Introduction to the special feature: amplify Black voices in optics and photonics.

This multi-journal special issue highlights the work of Black scientists and engineers in optics and photonics to accomplish the goal of engaging the entire optics and photonics community and bring awareness to the quality of their research and contributions to the field.

DiffuserSpec: spectroscopy with Scotch tape.

Computational spectroscopy breaks the inherent one-to-one spatial-to-spectral pixel mapping of traditional spectrometers by multiplexing spectral data over a given sensor region. Most computational spectrometers require components that are complex to design, fabricate, or both. DiffuserSpec is a simple computational spectrometer that uses the inherent spectral dispersion of commercially available diffusers to generate speckle patterns that are unique to each wavelength. Using Scotch tape as a diffuser, we demonstrate narrowband and broadband spectral reconstructions with 2-nm spectral resolution over an 85-nm bandwidth in the near-infrared, limited only by the bandwidth of the calibration dataset. We also investigate the effect of spatial sub-sampling of the 2D speckle pattern on resolution performance.

A multi-channel smartphone-based spectroscopic system for high-throughput biosensing in low-resource settings.

Primary healthcare centers (PHC) are the first point of contact for people in low-resource settings, and laboratory services play a critical role in early diagnosis of any disease. In recent years, several smartphone-based spectroscopic systems have been demonstrated to translate lab-confined healthcare applications into point-of-care environments to improve their accessibility. Due to constraints, such as the low availability of skilled personnel and consumables in a PHC, batch processing would be ideal for a large number of samples. Therefore, high-throughput and multi-channel detection is equally critical as affordability and portability. To date, most point-of-care systems are designed to perform a single type of analysis at a time. Herein, we introduce a smartphone-based spectroscopic system based on the use of line-beam illumination to achieve high-throughput sensing (15 channels simultaneously) within a 3d-printed microfluidic device. We also developed a smartphone application to process the spectral data and provide the results in real-time. Bland-Altman analysis revealed that the proposed device performs similarly to a laboratory spectrophotometer. The availability of the developed system will enable detection of multiple samples rapidly in low-resource settings with the existing limited manpower and infrastructures. The fast turnaround time may eventually help in timely diagnosis of patients during situations of high sample load, such as during disease outbreaks.

Two-Dimensional Cochlear Micromechanics Measured In Vivo Demonstrate Radial Tuning within the Mouse Organ of Corti.

UNLABELLED: The exquisite sensitivity and frequency discrimination of mammalian hearing underlie the ability to understand complex speech in noise. This requires force generation by cochlear outer hair cells (OHCs) to amplify the basilar membrane traveling wave; however, it is unclear how amplification is achieved with sharp frequency tuning. Here we investigated the origin of tuning by measuring sound-induced 2-D vibrations within the mouse organ of Corti in vivo Our goal was to determine the transfer function relating the radial shear between the structures that deflect the OHC bundle, the tectorial membrane and reticular lamina, to the transverse motion of the basilar membrane. We found that, after normalizing their responses to the vibration of the basilar membrane, the radial vibrations of the tectorial membrane and reticular lamina were tuned. The radial tuning peaked at a higher frequency than transverse basilar membrane tuning in the passive, postmortem condition. The radial tuning was similar in dead mice, indicating that this reflected passive, not active, mechanics. These findings were exaggerated in Tecta(C1509G/C1509G) mice, where the tectorial membrane is detached from OHC stereocilia, arguing that the tuning of radial vibrations within the hair cell epithelium is distinct from tectorial membrane tuning. Together, these results reveal a passive, frequency-dependent contribution to cochlear filtering that is independent of basilar membrane filtering. These data argue that passive mechanics within the organ of Corti sharpen frequency selectivity by defining which OHCs enhance the vibration of the basilar membrane, thereby tuning the gain of cochlear amplification. SIGNIFICANCE STATEMENT: Outer hair cells amplify the traveling wave within the mammalian cochlea. The resultant gain and frequency sharpening are necessary for speech discrimination, particularly in the presence of background noise. Here we measured the 2-D motion of the organ of Corti in mice and found that the structures that stimulate the outer hair cell stereocilia, the tectorial membrane and reticular lamina, were sharply tuned in the radial direction. Radial tuning was similar in dead mice and in mice lacking a tectorial membrane. This suggests that radial tuning comes from passive mechanics within the hair cell epithelium, and that these mechanics, at least in part, may tune the gain of cochlear amplification.

Iterative re-weighted approach to high-resolution optical coherence tomography with narrow-band sources.

