Agarose-based structured optical fibre

Low-cost, real-time detection of bacterial growth via diffraction-based sensing

The emergence of antibacterial resistance impacts healthcare networks globally, with mortality rates and linked burdens of infection disproportionately affecting the developing world. Rapid alternatives to antibiotic susceptibility testing (AST) allow for swifter, more effective treatment, though they are limited in use in low-resource settings due to significant cost barriers. Herein we demonstrate a simple, cost-effective diffraction sensing-based approach for rapidly detecting bacterial growth (a precursor to AST). Diffraction gratings (1D, lined) directly comprised of our test bacteria (Escherichia coli DH5α) were produced using soft agar-based gel templates designed to direct bacterial attachment and produce a near-zero background signal. The diffraction spot intensities from the live bacterial gratings were monitored in growth and no growth (ampicillin) conditions at room temperature, using a simple fixed laser and photodetector setup. Growth-induced differences in signal were observed within 10-20 minutes, highlighting the sensitivity of this approach and its potential to be adapted as a rapid and accessible AST alternative.

A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell

We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.

Mechanically Robust Biopolymer Optical Fibers with Enhanced Performance in the Near-Infrared Region

Polymer optical fibers (POFs) are lightweight, fatigue-tolerant, and suitable for local area networks, automobiles, aerospace, smart textiles, supercomputers, and servers. However, commercially available POFs are exclusively fabricated using synthetic polymers derived from nonrenewable resources. Recently, attempts have been made to fabricate biocompatible and biopolymeric optical fibers. However, their limitations in mechanical performance, thermal stability, and optical properties foil practical applications in waveguiding. Here, we report a comprehensive study of the preparation of biopolymer optical fibers with tailored mechanical strength, thermal properties, and their short-distance applications. Specifically, we use alginate as one of the key components with methylcelluloses to promote readily scalable wet spinning at ambient conditions to fabricate 21 combinations of composite fibers. The fibers display high maximum strain (up to 58%), Young's modulus (up to 11 GPa), modulus of toughness (up to 63 MJ/m3), and a high strength (up to 195 MPa), depending on the composition and fabrication conditions. The modulus of toughness is comparable to that of glass optical fibers, while the maximum strain is nearly 15 times higher. The mechanically robust fibers with high thermal stability allow rapid humidity, touch sensing, and complex shapes such as serpentine, coil, or twisted structures without losing their light transmission properties. More importantly, the fibers display enhanced optical performance and sensitivity in the near-infrared (NIR) region, making them suitable for advanced biomedical applications. Our work suggests that biobased materials offer innovative solutions to create short-distance optical fibers from fossil fuel-free resources with novel functionalities.

Hydrogel for light delivery in biomedical applications

Traditional optical waveguides or mediums are often silica-based materials, but their applications in biomedicine and healthcare are limited due to the poor biocompatibility and unsuitable mechanical properties. In term of the applications in human body, a biocompatible hydrogel system with excellent optical transparency and mechanical flexibility could be beneficial. In this review, we explore the different designs of hydrogel-based optical waveguides derived from natural and synthetic sources. We highlighted key developments such as light emitting contact lenses, implantable optical fibres, biosensing systems, luminating and fluorescent materials. Finally, we expand further on the challenges and perspectives for hydrogel waveguides to achieve clinical applications.

Imperfect refractive index matching in scanning laser optical tomography and a method for digital correction

Significance

Scanning laser optical tomography (SLOT) is a volumetric multi-modal imaging technique that is comparable to optical projection tomography and computer tomography. Image quality is crucially dependent on matching the refractive indexes (RIs) of the sample and surrounding medium, but RI matching often requires some effort and is never perfect.

Aim

Reducing the burden of RI matching between the immersion medium and sample in biomedical imaging is a challenging and interesting task. We aim at implementing a post processing strategy for correcting SLOT measurements that have errors caused by RI mismatch.

Approach

To better understand the problems with poorly matched Ris, simulated SLOT measurements with imperfect RI matching of the sample and medium are performed and presented here. A method to correct distorted measurements was developed and is presented and evaluated. This method is then applied to a sample containing fluorescent polystyrene beads and a sample made of olydimethylsiloxane with embedded fluorescent nanoparticles.

