by dermatoscopy using a Delta 30 dermatoscope and Vidix 4.0 videodermoscope (VD), by cutaneous ultrasound (US) using a high-resolution 20 MHz linear probe, and by confocal microscopy, along with histopathological analysis. (3) Results: the study included fifteen patients with vulgar psoriasis, diagnosed histopathologically, of whom six were women and nine were men, with an average age of 55. Between two and six plaques per patient were selected and a total of sixty psoriasis plaques were analyzed by non-invasive imaging techniques. Twelve lesions were analyzed with ex vivo fluorescence confocal microscopy (FCM), compared to histology. US showed that the hyperechoic band and the lack of damage to the subcutaneous tissue were the most common criteria. The epidermis and dermis were found to be thicker in the area of psoriasis plaques compared to healthy skin. Dermatoscopy showed that the specific aspect of psoriasis plaques localized on the limbs and trunk was a lesion with an erythematous background, with dotted vessels with regular distribution on the surface and covered by white scales with diffuse distribution. The presence of bushy vessels with medium condensation was the most frequently identified pattern on VD. Good correlations were identified between the histological criteria and those obtained through confocal microscopy. (4) Conclusions: the assessment and monitoring of patients with psoriasis vulgaris can be conducted in a more complete and all-encompassing manner by incorporating dermatoscopy, ultrasonography, and confocal microscopy in clinical practice.

Comparison between Conventional and Digital Impressions for Determining Axes and Distances of Three Implants in Straight and Curved Lines: An In Vitro Study

Background: In this study, we aimed to compare the effects of conventional and digital impressions on several parameters (inter-implant distance, intra-implant distance, inter-implant axis, and intra-implant axis) of three implants in curved lines and straight lines by using a laboratory scanner (LBS) versus an intra-oral scanner (IOS). Methods: Two 3D models were fabricated using a printer, each model with three internal hex implants analogues at the positions of 15#,16#,17# (straight line) and 12#,13#,14# (curved line). Standard intra-oral scan bodies (ISBs) were used, and the two models were scanned using 7 Series dental wings (LBS, reference model), followed by ten scans with Primescan (digital method). Standard Tessellation Language (STL) files were created. Five polyether impressions were taken from each model (straight and curved), and gypsum type 4 models were poured; each model was scanned five times to create a total of 25 STL files for each group (conventional method). The comparison between all the STL files (conventional and digital) was made by superimposition of the STL files on the STL reference model laboratory file using a 3D analyzing software. A Kolmogorov-Smirnov test was performed, followed by Mann-Whitney tests and Wilcoxon signed-rank tests. (p < 0.05). Results: For the conventional method, the mean errors were significantly higher for the curved line model (12-14) compared to the straight line model (15-17) for most parameters (p < 0.05). For the digital method, the mean errors were significantly higher for the curved-line model (12-14) compared to the straight line model (15-17) in half of the parameters (p < 0.05). Within the curved line model (12-14) and the straight line model (15-17), the mean errors between the conventional method and the digital method were not significant for most variables. Conclusions: The difference between curved lines and straight lines has an impact on the mean error of the conventional method. Both methods are reliable for straight and curved lines in partially dentate situations.

Real-time, depth-resolved, in vivo multiphoton fluorescence lifetime imaging microscopy of agricultural herbicide treatments in plants

The development of effective and safe agricultural treatments requires sub-cellular insight of the biochemical effects of treatments in living tissue in real-time. Industry-standard mass spectroscopic imaging lacks real-time in vivo capability. As an alternative, multiphoton fluorescence lifetime imaging microscopy (MPM-FLIM) allows for 3D sub-cellular quantitative metabolic imaging but is often limited to low frame rates. To resolve relatively fast effects (e.g., photosynthesis inhibiting treatments), high-frame-rate MPM-FLIM is needed. In this paper, we demonstrate and evaluate a high-speed MPM-FLIM system, "Instant FLIM", as a time-resolved 3D sub-cellular molecular imaging system in highly scattering, living plant tissues. We demonstrate simultaneous imaging of cellular autofluorescence and crystalline agrochemical crystals within plant tissues. We further quantitatively investigate the herbicidal effects of two classes of agricultural herbicide treatments, photosystem II inhibiting herbicide (Basagran) and auxin-based herbicide (Arylex), and successfully demonstrate the capability of the MPM-FLIM system to measure biological changes over a short time with enhanced imaging speed. Results indicate that high-frame-rate 3D MPM-FLIM achieves the required fluorescence lifetime resolution, temporal resolution, and spatial resolution to be a useful tool in basic plant cellular biology research and agricultural treatment development.

Scan-less microscopy based on acousto-optic encoded illumination

Several optical microscopy methods are now available for characterizing scientific and industrial processes at sub-micron resolution. However, they are often ill-suited for imaging rapid events. Limited by the trade-off between camera frame-rate and sensitivity, or the need for mechanical scanning, current microscopes are optimized for imaging at hundreds of frames-per-second (fps), well-below what is needed in processes such as neuronal signaling or moving parts in manufacturing lines. Here, we present a scan-less technology that allows sub-micrometric imaging at thousands of fps. It is based on combining a single-pixel camera with parallelized encoded illumination. We use two acousto-optic deflectors (AODs) placed in a Mach-Zehnder interferometer and drive them simultaneously with multiple and unique acoustic frequencies. As a result, orthogonal light stripes are obtained that interfere with the sample plane, forming a two-dimensional array of flickering spots - each with its modulation frequency. The light from the sample is collected with a single photodiode that, after spectrum analysis, allows for image reconstruction at speeds only limited by the AOD's bandwidth and laser power. We describe the working principle of our approach, characterize its imaging performance as a function of the number of pixels - up to 400 × 400 - and characterize dynamic events at 5000 fps.

Concordance of in vivo reflectance confocal microscopy and horizontal-sectioning histology in skin tumours

BACKGROUND

In vivo reflectance confocal microscopy (RCM) enables the study of architectural and cytological aspects in horizontal sections, which closely correlate with histologic features. However, traditional histopathological vertical sections cannot totally reproduce the image of the in vivo RCM horizontal section.

