Open-source controller for low-cost and high-speed atomic force microscopy imaging of skin corneocyte nanotextures

An open-source combined atomic force microscope and optical microscope for mechanobiology studies

Atomic Force Microscopy (AFM) has become the gold standard tool for measuring mechanical properties of biological samples including proteins, single cells and tissues. However, investment in this specialized equipment and gaining expertise in its operation are significant obstacles for non-experts looking to adopt this technique. To address this, we have designed an AFM based mechanical measurement system for measuring cell mechanical properties which is combined with a custom inverted fluorescence microscope which can be used for characterizing mechanosensitive responses. This system, through its ease of use and low setup cost, will promote interdisciplinary research leading to new insights into the role of cell mechanics and mechanosensitive responses in physiology and disease.

A Review of Atomic-Force Microscopy in Skin Barrier Function Assessment

Skin barrier function (SBF) disorders are a class of pathologies that affect a significant portion of the world population. These disorders cause skin lesions with intense itch, impacting patients' physical and psychological well-being as well as their social functioning. It is in the interest of patients that their disorder be monitored closely while under treatment to evaluate the effectiveness of the ongoing therapy and any potential adverse reactions. Symptom-based assessment techniques are widely used by clinicians; however, they carry some limitations. Techniques to assess skin barrier impairment are critical for understanding the nature of the disease and for helping personalize treatment. This review recalls the anatomy of the skin barrier and describes an atomic-force microscopy approach to quantitatively monitor its disorders and their response to treatment. We review a panel of studies that show that this technique is highly relevant for SBF disorder research, and we aim to motivate its adoption into clinical settings.

Atomic force microscopy in disease-related studies: Exploring tissue and cell mechanics

Despite significant progress in human medicine, certain diseases remain challenging to promptly diagnose and treat. Hence, the imperative lies in the development of more exhaustive criteria and tools. Tissue and cellular mechanics exhibit distinctive traits in both normal and pathological states, suggesting that "force" represents a promising and distinctive target for disease diagnosis and treatment. Atomic force microscopy (AFM) holds great promise as a prospective clinical medical device due to its capability to concurrently assess surface morphology and mechanical characteristics of biological specimens within a physiological setting. This review presents a comprehensive examination of the operational principles of AFM and diverse mechanical models, focusing on its applications in investigating tissue and cellular mechanics associated with prevalent diseases. The findings from these studies lay a solid groundwork for potential clinical implementations of AFM. RESEARCH HIGHLIGHTS: By examining the surface morphology and assessing tissue and cellular mechanics of biological specimens in a physiological setting, AFM shows promise as a clinical device to diagnose and treat challenging diseases.

Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a noninvasive tool for skin barrier assessment

BACKGROUND

Corneocyte surface nanoscale topography (nanotexture) has recently emerged as a potential biomarker for inflammatory skin diseases, such as atopic dermatitis (AD). This assessment method involves quantifying circular nano-size objects (CNOs) in corneocyte nanotexture images, enabling noninvasive analysis via stratum corneum (SC) tape stripping. Current approaches for identifying CNOs rely on computer vision techniques with specific geometric criteria, resulting in inaccuracies due to the susceptibility of nano-imaging techniques to environmental noise and structural occlusion on the corneocyte.

RESULTS

This study recruited 45 AD patients and 15 healthy controls, evenly divided into 4 severity groups based on their Eczema Area and Severity Index scores. Subsequently, we collected a dataset of over 1,000 corneocyte nanotexture images using our in-house high-speed dermal atomic force microscope. This dataset was utilized to train state-of-the-art deep learning object detectors for identifying CNOs. Additionally, we implemented a kernel density estimator to analyze the spatial distribution of CNOs, excluding ineffective regions with minimal CNO occurrence, such as ridges and occlusions, thereby enhancing accuracy in density calculations. After fine-tuning, our detection model achieved an overall accuracy of 91.4% in detecting CNOs.

CONCLUSIONS

By integrating deep learning object detector with spatial analysis algorithms, we developed a precise methodology for calculating CNO density, termed the Effective Corneocyte Topographical Index (ECTI). The ECTI demonstrated exceptional robustness to nano-imaging artifacts and presents substantial potential for advancing AD diagnostics by effectively distinguishing between SC samples of varying AD severity and healthy controls.

Open hardware in microscopy

The field of microscopy has been empowering humankind for many centuries by enabling the observation of objects that are otherwise too small to detect for the naked human eye. Microscopy techniques can be loosely divided into three main branches, namely photon-based optical microscopy, electron microscopy, and scanning probe microscopy with optical microscopy being the most prominent one. On the high-end level, optical microscopy nowadays enables nanometer resolution covering many scientific disciplines ranging from material sciences over the natural sciences and life sciences to the food sciences. On the lower-end level, simplified hardware and openly available description and blueprints have helped to make powerful microscopes widely available to interested scientists and researchers. For this special issue, we invited contributions from the community to share their latest ideas, designs, and research results on open-source hardware in microscopy. With this collection of articles, we hope to inspire the community to further increase the accessibility, interoperability, and reproducibility of microscopy. We further touch on the standardization of methodologies and devices including the use of computerized control of data acquisition and data analysis to achieve high quality and efficiency in research and development.

MicroFPGA: An affordable FPGA platform for microscope control

Modern microscopy relies increasingly on microscope automation to improve throughput, ensure reproducibility or observe rare events. Automation requires computer control of the important elements of the microscope. Furthermore, optical elements that are usually fixed or manually movable can be placed on electronically-controllable elements. In most cases, a central electronics board is necessary to generate the control signals they require and to communicate with the computer. For such tasks, Arduino microcontrollers are widely used due to their low cost and programming entry barrier. However, they are limiting in their performance for applications that require high-speed or multiple parallel processes. Field programmable gate arrays (FPGA) are the perfect technology for high-speed microscope control, as they are capable of processing signals in parallel and with high temporal precision. While plummeting prices made the technology available to consumers, a major hurdle remaining is the complex languages used to configure them. In this work, we used an affordable FPGA, delivered with an open-source and friendly-to-use programming language, to create a versatile microscope control platform called MicroFPGA. It is capable of synchronously triggering cameras and multiple lasers following complex patterns, as well as generating various signals used to control microscope elements such as filter wheels, servomotor stages, flip-mirrors, laser power or acousto-optic modulators. MicroFPGA is open-source and we provide online Micro-Manager, Java, Python and LabVIEW libraries, together with blueprints and tutorials.