Results

From the simulations, it is evident that measurements with an RI mismatch larger than 0.02 and no correction yield considerably worse results compared to perfectly matched measurements. RI mismatches larger than 0.05 make it almost impossible to resolve finer details and structures. By contrast, the simulations imply that a measurement with an RI mismatch of up to 0.1 can still yield reasonable results if the presented correction method is applied. The experiments validate the simulated results for an RI mismatch of about 0.09.

Conclusions

The method significantly improves the SLOT image quality for samples with imperfectly matched Ris. Although the absolutely best imaging quality will be achieved with perfect RI matching, these results pave the way for imaging in SLOT with RI mismatches while maintaining high image quality.

Femtosecond Laser Inscribed Excessively Tilted Fiber Grating for Humidity Sensing

We propose a humidity sensor using an excessively tilted fiber grating (Ex-TFG) coated with agarose fabricated using femtosecond laser processing. The processed grating showcases remarkable differentiation between TE and TM modes, achieving an exceptionally narrow bandwidth of approximately 1.5 nm and an impressive modulation depth of up to 15 dB for both modes. We exposed the agarose-coated TFG sensor to various relative humidity levels and monitored the resonance wavelength to test its humidity sensing capability. Our findings demonstrated that the sensor exhibited a rapid response time (2-4 s) and showed a high response sensitivity (18.5 pm/%RH) between the humidity changes and the resonant wavelength shifts. The high sensitivity, linearity, repeatability, low hysteresis, and excellent long-term stability of the TFG humidity sensor, as demonstrated in our experimental results, make it an attractive option for environmental monitoring or biomedical diagnosis.

Recent Insights about the Role of Gels in Organic Photonics and Electronics

This review article provides an in-depth exploration of the role of gels in the fields of organic electronics and photonics, focusing on their unique properties and applications. Despite their remarkable potential, gel-based innovations remain relatively uncharted in these domains. This brief review aims to bridge the knowledge gap by shedding light on the diverse roles that gels can fulfil in the enhancement of organic electronic and photonic devices. From flexible electronics to light-emitting materials, we delve into specific examples of gel applications, highlighting their versatility and promising outcomes. This work serves as an indispensable resource for researchers interested in harnessing the transformative power of gels within these cutting-edge fields. The objective of this review is to raise awareness about the overlooked research potential of gels in optoelectronic materials, which have somewhat diminished in recent years.

Validation of Point-of-Care Device for Rapid Detection of Salmonella enterica in Meat Products

Accurate and rapid detection of pathogens in foods of animal origin has been a critical part of the One Health Action Plan of the European Union (EU). Biosensors have the potential in bringing required technologies to accomplish this on the field, wherein loop-mediated isothermal amplification (LAMP) and lab-on-a-chip have proven to be ideal. We have developed a LAMP-based point-of-care (POC) device, the VETPOD, as a solution to the contemporary challenges in the rapid detection of Salmonella spp. The core technology in the VETPOD is a ready-to-use cartridge that included an injection-molded polymer chip with pyramid-shaped optical structures embedded within the chip. These pyramid-shaped optical structures direct the incident light, due to total internal reflection (TIR), through the reaction chambers to the phototransistor. The VETPOD was validated against the ISO 6579-1 reference method. A total of 310 samples were tested that included 180 Salmonella spiked samples in 6 different meat categories and 130 strains to determine the specificity. The overall results were satisfactory, wherein the VETPOD had an acceptable sensitivity (96.51%) compared to the reference (98.81%) and near perfect agreement with ISO 6579-1 with an overall Cohen's kappa of 0.94. The relative level of detection (RLOD) for the VETPOD was 1.38 CFU/25 g that was found to be 1.17 times higher than the reference. The VETPOD showed 98% precision for inclusivity and 100% precision for the exclusivity samples. The VETPOD proved as a useful alternative to detect Salmonella spp. that can be adaptable to a broader spectrum of pathogens in future.