OBJECTIVE

To evaluate the concordance between in vivo RCM and histopathologic transverse sections for melanocytic lesions, basal cell carcinoma and seborrheic keratoses.

METHODS

Prospectively collected benign melanocytic and non-melanocytic tumours diagnosed by dermoscopy were evaluated for common RCM features and compared to histopathology in horizontal sections with haematoxylin and eosin staining.

RESULTS

A total of 44 skin tumours including 19 melanocytic lesions (nine compound, five junctional and five intradermal nevi), 12 basal cell carcinomas and 13 seborrheic keratoses were collected in the Department of Dermatology of Hospital Clinic of Barcelona. The RCM features that had statistically significant agreement with the histopathological horizontal sections were the preserved and visible honeycomb pattern, well defined DEJ, small bright particles, dermal nests, tumour islands and dark silhouettes, clefting, collagen bundles, thickened collagen bundles and cytologic atypia.

CONCLUSIONS

Histopathology evaluation of horizontal sections of skin tumours can be correlated with main RCM findings. The results of this study have improved the understanding and interpretation of RCM features in relation to skin tumours, thus reinforcing the utility of RCM as a diagnostic tool.

In vivo evaluation of skin of children with LC-OCT: An objective assessment

BACKGROUND

Several non-invasive skin imaging methods have been developed in recent years. Line-field confocal optical coherence tomography (LC-OCT) is one of them, leading to the best compromise in terms of resolution and penetration depth. Skin biopsies are an essential technique in paediatric dermatology, but they are a major stressful event for the child and their parents. Current LC-OCT studies have not been dedicated to a paediatric population. If, however, LC-OCT proves to be helpful in children, it may help guide and decrease a certain number of skin biopsies.

OBJECTIVES

(1) To evaluate the feasibility of using LC-OCT in paediatric patients, and (2) to assess the maturation of skin structures in children over time with this method.

METHODS

In vivo LC-OCT images were collected on six specific body regions (forehead, forearm, chest, back, dorsum of the hand and palmar surface) and in six age groups (between the ages of 0 and 16 years).

RESULTS

In all body areas and age groups assessed, 9 of 10 images were rated as good-to-excellent, the only exception were the images acquired on the palmar surface. LC-OCT allowed visualizing very well the skin structures up to a penetration of 500 μm. We observed that the body regions located on the upper extremities of the body (forearm, dorsum of the hand and palmar surface) showed both a maturation on their structure and differences in thickness with respect to the other regions evaluated.

CONCLUSIONS

LC-OCT can easily be used for non-invasive imaging of children's skin and allows to document progressive skin changes in the different age groups. It may be a useful asset for imaging and diagnosing superficial skin disorders and as such reducing the number of invasive procedures while increasing the speed of diagnosis in the paediatric population.

A weak-labelling and deep learning approach for in-focus object segmentation in 3D widefield microscopy

Three-dimensional information is crucial to our understanding of biological phenomena. The vast majority of biological microscopy specimens are inherently three-dimensional. However, conventional light microscopy is largely geared towards 2D images, while 3D microscopy and image reconstruction remain feasible only with specialised equipment and techniques. Inspired by the working principles of one such technique-confocal microscopy, we propose a novel approach to 3D widefield microscopy reconstruction through semantic segmentation of in-focus and out-of-focus pixels. For this, we explore a number of rule-based algorithms commonly used for software-based autofocusing and apply them to a dataset of widefield focal stacks. We propose a computation scheme allowing the calculation of lateral focus score maps of the slices of each stack using these algorithms. Furthermore, we identify algorithms preferable for obtaining such maps. Finally, to ensure the practicality of our approach, we propose a surrogate model based on a deep neural network, capable of segmenting in-focus pixels from the out-of-focus background in a fast and reliable fashion. The deep-neural-network-based approach allows a major speedup for data processing making it usable for online data processing.

Acquisition and annotation in high resolution in vivo digital biopsy by confocal microscopy for diagnosis in oral precancer and cancer

Introduction

Scanned fibre endomicroscopes are full point-scanning confocal microscopes with submicron lateral resolution with an optical slice thickness thin enough to isolate individual cell layers, allow active positioning of the optical slice in the z-axis and collection of megapixel images. Here we present descriptive findings and a brief atlas of an acquisition and annotation protocol high resolution in vivo capture of oral mucosal pathology including oral squamous cell carcinoma and dysplasia using a fluorescence scanned fibre endomicroscope with 3 topical fluorescent imaging agents: fluorescein, acriflavine and PARPi-FL.

Methods

Digital biopsy was successfully performed via an acquisition protocol in seventy-one patients presenting for investigation of oral mucosal abnormalities using a miniaturized, handheld scanned fibre endoscope. Multiple imaging agents were utilized and multiple time points sampled. Fifty-nine patients had a matched histopathology correlating in location with imaging. The images were annotated back to macrographic location using a purpose-built software, MouthMap™.

Results

Acquisition and annotation of cellular level resolved images was demonstrated with all 3 topical agents. Descriptive observations between clinically or histologically normal oral mucosa showed regular intranuclear distance, a regular nuclear profile and fluorescent homogeneity. This was dependent on the intraoral location and type of epithelium being observed. Key features of malignancy were a loss of intranuclear distance, disordered nuclear clustering and irregular nuclear fluorescence intensity and size. Perinuclear fluorescent granules were seen in the absence of irregular nuclear features in lichenoid inflammation.

Discussion

High resolution oral biopsy allows for painless and rapid capture of multiple mucosal sites, resulting in more data points to increase diagnostic precision. High resolution digital micrographs can be easily compared serially across multiple time points utilizing an annotation software. In the present study we have demonstrated realization of a high-resolution digital biopsy protocol of the oral mucosa for utility in the diagnosis of oral cancer and precancer..