Optical coherence tomography (OCT) is a non-invasive optical imaging modality capable of high resolution imaging of internal tissue structures. It is widely believed that the high axial resolution in OCT systems requires a wide-bandwidth light source. As a result, often the potential advantages of narrow-bandwidth sources (in terms of cost and/or imaging speed) are understood to come at the cost of significant reduction in imaging resolution. In this paper, we argue that this trade-off between resolution and speed is a shortcoming imposed by the-state-of-the-art A-scan reconstruction algorithm, Fast Fourier Transform, and can be circumvented through use of alternative processing methods. In particular, we investigate the shortcomings of the FFT as well as previously proposed alternatives and demonstrate the first application of an iterative regularized re-weighted l(2) norm method to improve the axial resolution of fast scan rate OCT systems in the narrow-bandwidth imaging conditions. We validate our claims via experimental results generated from a home-built OCT system used to image layered phantom and in vivo data. Our results rely on new, sophisticated signal processing algorithms to generate higher precision (i.e., higher resolution) OCT images at correspondingly fast scan rates. In other words, our work demonstrates the feasibility of simultaneously more reliable and more comfortable medical imaging systems for patients by reducing the overall scan time, without sacrificing image quality.

Enhanced depolarization contrast in polarization-sensitive optical coherence tomography.

We demonstrate the first application of the differential depolarization index (DDI) for depolarization imaging in polarization-sensitive optical coherence tomography (PS-OCT). Unlike the widely used degree of polarization uniformity (DOPU), the DDI is independent of the incident polarization state and, therefore, more robust to varying system and sample parameters. Moreover, it can be applied to single-input-polarization-state PS-OCT systems, and it overcomes several limitations of the emerging depolarization index used in multiple-input-polarization-state systems. Our results on tissue phantoms and human skin prove that DDI yields significant depolarization contrast improvements compared to DOPU, which highlights its potential for depolarization imaging in PS-OCT.

Label-Free Optical Technologies to Enhance Noninvasive Endoscopic Imaging of Early-Stage Cancers.

White light endoscopic imaging allows for the examination of internal human organs and is essential in the detection and treatment of early-stage cancers. To facilitate diagnosis of precancerous changes and early-stage cancers, label-free optical technologies that provide enhanced malignancy-specific contrast and depth information have been extensively researched. The rapid development of technology in the past two decades has enabled integration of these optical technologies into clinical endoscopy. In recent years, the significant advantages of using these adjunct optical devices have been shown, suggesting readiness for clinical translation. In this review, we provide an overview of the working principles and miniaturization considerations and summarize the clinical and preclinical demonstrations of several such techniques for early-stage cancer detection. We also offer an outlook for the integration of multiple technologies and the use of computer-aided diagnosis in clinical endoscopy. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 17 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

SpecReFlow: an algorithm for specular reflection restoration using flow-guided video completion.

Purpose: Specular reflections (SRs) are highlight artifacts commonly found in endoscopy videos that can severely disrupt a surgeon's observation and judgment. Despite numerous attempts to restore SR, existing methods are inefficient and time consuming and can lead to false clinical interpretations. Therefore, we propose the first complete deep-learning solution, SpecReFlow, to detect and restore SR regions from endoscopy video with spatial and temporal coherence. Approach: SpecReFlow consists of three stages: (1) an image preprocessing stage to enhance contrast, (2) a detection stage to indicate where the SR region is present, and (3) a restoration stage in which we replace SR pixels with an accurate underlying tissue structure. Our restoration approach uses optical flow to seamlessly propagate color and structure from other frames of the endoscopy video. Results: Comprehensive quantitative and qualitative tests for each stage reveal that our SpecReFlow solution performs better than previous detection and restoration methods. Our detection stage achieves a Dice score of 82.8% and a sensitivity of 94.6%, and our restoration stage successfully incorporates temporal information with spatial information for more accurate restorations than existing techniques. Conclusions: SpecReFlow is a first-of-its-kind solution that combines temporal and spatial information for effective detection and restoration of SR regions, surpassing previous methods relying on single-frame spatial information. Future work will look to optimizing SpecReFlow for real-time applications. SpecReFlow is a software-only solution for restoring image content lost due to SR, making it readily deployable in existing clinical settings to improve endoscopy video quality for accurate diagnosis and treatment.

Towards improved 3D reconstruction of cystoscopies through real-time feedback for frame reacquisition.

Cystoscopic video can be cumbersome to review; however, preservation of data in the form of 3D bladder reconstructions has the potential to improve patient care. Unfortunately, not all cystoscopy videos produce viable reconstructions, because their underlying frames contain artifacts such as motion blur and bladder debris, which consequently make them unusable for 3D reconstructions. Here, we develop a real-time pipeline, termed the Assessment and Feedback Pipeline (AFP), that alerts clinicians when unusable frames are detected and encourages them to recollect the last few seconds of data. We show that the AFP classifies frames as usable or unusable with a balanced accuracy of 81.60% and demonstrate that use of the AFP improves 3D reconstruction coverage. These results suggest that clinical implementation of the AFP would improve 3D reconstruction quality through real-time detection and recollection of unusable frames.