Agar-based optical sensors for electric current measurements

Biodegradable optical waveguides are breakthrough technologies to light delivery and sensing in biomedical and environmental applications. Agar emerges as an edible, soft, low-cost, and renewable alternative to traditional biopolymers, presenting remarkable optical and mechanical characteristics. Previous works introduced agar-made optical fibers for chemical measurements based on their inherent response to humidity and surrounding concentration. Therefore, we propose, for the first time, an all-optical, biodegradable electric current sensor. As flowing charges heat the agar matrix and modulate its refractive index, we connect the optical device to a DC voltage source using pin headers and excite the agar sample with coherent light to project spatiotemporally deviating speckle fields. Experiments proceeded with spheres and no-core fibers comprising 2 wt% agar/water. Once the increasing current stimulates the speckles' motion, we acquire such images with a camera and evaluate their correlation coefficients, yielding exponential decay-like functions whose time constants provide the input amperage. Furthermore, the light granules follow the polarization of the applied voltage drop, providing visual information about the current direction. The results indicate a maximum resolution of [Formula: see text]0.4 [Formula: see text]A for electrical stimuli [Formula: see text] 100 [Formula: see text]A, which fulfills the requirements for bioelectrical signal assessment.

Phase-Resolved Optical Coherence Elastography: An Insight into Tissue Displacement Estimation

Robust methods to compute tissue displacements in optical coherence elastography (OCE) data are paramount, as they play a significant role in the accuracy of tissue elastic properties estimation. In this study, the accuracy of different phase estimators was evaluated on simulated OCE data, where the displacements can be accurately set, and on real data. Displacement (∆d) estimates were computed from (i) the original interferogram data (Δφori) and two phase-invariant mathematical manipulations of the interferogram: (ii) its first-order derivative (Δφd) and (iii) its integral (Δφint). We observed a dependence of the phase difference estimation accuracy on the initial depth location of the scatterer and the magnitude of the tissue displacement. However, by combining the three phase-difference estimates (Δdav), the error in phase difference estimation could be minimized. By using Δdav, the median root-mean-square error associated with displacement prediction in simulated OCE data was reduced by 85% and 70% in data with and without noise, respectively, in relation to the traditional estimate. Furthermore, a modest improvement in the minimum detectable displacement in real OCE data was also observed, particularly in data with low signal-to-noise ratios. The feasibility of using Δdav to estimate agarose phantoms' Young's modulus is illustrated.

A silk-based self-adaptive flexible opto-electro neural probe

The combination of optogenetics and electrophysiological recording enables high-precision bidirectional interactions between neural interfaces and neural circuits, which provides a promising approach for the study of progressive neurophysiological phenomena. Opto-electrophysiological neural probes with sufficient flexibility and biocompatibility are desirable to match the low mechanical stiffness of brain tissue for chronic reliable performance. However, lack of rigidity poses challenges for the accurate implantation of flexible neural probes with less invasiveness. Herein, we report a hybrid probe (Silk-Optrode) consisting of a silk protein optical fiber and multiple flexible microelectrode arrays. The Silk-Optrode can be accurately inserted into the brain and perform synchronized optogenetic stimulation and multichannel recording in freely behaving animals. Silk plays an important role due to its high transparency, excellent biocompatibility, and mechanical controllability. Through the hydration of the silk optical fiber, the Silk-Optrode probe enables itself to actively adapt to the environment after implantation and reduce its own mechanical stiffness to implant into the brain with high fidelity while maintaining mechanical compliance with the surrounding tissue. The probes with 128 recording channels can detect high-yield well-isolated single units while performing intracranial light stimulation with low optical losses, surpassing previous work of a similar type. Two months of post-surgery results suggested that as-reported Silk-Optrode probes exhibit better implant-neural interfaces with less immunoreactive glial responses and tissue lesions. A silk optical fiber-based Silk-Optrode probe consisting of a natural silk optical fiber and a flexible micro/nano electrode array is reported. The multifunctional soft probe can modify its own Young's modulus through hydration to achieve accurate implantation into the brain. The low optical loss and single-unit recording abilities allow simultaneous optogenetic stimulation and multichannel readout, which expands the applications in the operation and parsing of neural circuits in behavioral animals.

Biomolecule-Based Optical Metamaterials: Design and Applications

Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.