In vivo detection of healthy skin: Comparison of multiphoton microscopy and reflectance confocal microscopy

BACKGROUND

Noninvasive skin examination evolved rapidly in recent years, with multiphoton microscopy (MPM) and reflectance confocal microscopy (RCM) being used to image in-vivo skin at high resolution. The aim of this study is to compare the imaging clarity between the two techniques and measure the thickness of the epidermis in different body sites. We also measured the degree of skin aging with noninvasive tools.

METHODS

Fifty-six volunteers were evaluated and measured at three different body sites, including the cheek, volar forearm, and back. We used RCM and MPM to evaluate the clarity of each skin layer, including stratum corneum, stratum granulosum, stratum spinosum, dermo-epidermal junction, and dermis. We measured epidermal thickness (ET) at the three body sites in individuals of different ages and genders. We assessed skin aging by the second harmonic to autofluorescence aging index of dermis (SAAID), and multiple linear regression was used to analyze the factors affecting SAAID.

RESULTS

MPM had advantages in observation of stratum granulosum, collagen fiber, and elastic fiber (p < 0.001), but RCM provided better observation in dermo-epidermal junction layer (p < 0.001). The epidermis was thicker in the cheek area than the volar forearm and back in both RCM and MPM detection, and the average ET measured by MPM was lower than RCM. ET varied among the three body sites with significant differences (p < 0.05). ET was significantly lower at almost all sites in individuals above 40y (p < 0.05). SAAID decreased with age, and more rapidly in women. Cheeks have lower SAAID scores than other body sites.

CONCLUSION

MPM and RCM provide noninvasive methods for imaging skin and each method has its own advantages. Epidermal thickness and SAAID correlated with age, gender, and different body sites. MPM could also assess the degree of skin aging, which could guide the clinical treatment of patients with diffferent ages and genders in the above body sites.

Super-resolution reconstruction, recognition, and evaluation of laser confocal images of hyperaccumulator Solanum nigrum endocytosis vesicles based on deep learning: Comparative study of SRGAN and SRResNet

It is difficult for laser scanning confocal microscopy to obtain high- or ultra-high-resolution laser confocal images directly, which affects the deep mining and use of the embedded information in laser confocal images and forms a technical bottleneck in the in-depth exploration of the microscopic physiological and biochemical processes of plants. The super-resolution reconstruction model (SRGAN), which is based on a generative adversarial network and super-resolution reconstruction model (SRResNet), which is based on a residual network, was used to obtain single and secondary super-resolution reconstruction images of laser confocal images of the root cells of the hyperaccumulator Solanum nigrum. Using the peak signal-to-noise ratio (PSNR), structural similarity (SSIM) and mean opinion score (MOS), the models were evaluated by the image effects after reconstruction and were applied to the recognition of endocytic vesicles in Solanum nigrum root cells. The results showed that the single reconstruction and the secondary reconstruction of SRGAN and SRResNet improved the resolution of laser confocal images. PSNR, SSIM, and MOS were clearly improved, with a maximum PSNR of 47.690. The maximum increment of PSNR and SSIM of the secondary reconstruction images reached 21.7% and 2.8%, respectively, and the objective evaluation of the image quality was good. However, overall MOS was less than that of the single reconstruction, the perceptual quality was weakened, and the time cost was more than 130 times greater. The reconstruction effect of SRResNet was better than that of SRGAN. When SRGAN and SRResNet were used for the recognition of endocytic vesicles in Solanum nigrum root cells, the clarity of the reconstructed images was obviously improved, the boundary of the endocytic vesicles was clearer, and the number of identified endocytic vesicles increased from 6 to 9 and 10, respectively, and the mean fluorescence intensity was enhanced by 14.4% and 7.8%, respectively. Relevant research and achievements are of great significance for promoting the application of deep learning methods and image super-resolution reconstruction technology in laser confocal image studies.

Multiscale microscopy to decipher plant cell structure and dynamics

New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.

Three-dimensional mouse cochlea imaging based on the modified Sca/eS using confocal microscopy

The three-dimensional stria vascularis (SV) and cochlear blood vessel structure is essential for inner ear function. Here, modified Sca/eS, a sorbitol-based optical-clearing method, was reported to visualize SV and vascular structure in the intact mouse cochlea. Cochlear macrophages as well as perivascular-resident macrophage-like melanocytes were detected as GFP-positive cells of the CX3CR1^+/GFP mice. This study's method was effective in elucidating inner ear function under both physiological and pathological conditions.

Emerging tools for studying receptor endocytosis and signaling

Ligands, agonists, or antagonists use receptor-mediated endocytosis (RME) to reach their intracellular targets. After the internalization of ligand-receptor complexes, it traffics through different subcellular organelles such as early endosome, recycling endosome, lysosome, etc. Further, after the ligand binding to the receptor, different second messengers are generated, such as cGMP, cAMP, IP₃, etc. Several methods have been used, such as radioligand binding assay, western blotting, co-immunoprecipitation (co-IP), qRT-PCR, immunofluorescence and confocal microscopy, microRNA/siRNA, and bioassays to understand the various events, such as internalization, subcellular trafficking, signaling, metabolic degradation, etc. This chapter briefly discusses the key principles and methods used to study internalization, subcellular trafficking, signaling, and metabolic degradation of numerous receptors.

Phase-quadrature quantum imaging with undetected photons

Sensing with undetected photons allows access to spectral regions with simultaneous detection of photons of another region and is based on nonlinear interferometry. To obtain the full information of a sample, the corresponding interferogram has to be analyzed in terms of amplitude and phase, which has been realized so far by multiple measurements followed by phase variation. Here, we present a polarization-optics-based phase-quadrature implementation in a nonlinear interferometer for imaging with undetected photons in the infrared region. This allows us to obtain phase and visibility with a single image acquisition without the need of varying optical paths or phases, thus enabling the detection of dynamic processes. We demonstrate the usefulness of our method on a static phase mask opaque to the detected photons as well as on dynamic measurement tasks as the drying of an isopropanol film and the stretching of an adhesive tape.