Fiberscopic pattern removal for optimal coverage in 3D bladder reconstructions of fiberscope cystoscopy videos.

Purpose: In the current clinical standard of care, cystoscopic video is not routinely saved because it is cumbersome to review. Instead, clinicians rely on brief procedure notes and still frames to manage bladder pathology. Preserving discarded data via 3D reconstructions, which are convenient to review, has the potential to improve patient care. However, many clinical videos are collected by fiberscopes, which are lower cost but induce a pattern on frames that inhibit 3D reconstruction. The aim of our study is to remove the honeycomb-like pattern present in fiberscope-based cystoscopy videos to improve the quality of 3D bladder reconstructions. Approach: Our study introduces an algorithm that applies a notch filtering mask in the Fourier domain to remove the honeycomb-like pattern from clinical cystoscopy videos collected by fiberscope as a preprocessing step to 3D reconstruction. We produce 3D reconstructions with the video before and after removing the pattern, which we compare with a metric termed the area of reconstruction coverage (ARC), defined as the surface area (in pixels) of the reconstructed bladder. All statistical analyses use paired t-tests. Results: Preprocessing using our method for pattern removal enabled reconstruction for all (n=5) cystoscopy videos included in the study and produced a statistically significant increase in bladder coverage (p=0.018). Conclusions: This algorithm for pattern removal increases bladder coverage in 3D reconstructions and automates mask generation and application, which could aid implementation in time-starved clinical environments. The creation and use of 3D reconstructions can improve documentation of cystoscopic findings for future surgical navigation, thus improving patient treatment and outcomes.

SmartOCT: smartphone-integrated optical coherence tomography.

Smartphone devices have seen unprecedented technical innovation in computational power and optical imaging capabilities, making them potentially invaluable tools in scientific imaging applications. The smartphone's compact form-factor and broad accessibility has motivated researchers to develop smartphone-integrated imaging systems for a wide array of applications. Optical coherence tomography (OCT) is one such technique that could benefit from smartphone-integration. Here, we demonstrate smartOCT, a smartphone-integrated OCT system that leverages built-in components of a smartphone for detection, processing and display of OCT data. SmartOCT uses a broadband visible-light source and line-field OCT design that enables snapshot 2D cross-sectional imaging. Furthermore, we describe methods for processing smartphone data acquired in a RAW data format for scientific applications that improves the quality of OCT images. The results presented here demonstrate the potential of smartphone-integrated OCT systems for low-resource environments.

Enhancing the image quality of blue light cystoscopy through green-hue correction and fogginess removal.

Blue light cystoscopy (BLC) is a guideline-recommended endoscopic tool to detect bladder cancer with high sensitivity. Having clear, high-quality images during cystoscopy is crucial to the sensitive, efficient detection of bladder tumors; yet, important diagnostic information is often missed or poorly visualized in images containing illumination artifacts or impacted by impurities in the bladder. In this study, we introduce computational methods to remove two common artifacts in images from BLC videos: green hue and fogginess. We also evaluate the effect of artifact removal on the perceptual quality of the BLC images through a survey study and computation of Blind/Referenceless Image Spatial Quality Evaluator scores on the original and enhanced images. We show that corrections and enhancements made to cystoscopy images resulted in a better viewing experience for clinicians during BLC imaging and reliably restored lost tissue features that were important for diagnostics. Incorporating these enhancements during clinical and OR procedures may lead to more comprehensive tumor detection, fewer missed tumors during TURBT procedures, more complete tumor resection and shorter procedure time. When used in off-line review of cystoscopy videos, it may also better guide surgical planning and allow more accurate assessment and diagnosis.

Multiparameter interferometric polarization-enhanced imaging differentiates carcinoma in situ from inflammation of the bladder: an ex vivo study.

Significance: Successful differentiation of carcinoma in situ (CIS) from inflammation in the bladder is key to preventing unnecessary biopsies and enabling accurate therapeutic decisions. Current standard-of-care diagnostic imaging techniques lack the specificity needed to differentiate these states, leading to false positives. Aim: We introduce multiparameter interferometric polarization-enhanced (MultiPIPE) imaging as a promising technology to improve the specificity of detection for better biopsy guidance and clinical outcomes. Approach: In this ex vivo study, we extract tissue attenuation-coefficient-based and birefringence-based parameters from MultiPIPE imaging data, collected with a bench-top system, to develop a classifier for the differentiation of benign and CIS tissues. We also analyze morphological features from second harmonic generation imaging and histology slides and perform imaging-to-morphology correlation analysis. Results: MultiPIPE enhances specificity to differentiate CIS from benign tissues by nearly 20% and reduces the false-positive rate by more than four-fold over clinical standards. We also show that the MultiPIPE measurements correlate well with changes in morphological features in histological assessments. Conclusions: The results of our study show the promise of MultiPIPE imaging to be used for better differentiation of bladder inflammation from flat tumors, leading to a fewer number of unnecessary procedures and shorter operating room (OR) time.