Transverse and axial resolution of femtosecond laser ablation

Femtosecond lasers are capable of precise ablation that produces surgical dissections in vivo. The transverse and axial resolutions of the laser damage inside the bulk are important parameters of ablation. The transverse resolution is routinely quantified; but the axial resolution is more difficult to measure and is less commonly performed. Using a 1040-nm, 400-fs pulsed laser, and a 1.4-NA objective, we performed ablation inside agarose and glass, producing clear, and persistent damage spots. Near the ablation threshold of both media, we found that the axial resolution is similar to the transverse resolution. We also ablated neuron cell bodies and fibers in Caenorhabditis elegans and demonstrate submicrometer resolution in both the transverse and axial directions, consistent with our results in agarose and glass. Using simple yet rigorous methods, we define the resolution of laser ablation in transparent media along all directions.

Single-tube collection and nucleic acid analysis of clinical samples for SARS-CoV-2 saliva testing

The SARS-CoV-2 pandemic has brought to light the need for expedient diagnostic testing. Cost and availability of large-scale testing capacity has led to a lag in turnaround time and hindered contact tracing efforts, resulting in a further spread of SARS-CoV-2. To increase the speed and frequency of testing, we developed a cost-effective single-tube approach for collection, denaturation, and analysis of clinical samples. The approach utilizes 1 µL microbiological inoculation loops to collect saliva, sodium dodecyl sulfate (SDS) to inactivate and release viral genomic RNA, and a diagnostic reaction mix containing polysorbate 80 (Tween 80). In the same tube, the SDS-denatured clinical samples are introduced to the mixtures containing all components for nucleic acids detection and Tween 80 micelles to absorb the SDS and allow enzymatic reactions to proceed, obviating the need for further handling of the samples. The samples can be collected by the tested individuals, further decreasing the need for trained personnel to administer the test. We validated this single-tube sample-to-assay method with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) and discovered little-to-no difference between Tween- and SDS-containing reaction mixtures, compared to control reactions. This approach reduces the logistical burden of traditional large-scale testing and provides a method of deployable point-of-care diagnostics to increase testing frequency.

Analysis of the Relative Humidity Response of Hydrophilic Polymers for Optical Fiber Sensing

Relative humidity (RH) monitorization is of extreme importance on scientific and industrial applications, and optical fiber sensors (OFS) may provide adequate solutions. Typically, these kinds of sensors depend on the usage of humidity responsive polymers, thus creating the need for the characterization of the optical and expansion properties of these materials. Four different polymers, namely poly(vinyl alcohol), poly(ethylene glycol), Hydromed™ D4 and microbiology agar were characterized and tested using two types of optical sensors. First, optical fiber Fabry–Perot (FP) tips were made, which allow the dynamical measurement of the polymers’ response to RH variations, in particular of refractive index, film thickness, and critical deliquescence RH. Using both FP tips and Long-Period fiber gratings, the polymers were then tested as RH sensors, allowing a comparison between the different polymers and the different OFS. For the case of the FP sensors, the PEG tips displayed excellent sensitivity above 80%RH, outperforming the other polymers. In the case of LPFGs, the 10% (wt/wt) PVA one displayed excellent sensitivity in a larger working range (60 to 100%RH), showing a valid alternative to lower RH environment sensing.

Envisioning Quantum Electrodynamic Frameworks Based on Bio-Photonic Cavities

A bio-photonic cavity quantum electrodynamic (C-QED) framework could be imagined as a system in which both the “cavity” and the “atom” participating in the light-matter interaction scenario are bio-inspired. Can a cavity be made of a bio-polymer? If so, how should such a cavity appear and what are the best polymers to fabricate it? Can a bioluminescent material stand the comparison with new-fashion semiconductors? In this review we answer these fundamental questions to pave the way toward an eco-friendly paradigm, in which the ever-increasing demand for more performing quantum photonics technologies meets the ever-increasing yet silent demand of our planet to reduce our environmental footprint.

Coupling plasmonic catalysis and nanocrystal growth through cyclic regeneration of NADH

In a typical colloidal synthesis, the molecules of the reducing agent are irreversibly oxidized during nanocrystal growth. Such a scenario is of questionable sustainability when confronted with naturally occurring processes in which reducing agent molecules are cyclically regenerated. Here we show that cofactor molecules once consumed in the nucleation and growth of metallic nanocrystals can be photoregenerated using metallic nanocrystals as photocatalysts and reused in the subsequent nucleation process. Cyclic regeneration of cofactor molecules opens up the possibilities for the sustainable synthesis of inorganic nanoparticles.