Developments and Clinical Applications of Noninvasive Optical Technologies for Skin Cancer Diagnosis

Skin cancer has shown a sharp increase in prevalence over the past few decades and currently accounts for one-third of all cancers diagnosed. The most lethal form of skin cancer is melanoma, which develops in 4% of individuals. The rising prevalence and increased number of fatalities of skin cancer put a significant burden on healthcare resources and the economy. However, early detection and treatment greatly improve survival rates for patients with skin cancer. Since the rising rates of both the incidence and mortality have been particularly noticeable with melanoma, significant resources have been allocated to research aimed at earlier diagnosis and a deeper knowledge of the disease. Dermoscopy, reflectance confocal microscopy, optical coherence tomography, multiphoton-excited fluorescence imaging, and dermatofluorescence are only a few of the optical modalities reviewed here that have been employed to enhance noninvasive diagnosis of skin cancer in recent years. This review article discusses the methodology behind newly emerging noninvasive optical diagnostic technologies, their clinical applications, and advantages and disadvantages of these techniques, as well as the potential for their further advancement in the future.

Non-contact optical in-vivo sensing of cilia motion by analyzing speckle patterns

Cilia motion is an indicator of pathological-ciliary function, however current diagnosis relies on biopsies. In this paper, we propose an innovative approach for sensing cilia motility. We present an endoscopic configuration for measuring the motion frequency of cilia in the nasal cavity. The technique is based on temporal tracking of the reflected spatial distribution of defocused speckle patterns while illuminating the cilia with a laser. The setup splits the optical signal into two channels; One imaging channel is for the visualization of the physician and another is, defocusing channel, to capture the speckles. We present in-vivo measurements from healthy subjects undergoing endoscopic examination. We found an average motion frequency of around 7.3 Hz and 9.8 Hz in the antero-posterior nasal mucus (an area rich in cilia), which matches the normal cilia range of 7–16 Hz. Quantitative and precise measurements of cilia vibration will optimize the diagnosis and treatment of pathological-ciliary function. This method is simple, minimally invasive, inexpensive, and promising to distinguish between normal and ciliary dysfunction.

In vivo tracking of individual stem cells labeled with nanowire lasers using multimodality imaging

Emerging cell-based regenerative medicine and stem cell therapies have drawn wide attention in medical research and clinical practice to treat tissue damage and numerous incurable diseases. In vivo observation of the distribution, migration, and development of the transplanted cells is important for both understanding the mechanism and evaluating the treatment efficacy and safety. However, tracking the 3D migration trajectories for individual therapeutic cells in clinically relevant pathological environments remains technically challenging. Using a laser photocoagulation model in living rabbit eyes, this study demonstrates a multimodality imaging technology integrating optical coherence tomography (OCT), fluorescence microscopy (FM), and lasing emission for in vivo longitudinal tracking of the 3D migration trajectories of individual human retinal pigment epithelium cells (ARPE-19) labeled with CdS nanowires. With unique lasing spectra generated from the subtle microcavity differences, the surface-modified nanowires perform as distinct spectral identifiers for labeling individual ARPE-19 cells. Meanwhile, with strong optical scattering and natural fluorescence emission, CdS nanowires also served as OCT and FM contrast agents to indicate the spatial locations of the transplanted ARPE-19 cells. A longitudinal study of tracking individual ARPE-19 cells in rabbit eyes over a duration of 28 days was accomplished. This method could potentially promote an understanding of the pharmacodynamics and pharmacokinetics of implanted cells in the development of cell-based therapies.

What is the best technic to dislodge Staphylococcus epidermidis biofilm on medical implants?

Background

Bacterial biofilm can occur on all medical implanted devices and lead to infection and/or dysfunction of the device.

In this study, artificial biofilm was formed on four different medical implants (silicone, piccline, peripheral venous catheter and endotracheal tube) of interest for our daily clinical and/or research practice. We investigated the best conventional technic to dislodge the biofilm on the implants and quantified the number of bacteria. Staphylococcus epidermidis previously isolated from a breast implant capsular contracture on a patient in the university hospital of Dijon was selected for its ability to produce biofilm on the implants. Different technics (sonication, Digest-EUR®, mechanized bead mill, combination of sonication plus Digest-EUR®) were tested and compared to detach the biofilm before quantifying viable bacteria by colony counting.

Results

For all treatments, the optical and scanning electron microscope images showed substantial less biofilm biomass remaining on the silicone implant compared to non-treated implant.

This study demonstrated that the US procedure was statistically superior to the other physical treatment: beads, Digest-EUR® alone and Digest-EUR® + US (p < 0.001) for the flexible materials (picc-line, PIV, and silicone). The number of bacteria released by the US is significantly higher with a difference of 1 log on each material. The result for a rigid endotracheal tube were different with superiority for the chemical treatment dithiothreitol: Digest-EUR®. Surprisingly the combination of the US plus Digest-EUR® treatment was consistently inferior for the four materials.

Conclusions

Depending on the materials used, the biofilm dislodging technique must be adapted. The US procedure was the best technic to dislodge S. epidermidis biofilm on silicone, piccline, peripheral venous catheter but not endotracheal tube. This suggested that scientists should compare themselves different methods before designing a protocol of biofilm study on a given material.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02606-x.

Foldscope microscope, an inexpensive alternative tool to conventional microscopy-Applications in research and education: A review

Microscope is a device used for the visualization of tiny objects which are not visible to the naked eye. Traditional microscopes have been crucial for the advancement of contemporary science and medicine. Recent advancements in the field of microscopy have fueled its exponential growth rate. However, due to their expensive cost and complicated structure, modern microscopes remain inaccessible to the majority of the public. Nonetheless, the foldscope paper microscope has made it possible for anyone to explore and understand the world of microbes and organisms. In this review, we have listed foldscope-based research projects in various domains, as well as their key properties when compared to traditional research microscopes. In addition, we have briefly explored the impact of a foldscope microscope on public health, clinical diagnostics, forensic science, agriculture, basic science, developmental biology, and education. Moreover, the major drawbacks of paper microscopes and the current steps being taken to upgrade foldscope and its features are discussed in this review. Finally, we have concluded with our perspective that the microscope may be updated to imitate the advancement of a conventional microscope. RESEARCH HIGHLIGHTS: The foldscope, a low-cost instrument for studying the microscopic world. Foldscope applications were compared to conventional microscopes in many sectors. The foldscope microscope's existing limitations and potential prospects are highlighted.