Birefringent tissue-mimicking phantom for polarization-sensitive optical coherence tomography imaging.

SIGNIFICANCE: Tissue birefringence is an important parameter to consider when designing realistic, tissue-mimicking phantoms. Options for suitable birefringent materials that can be used to accurately represent tissue scattering are limited. AIM: To introduce a method of fabricating birefringent tissue phantoms with a commonly used material-polydimethylsiloxane (PDMS)-for imaging with polarization-sensitive optical coherence tomography (PS-OCT). APPROACH: Stretch-induced birefringence was characterized in PDMS phantoms made with varying curing ratios, and the resulting phantom birefringence values were compared with those of biological tissues. RESULTS: We showed that, with induced birefringence levels up to 2.1 × 10 - 4, PDMS can be used to resemble the birefringence levels in weakly birefringent tissues. We demonstrated the use of PDMS in the development of phantoms to mimic the normal and diseased bladder wall layers, which can be differentiated by their birefringence levels. CONCLUSIONS: PDMS allows accurate control of tissue scattering and thickness, and it exhibits controllable birefringent properties. The use of PDMS as a birefringent phantom material can be extended to other birefringence imaging systems beyond PS-OCT and to mimic other organs.

Depth-resolved extraction of optical attenuation for glaucoma assessment in clinical settings: a pilot study.

We assessed the ability of the optical attenuation coefficient (AC) to detect early-stage glaucoma with two AC estimation algorithms: retinal layer intensity ratio (LIR) and depth-resolved confocal (DRC). We also introduced new depth-dependent AC parameters for retinal nerve fiber layer assessment. Optical coherence tomography B-scans were collected from 44 eyes of age-similar participants with eye health ranging from healthy to severe glaucoma, including glaucoma suspect patients. Mean AC values estimated from the DRC method are comparable to ratio-extracted values (p > 0.5 for all study groups), and the depth-dependent ACDRC parameters enhance the utility of the AC for detection of early-stage glaucoma.

Smartphone-based optical spectroscopic platforms for biomedical applications: a review [Invited].

Rapid advancements in smartphone technology have enabled the integration of many optical detection techniques that leverage the embedded functional components and software platform of these sophisticated devices. Over the past few years, several research groups have developed high-resolution smartphone-based optical spectroscopic platforms and demonstrated their usability in different biomedical applications. Such platforms provide unprecedented opportunity to develop point-of-care diagnostics systems, especially for resource-constrained environments. In this review, we discuss the development of smartphone systems for optical spectroscopy and highlight current challenges and potential solutions to improve the scope for their future adaptability.

Anti-Black racism in academia and what you can do about it.

The experiences of Black scientists and engineers reveal that science is not a meritocracy. Here is a list of recommendations to combat anti-Black racism in academic institutions.

Low-Cost, Volume-Controlled Dipstick Urinalysis for Home-Testing.

Dipstick urinalysis provides quick and affordable estimations of multiple physiological conditions but requires good technique and training to use accurately. Manual performance of dipstick urinalysis relies on good human color vision, proper lighting control, and error-prone, time-sensitive comparisons to chart colors. By automating the key steps in the dipstick urinalysis test, potential sources of error can be eliminated, allowing self-testing at home. We describe the steps necessary to create a customizable device to perform automated urinalysis testing in any environment. The device is cheap to manufacture and simple to assemble. We describe the key steps involved in customizing it for the dipstick of choice and for customizing a mobile phone app to analyze the results. We demonstrate its use to perform urinalysis and discuss the critical measurements and fabrication steps necessary to ensure robust operation. We then compare the proposed method to the dip-and-wipe method, the gold standard technique for dipstick urinalysis.

Recurrence monitoring for ovarian cancer using a cell phone-integrated paper device to measure the ovarian cancer biomarker HE4/CRE ratio in urine.

Ovarian cancer has a poor cure rate and rates of relapse are high. Current recurrence detection is limited by non-specific methods such as blood testing and ultrasound. Based on reports that human epididymis four (HE4) / creatinine (CRE) ratios found in urine are elevated in ovarian cancers, we have developed a paper-based device that combines lateral flow technology and cell phone analysis to quantitatively measure HE4/CRE. Surrogate samples were used to test the performance over clinically expected HE4/CRE ratios. For HE4/CRE ratios of 2 to 47, the percent error was found to be 16.0% on average whether measured by a flatbed scanner or cell phone. There was not a significant difference between the results from the cell phone or scanner. Based on published studies, error in this method was less than the difference required to detect recurrence. This promising new tool, with further development, could be used at home or in low-resource settings to provide timely detection of ovarian cancer recurrence.