Methylcellulose-Cellulose Nanocrystal Composites for Optomechanically Tunable Hydrogels and Fibers

Chemical modification of cellulose offers routes for structurally and functionally diverse biopolymer derivatives for numerous industrial applications. Among cellulose derivatives, cellulose ethers have found extensive use, such as emulsifiers, in food industries and biotechnology. Methylcellulose, one of the simplest cellulose derivatives, has been utilized for biomedical, construction materials and cell culture applications. Its improved water solubility, thermoresponsive gelation, and the ability to act as a matrix for various dopants also offer routes for cellulose-based functional materials. There has been a renewed interest in understanding the structural, mechanical, and optical properties of methylcellulose and its composites. This review focuses on the recent development in optically and mechanically tunable hydrogels derived from methylcellulose and methylcellulose-cellulose nanocrystal composites. We further discuss the application of the gels for preparing highly ductile and strong fibers. Finally, the emerging application of methylcellulose-based fibers as optical fibers and their application potentials are discussed.

Bioresorbable Photonics: Materials, Devices and Applications

Bio-photonic devices that utilize the interaction between light and biological substances have been emerging as an important tool for clinical diagnosis and/or therapy. At the same time, implanted biodegradable photonic devices can be disintegrated and resorbed after a predefined operational period, thus avoiding the risk and cost associated with the secondary surgical extraction. In this paper, the recent progress on biodegradable photonics is reviewed, with a focus on material strategies, device architectures and their biomedical applications. We begin with a brief introduction of biodegradable photonics, followed by the material strategies for constructing biodegradable photonic devices. Then, various types of biodegradable photonic devices with different functionalities are described. After that, several demonstration examples for applications in intracranial pressure monitoring, biochemical sensing and drug delivery are presented, revealing the great potential of biodegradable photonics in the monitoring of human health status and the treatment of human diseases. We then conclude with the summary of this field, as well as current challenges and possible future directions.

Engineering Hydrogel-Based Biomedical Photonics: Design, Fabrication, and Applications

Light guiding and manipulation in photonics have become ubiquitous in events ranging from everyday communications to complex robotics and nanomedicine. The speed and sensitivity of light-matter interactions offer unprecedented advantages in biomedical optics, data transmission, photomedicine, and detection of multi-scale phenomena. Recently, hydrogels have emerged as a promising candidate for interfacing photonics and bioengineering by combining their light-guiding properties with live tissue compatibility in optical, chemical, physiological, and mechanical dimensions. Herein, the latest progress over hydrogel photonics and its applications in guidance and manipulation of light is reviewed. Physics of guiding light through hydrogels and living tissues, and existing technical challenges in translating these tools into biomedical settings are discussed. A comprehensive and thorough overview of materials, fabrication protocols, and design architectures used in hydrogel photonics is provided. Finally, recent examples of applying structures such as hydrogel optical fibers, living photonic constructs, and their use as light-driven hydrogel robots, photomedicine tools, and organ-on-a-chip models are described. By providing a critical and selective evaluation of the field's status, this work sets a foundation for the next generation of hydrogel photonic research.

Challenges in the Fabrication of Biodegradable and Implantable Optical Fibers for Biomedical Applications

The limited penetration depth of visible light in biological tissues has encouraged researchers to develop novel implantable light-guiding devices. Optical fibers and waveguides that are made from biocompatible and biodegradable materials offer a straightforward but effective approach to overcome this issue. In the last decade, various optically transparent biomaterials, as well as different fabrication techniques, have been investigated for this purpose, and in view of obtaining fully fledged optical fibers. This article reviews the state-of-the-art in the development of biocompatible and biodegradable optical fibers. Whilst several reviews that focus on the chemical properties of the biomaterials from which these optical waveguides can be made have been published, a systematic review about the actual optical fibers made from these materials and the different fabrication processes is not available yet. This prompted us to investigate the essential properties of these biomaterials, in view of fabricating optical fibers, and in particular to look into the issues related to fabrication techniques, and also to discuss the challenges in the use and operation of these optical fibers. We close our review with a summary and an outline of the applications that may benefit from these novel optical waveguides.