MIL-125-based nanocarrier decorated with Palladium complex for targeted drug delivery

The aim of this work was to provide a novel approach to designing and synthesizing a nanocomposite with significant biocompatibility, biodegradability, and stability in biological microenvironments. Hence, the porous ultra-low-density materials, metal–organic frameworks (MOFs), have been considered and the MIL-125(Ti) has been chosen due to its distinctive characteristics such as great biocompatibility and good biodegradability immobilized on the surface of the reduced graphene oxide (rGO). Based on the results, the presence of transition metal complexes next to the drug not only can reinforce the stability of the drug on the structure by preparing π–π interaction between ligands and the drug but also can enhance the efficiency of the drug by preventing the spontaneous release. The effect of utilizing transition metal complex beside drug (Doxorubicin (DOX)) on the drug loading, drug release, and antibacterial activity of prepared nanocomposites on the P. aeruginosa and S. aureus as a model bacterium has been investigated and the results revealed that this theory leads to increasing about 200% in antibacterial activity. In addition, uptake, the release of the drug, and relative cell viabilities (in vitro and in vivo) of prepared nanomaterials and biomaterials have been discussed. Based on collected data, the median size of prepared nanocomposites was 156.2 nm, and their biological stability in PBS and DMEM + 10% FBS was screened and revealed that after 2.880 min, the nanocomposite’s size reached 242.3 and 516 nm respectively. The MTT results demonstrated that immobilizing PdL beside DOX leads to an increase of more than 15% in the cell viability. It is noticeable that the AST:ALT result of prepared nanocomposite was under 1.5.

Real-time observation of neutrophil extracellular trap formation in the inflamed mouse brain via two-photon intravital imaging

Intravital imaging via two-photon microscopy (TPM) is a useful tool for observing and delineating biological events at the cellular and molecular levels in live animals in a time-lapse manner. This imaging method provides spatiotemporal information with minimal phototoxicity while penetrating a considerable depth of intact organs in live animals. Although various organs can be visualized using intravital imaging, in the field of neuroscience, the brain is the main organ whose cell-to-cell interactions are imaged using this technique. Intravital imaging of brain disease in mouse models acts as an abundant source of novel findings for studying cerebral etiology. Neutrophil infiltration is a well-known hallmark of inflammation; in particular, the crucial impact of neutrophils on the inflamed brain has frequently been reported in literature. Neutrophil extracellular traps (NETs) have drawn attention as an intriguing feature over the last couple of decades, opening a new era of research on their underlying mechanisms and biological effects. However, the actual role of NETs in the body is still controversial and is in parallel with a poor understanding of NETs in vivo. Although several experimental methods have been used to determine NET generation in vitro, some research groups have applied intravital imaging to detect NET formation in the inflamed organs of live mice. In this review, we summarize the advantages of intravital imaging via TPM that can also be used to characterize NET formation, especially in inflamed brains triggered by systemic inflammation. To study the function and migratory pattern of neutrophils, which is critical in triggering the innate immune response in the brain, intravital imaging via TPM can provide new perspectives to understand inflammation and the resolution process.

Research Techniques Made Simple: Emerging Imaging Technologies for Noninvasive Optical Biopsy of Human Skin

Over the past few years, high-resolution optical imaging technologies such as optical coherence tomography (OCT), reflectance confocal microscopy (RCM), and multiphoton microscopy (MPM) have advanced significantly as new methodologies for clinical research and for real-time detection, diagnosis, and therapy monitoring of skin diseases. Implementation of these technologies into clinical research and practice requires clinicians to have an understanding of their capabilities, benefits, and limitations. This concise review provides insights on the application of OCT, RCM, and MPM for clinical skin imaging through images acquired in vivo from the same lesions. The presented data are limited to pigmented lesions and basal cell carcinoma.

Optical Modalities for Research, Diagnosis, and Treatment of Stroke and the Consequent Brain Injuries

Stroke is the second most common cause of death and third most common cause of disability worldwide. Therefore, it is an important disease from a medical standpoint. For this reason, various studies have developed diagnostic and therapeutic techniques for stroke. Among them, developments and applications of optical modalities are being extensively studied. In this article, we explored three important optical modalities for research, diagnostic, and therapeutics for stroke and the brain injuries related to it: (1) photochemical thrombosis to investigate stroke animal models; (2) optical imaging techniques for in vivo preclinical studies on stroke; and (3) optical neurostimulation based therapy for stroke. We believe that an exploration and an analysis of previous studies will help us proceed from research to clinical applications of optical modalities for research, diagnosis, and treatment of stroke.

New Label-Free Biosensing for the Evaluation of the AX-024 Inhibitor: Case Study for the Development of New Drugs in Autoimmune Diseases

We developed a new label-free assay to evaluate the inhibition capacity of AX-024 by means of a new Point-of-Care (PoC) device for application in the development of new drugs in autoimmune diseases. The technology of PoC is based on interferometric optical detection method (IODM). For this purpose, we have optimized and developed an assay protocol whereby a Glutathione S-Transferase modified protein (GST-SH3.1), which contains a functional domain of a protein involved in T-cell activation, together with the AX-024 inhibitor has been studied. The chips used are a sensing surface based on nitrocellulose. We used streptavidin and a biotinylated peptide as links for the immobilization process on the sensing surface. The biotinylated peptide and AX-024 inhibitor compete for the same functional group of the GST-SH3.1 modified protein. When the inhibitor binds its binding site on GST-SH3.1, the biotinylated peptide cannot bind to its pocket on the protein. This competition reduces the total molecular mass of protein fixed onto the biosensor. In order to quantify the inhibition capacity of AX-024, several Ax-024:GST-SH3.1 ratios have been studied. We have compared the read-out signal for GST-SH3.1 protein not interfered by the drug, which served as a positive blank, and the response of the GST-SH3.1 modified protein blocked by the inhibitor. The technology has been correlated with confocal fluorescence microscopy.

Fluorescence Microscopy-Based Quantitation of GLUT4 Translocation

Postprandial insulin-stimulated glucose uptake into target tissue is crucial for the maintenance of normal blood glucose homeostasis. This step is rate-limited by the number of facilitative glucose transporters type 4 (GLUT4) present in the plasma membrane. Since insulin resistance and impaired GLUT4 translocation are associated with the development of metabolic disorders such as type 2 diabetes, this transporter has become an important target of antidiabetic drug research. The application of screening approaches that are based on the analysis of GLUT4 translocation to the plasma membrane to identify substances with insulinomimetic properties has gained global research interest in recent years. Here, we review methods that have been implemented to quantitate the translocation of GLUT4 to the plasma membrane. These methods can be broadly divided into two sections: microscopy-based technologies (e.g., immunoelectron, confocal or total internal reflection fluorescence microscopy) and biochemical and spectrometric approaches (e.g., membrane fractionation, photoaffinity labeling or flow cytometry). In this review, we discuss the most relevant approaches applied to GLUT4 thus far, highlighting the advantages and disadvantages of these approaches, and we provide a critical discussion and outlook into new methodological opportunities.

Use of Reflectance Confocal Microscopy to Predict Treatment Efficacy in Café Au Lait Macules

BACKGROUND

Multiple lasers have been used for the treatment of café au lait macules (CALMs) with various results. Objective tools to predict therapeutic efficacy of CALMs treatment is lacking.

OBJECTIVE

To determine whether reflectance confocal microscopy (RCM) characteristics correlate with CALMs response to laser treatment.

MATERIALS AND METHODS

All CAMLs underwent RCM examination of length and density of dermal papillae followed by 3 sessions of Q-switched alexandrite laser (QSAL). A visual analog scale was used to assess clinical treatment efficacy.

RESULTS

Forty-three patients were included, 22 had CALMs with irregular borders and 21 with smooth borders. Café au lait macules with irregular border had shorter rete pegs and less papillae (p < .05) on RCM compared with smooth border CAMLs and responded better to QSAL treatment (2.32 vs 1.10).

CONCLUSION

Reflectance confocal microscopy measurement of length and density of papillae were inversely correlated with treatment response. Reflectance confocal microscopy may be a useful tool to predict CALMs response to laser treatment.

3D monitoring of the surface slippage effect on micro-particle sedimentation by digital holographic microscopy

In several phenomena in biology and industry, it is required to understand the comprehensive behavior of sedimenting micro-particles in fluids. Here, we use the numerical refocusing feature of digital holographic microscopy (DHM) to investigate the slippage effect on micro-particle sedimentation near a flat wall. DHM provides quantitative phase contrast and three-dimensional (3D) imaging in arbitrary time scales, which suggests it as an elegant approach to investigate various phenomena, including dynamic behavior of colloids. 3D information is obtained by post-processing of the recorded digital holograms. Through analysis of 3D trajectories and velocities of multiple sedimenting micro-particles, we show that proximity to flat walls of higher slip lengths causes faster sedimentation. The effect depends on the ratio of the particle size to (1) the slip length and (2) its distance to the wall. We corroborate our experimental findings by a theoretical model which considers both the proximity and the particle interaction to a wall of different hydrophobicity in the hydrodynamic forces.

Transmissive Single-Pixel Microscopic Imaging through Scattering Media

Microscopic imaging is of great significance for medical diagnosis. However, due to the strong scattering and absorption of tissue, the implementation of non-invasive microscopic imaging is very difficult. Traditional single-pixel microscopes, based on reflective optical systems, provide an alternative solution for scattering media imaging. Here, the single-pixel microscope with transmissive liquid crystal modulation is proposed. The microscopic ability of the proposed microscope is calibrated. The multi-spectral microscopic imaging of the object is demonstrated. The transmissive imaging of the object behind the scattering media is analyzed. The proposed prototype of the transmissive single-pixel microscope is expected to be applied in microscopic imaging through scattering media and medical imaging.

Non-invasive optical methods for melanoma diagnosis

Cutaneous melanoma is one of the most common malignancies with increased incidence in the past few decades, making it a significant public health problem. The early diagnosis of melanoma is a major factor in improving patient's survival. The traditional pathway to melanoma diagnosis starts with a visual diagnosis, followed by subsequent biopsy and histopathologic evaluation. Recently, multiple innovative optical technology-based methods, including dermoscopy, reflectance confocal microscopy, optical coherence tomography, multiphoton excited fluorescence imaging and stepwise two-photon excited fluorescence (dermatofluoroscopy), have been developed to increase the diagnostic accuracy for the non-invasive melanoma diagnosis. Some of them have already been applied to real-life clinical settings, others require more research and development. These technologies show promise in facilitating the diagnosis of melanoma since they are non-invasive, sensitive, objective and easy to apply. Diagnostic accuracy, detection time, portability and the cost-effectiveness of the device are all aspects that need to be improved. This article reviews the method of these emerging optical non-invasive diagnostic technologies, their clinical application, their benefits and limitations, as well as their possible future development.

Pathogens electrogenicity as a tool for in-situ metabolic activity monitoring and drug assessment in biofilms

Concerns regarding increased antibiotic resistance arising from the emergent properties of biofilms have spurred interest in the discovery of novel antibiotic agents and techniques to directly estimate metabolic activity in biofilms. Although a number of methods have been developed to quantify biofilm formation, real-time quantitative assessment of metabolic activity in label-free biofilms remains a challenge. Production of electrical current via extracellular electron transport (EET) has recently been found in pathogens and appears to correlate with their metabolic activity. Accordingly, monitoring the production of electrical currents as an indicator of cellular metabolic activity in biofilms represents a new direction for research aiming to assess and screen the effects of antimicrobials on biofilm activity. In this article, we reviewed EET-capable pathogens and the methods to monitor biofilm activity to discuss advantages of using the capability of pathogens to produce electrical currents and effective combination of these methods. Moreover, we discussed EET mechanisms by pathogenic and environmental bacteria and open questions for the physiological roles of EET in pathogen's biofilm. The present limitations and possible future directions of in situ biofilm metabolic activity assessment for large-scale screening of antimicrobials are also discussed.

Cationic Dendrimers for siRNA Delivery: An Overview of Methods for In Vitro/In Vivo Characterization

This chapter reviews the different techniques for analyzing the chemical-physical properties, transfection efficiency, cytotoxicity, and stability of covalent cationic dendrimers (CCDs) and self-assembled cationic dendrons (ACDs) for siRNA delivery in the presence and absence of their nucleic cargos. On the basis of the reported examples, a standard essential set of techniques is described for each step of a siRNA/nanovector (NV) complex characterization process: (1) analysis of the basic chemical-physical properties of the NV per se; (2) characterization of the morphology, size, strength, and stability of the siRNA/NV ensemble; (3) characterization and quantification of the cellular uptake and release of the siRNA fragment; (4) in vitro and (5) in vivo experiments for the evaluation of the corresponding gene silencing activity; and (6) assessment of the intrinsic toxicity of the NV and the siRNA/NV complex.

High-quality Fluorescence Imaging of the Human Acrosyringium Using a Transparency: Enhancing Technique and an Improved, Fluorescent Solvatochromic Pyrene Probe

Two-photon, excitation fluorescent microscopy featuring autofluorescence or immunofluorescence, combined with optical clearance using a transparency-enhancing technique, allows deep imaging of three-dimensional (3D) skin structures. However, it remains difficult to obtain high-quality images of individual cells or 3D structures. We combined a new dye with a transparency-enhancing technology and performed high-quality structural analysis of human epidermal structures, especially the acrosyringium. Human fingertip skin samples were collected, formalin-fixed, embedded in both frozen and paraffin blocks, sliced, stained with propidium iodide, optically cleared using a transparency-enhancing technique, and stained with a new fluorescent, solvatochromic pyrene probe. Microscopy revealed fine skin features and detailed epidermal structures including the stratum corneum (horny layer), keratinocytes, eccrine sweat glands, and peripheral nerves. Three-dimensional reconstruction of an entire acrosyringium was possible in one sample. This new fluorescence microscopy technique yields high-quality epidermal images and will aid in histopathological analyses of skin disorders.

The use of the laser confocal scanning microscopy to measure resin remnants on customized lingual bracket

Background

The study aimed to evaluate the permanence of resin and enamel remains on lingual brackets at the end of orthodontic treatment and after the debonding procedure. The evaluation of resin remnants on customized lingual brackets bases has never done before in other studies because they are curved, and traditional techniques are not applicable.

Methods

The sample consisted of 100 lingual brackets (25 incisors, 25 canines, 25 premolars, 25 molars) scanned with a confocal laser microscope (OLS4000). We measured the brackets' surface and the area of resin remnants with the software of the microscope. Median and quartiles were presented to describe the data. ARI calculation was indirect for each tooth, measuring the resin remnants to the total surface of the bracket. The Kruskal-Wallis test and Fisher test were applied respectively to compare the percentages of remnants and the frequencies of the ARI between the four groups.

Results

After the analyses, 13 brackets had no adhesive remnants (ARI 0), 29 brackets had less than 50% of resin remnants (ARI 1), 50 brackets had more than 50% of resin remnants (ARI 2), and 8 brackets had 100% of adhesive (ARI 3). Canines brackets presented the lower amount of resin followed by premolars, incisors, and molars.

Conclusion

Lingual brackets showed a high frequency of ARI = 2. The median percentage of the bracket surface covered by resin was 41%. We observed a slight tendency of more resin remnants on molar brackets, due to half-pad configuration. The authors suggest paying attention during the debonding procedure of molar brackets since a stronger connection between the adhesive and the bracket mesh means a higher risk of enamel damage.

Basal Cell Carcinoma: From Pathophysiology to Novel Therapeutic Approaches

Basal cell carcinoma (BCC) is the most common human cancer worldwide, and is a subtype of nonmelanoma skin cancer, characterized by a constantly increasing incidence due to an aging population and widespread sun exposure. Although the mortality from BCC is negligible, this tumor can be associated with significant morbidity and cost. This review presents a literature overview of BCC from pathophysiology to novel therapeutic approaches. Several histopathological BCC subtypes with different prognostic values have been described. Dermoscopy and, more recently, reflectance confocal microscopy have largely improved BCC diagnosis. Although surgery is the first-line treatment for localized BCC, other nonsurgical local treatment options are available. BCC pathogenesis depends on the interaction between environmental and genetic characteristics of the patient. Specifically, an aberrant activation of Hedgehog signaling pathway is implicated in its pathogenesis. Notably, Hedgehog signaling inhibitors, such as vismodegib and sonidegib, are successfully used as targeted treatment for advanced or metastatic BCC. Furthermore, the implementation of prevention measures has demonstrated to be useful in the patient management.

Role of gold nanoparticles in advanced biomedical applications

Gold nanoparticles (GNPs) have generated keen interest among researchers in recent years due to their excellent physicochemical properties. In general, GNPs are biocompatible, amenable to desired functionalization, non-corroding, and exhibit size and shape dependent optical and electronic properties. These excellent properties of GNPs exhibit their tremendous potential for use in diverse biomedical applications. Herein, we have evaluated the recent advancements of GNPs to highlight their exceptional potential in the biomedical field. Special focus has been given to emerging biomedical applications including bio-imaging, site specific drug/gene delivery, nano-sensing, diagnostics, photon induced therapeutics, and theranostics. We have also elaborated on the basics, presented a historical preview, and discussed the synthesis strategies, functionalization methods, stabilization techniques, and key properties of GNPs. Lastly, we have concluded this article with key findings and unaddressed challenges. Overall, this review is a complete package to understand the importance and achievements of GNPs in the biomedical field.

From 2D to 3D: Promising Advances in Imaging Lung Structure

The delicate structure of murine lungs poses many challenges for acquiring high-quality images that truly represent the living lung. Here, we describe several optimized procedures for obtaining and imaging murine lung tissue. Compared to traditional paraffin cross-section and optimal cutting temperature (OCT), agarose-inflated vibratome sections (aka precision-cut lung slices), combines comparable structural preservation with experimental flexibility. In particular, we discuss an optimized procedure to precision-cut lung slices that can be used to visualize three-dimensional cell-cell interactions beyond the limitations of two-dimensional imaging. Super-resolution microscopy can then be used to reveal the fine structure of lung tissue's cellular bodies and processes that regular confocal cannot. Lastly, we evaluate the entire lung vasculature with clearing technology that allows imaging of the entire volume of the lung without sectioning. In this manuscript, we combine the above procedures to create a novel and evolutionary method to study cell behavior ex vivo, trace and reconstruct pulmonary vasculature, address fundamental questions relevant to a wide variety of vascular disorders, and perceive implications to better imaging clinical tissue.

Recent Advances in Luminescence Imaging of Biological Systems Using Lanthanide(III) Luminescent Complexes

The use of luminescence in biological systems allows one to diagnose diseases and understand cellular processes. Molecular systems, particularly lanthanide(III) complexes, have emerged as an attractive system for application in cellular luminescence imaging due to their long emission lifetimes, high brightness, possibility of controlling the spectroscopic properties at the molecular level, and tailoring of the ligand structure that adds sensing and therapeutic capabilities. This review aims to provide a background in luminescence imaging and lanthanide spectroscopy and discuss selected examples from the recent literature on lanthanide(III) luminescent complexes in cellular luminescence imaging, published in the period 2016-2020. Finally, the challenges and future directions that are pointing for the development of compounds that are capable of executing multiple functions and the use of light in regions where tissues and cells have low absorption will be discussed.

Spectroscopic Methods Used in Implant Material Studies

It is recognized that interactions between most materials are governed by their surface properties and manifest themselves at the interface formed between them. To gain more insight into this thin layer, several methods have been deployed. Among them, spectroscopic methods have been thoroughly evaluated. Due to their exceptional sensitivity, data acquisition speed, and broad material tolerance they have been proven to be invaluable tools for surface analysis, used by scientists in many fields, for example, implant studies. Today, in modern medicine the use of implants is considered standard practice. The past two decades of constant development has established the importance of implants in dentistry, orthopedics, as well as extended their applications to other areas such as aesthetic medicine. Fundamental to the success of implants is the knowledge of the biological processes involved in interactions between an implant and its host tissue, which are directly connected to the type of implant material and its surface properties. This review aims to demonstrate the broad applications of spectroscopic methods in implant material studies, particularly discussing hard implants, surface composition studies, and surface-cell interactions.

FeSe quantum dots for in vivo multiphoton biomedical imaging

An immense demand in biomedical imaging is to develop efficient photoluminescent probes with high biocompatibility and quantum yield, as well as multiphoton absorption performance to improve penetration depth and spatial resolution. Here, iron selenide (FeSe) quantum dots (QDs) are reported to meet these criteria. The synthesized QDs exhibit two- and three-photon excitation property at 800- and 1080-nm wavelengths and high quantum yield (ca. 40%), which are suitable for second-window imaging. To verify their biosuitability, poly(ethylene glycol)-conjugated QDs were linked with human epidermal growth factor receptor 2 (HER2) antibodies for in vitro/in vivo two-photon imaging in HER2-overexpressed MCF7 cells and a xenograft breast tumor model in mice. Imaging was successfully carried out at a depth of up to 500 μm from the skin using a nonlinear femtosecond laser at an excitation wavelength of 800 nm. These findings may open up a way to apply biocompatible FeSe QDs to multiphoton cancer imaging.

Reflectance Confocal Microscopy Can Help the Dermatopathologist in the Diagnosis of Challenging Skin Lesions

Despite the successful assignment of Current Procedural Terminology codes, there are barriers to incorporating in vivo reflectance confocal microscopy (RCM) into daily practice. Importantly, the dermatopathologist can play a key role in interpreting RCM images and can use these images to correlate with histopathology. Herein, we describe, using a case series, how RCM can be incorporated into the dermatopothalogist's practice. We also summarize the criteria for RCM diagnosis of common neoplasms.

Improved identification of DNA double strand breaks: γ-H2AX-epitope visualization by confocal microscopy and 3D reconstructed images

Currently, in the context of radiology, irradiation-induced and other genotoxic effects are determined by visualizing DSB-induced DNA repair through γ-H2AX immunofluorescence and direct counting of the foci by epifluorescence microscopy. This procedure, however, neglects the 3D nature of the nucleus. The aim of our study was to use confocal microscopy and 3D reconstructed images to improve documentation and analysis of γ-H2AX fluorescence signals after diagnostic examinations. Confluent, non-dividing MRC-5 lung fibroblasts were irradiated in vitro with a Cs-137 source and exposed to radiation doses up to 1000 mGy before fixation and staining with an antibody recognizing the phosphorylated histone variant γ-H2AX. The 3D distribution of γ-H2AX foci was visualized using confocal laser scanning microscopy. 3D reconstruction of the optical slices and γ-H2AX foci counting were performed using Imaris Image Analysis software. In parallel, γ-H2AX foci were counted visually by epifluorescence microscopy. In addition, whole blood was exposed ex vivo to the radiation doses from 200 to 1600 mGy. White blood cells (WBCs) were isolated and stained for γ-H2AX. In fibroblasts, epifluorescence microscopy alone visualized the entirety of fluorescence signals as integral, without correct demarcation of single foci, and at 1000 mGy yielded on average 11.1 foci by manual counting of 2D images in comparison to 36.1 foci with confocal microscopy and 3D reconstruction (p < 0.001). The procedure can also be applied for studies on WBCs. In contrast to epifluorescence microscopy, confocal microscopy and 3D reconstruction enables an improved identification of DSB-induced γ-H2AX foci, allowing for an unbiased, ameliorated quantification.