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At least 19 records

Analysis of an optical imaging system prototype for autonomously monitoring zooplankton in an aquaculture facility

Traditional approaches to biomonitoring in aquatic systems, such as sample collection, sorting, and identification, require significant time and effort, thereby limiting the spatiotemporal resolution of sample collection. Additionally, collection and preservation of samples for subsequent taxonomic identification and enumeration leads to mortality of organisms. Recent advances in technologies that utilize optical imaging and machine learning have provided new opportunities to expedite biomonitoring and lead to significant cost savings. These technologies can be advantageous to scientists or managers that conduct routine biomonitoring to inform operations, as in the case of aquaculture facilities. The Small Aquatic Organism optical imaging system (SAO) is a high-throughput optical imaging and classification prototype system that relies on computer vision and machine learning (Support Vector Machines, or SVMs) to autonomously identify and enumerate aquatic organisms. The SAO provides a more sustainable method of collecting large volumes of data and has the benefit of being used in situ. In this study, we tested the performance of the SAO in providing comparable results to manual zooplankton community monitoring in ten ponds at an aquaculture facility. We performed a side-by-side study comparing the sampling methods of plankton tow nets, where major zooplankton taxonomic classes were manually identified and enumerated, to sampling with the SAO. Vouchered samples were used to develop a training library for the SAO, where classes consisted of water boatman and zooplankton groups: cladocerans, copepod adults, copepod nauplii, and rotifers. SAO imagery was manually classified and compared with predicted results for validation. Accuracy for the SVM classifier of the SAO was 37.4 %. Convolutional Neural Networks (CNN) and Random Forest classifiers were also applied to SAO imagery and image features for comparison. The best CNN model and our Random Forest model had accuracies of 80.4 % and 46.6 % respectively. Challenges faced included the small size of copepod nauplii and rotifers and the limited resolution of the imaging camera, although there are tradeoffs between imaging resolution and the sample processing rate. Furthermore, our comparison shows that advancement in both optical imaging and ML are needed in order for the SAO prototype to yield comparable results to manual community monitoring in an aquaculture facility.

54 ENVIRONMENTAL SCIENCES↗

Optical image analysis for graphene layer detection: Enhanced green channel methodology

Graphene, a material of increasing research interest, requires accurate layer identification due to its sensitivity to layer count. Existing methods for graphene layer number identification are either time-consuming or of low accuracy, with high-accuracy methods often requiring expensive processes. This paper aims to address this challenge by proposing a cost-effective and efficient approach. Specifically, the current work highlights only the green channel—one of the three primary color channels (red, green, blue) that make up an optical image—from images of exfoliated graphene flakes for layer count identification. A linear regression is performed between pixel position and substrate green channel value, and this effect is subtracted from the entire optical image to mitigate background effects. By storing the range of green channel values for each type of flake (monolayer, bilayer, or tri-layer) based on a few images, we establish thresholds for identifying different types of layers in a particular setup. Additionally, our methodology allows for flexible threshold tuning using a single reference image, enabling adjustment to changes in detection setup such as illumination level, magnification, or microscope used. Finally, demonstrating high accuracy and flexibility, this methodology presents a suitable technique for graphene layer number identification without the need for large datasets or expensive instruments.

2D materials↗

Simultaneous measurements of volume, pressure, optical images, and crystal structure with a dynamic diamond anvil cell: A real-time event monitoring system

The dynamic diamond anvil cell (dDAC) technique has attracted great interest because it possibly provides a bridge between static and dynamic compression studies with fast, repeatable, and controllable compression rates. The dDAC can be a particularly useful tool to study the pathways and kinetics of phase transitions under dynamic pressurization if simultaneous measurements of physical quantities are possible as a function of time. We report the development of a real-time event monitoring (RTEM) system with dDAC, which can simultaneously record the volume, pressure, optical image, and structure of materials during dynamic compression runs. In particular, the volume measurement using both Fabry–Pérot interferogram and optical images facilitates the construction of an equation of state (EoS) using the dDAC in a home-laboratory. We also developed an in-line ruby pressure measurement (IRPM) system to be deployed at a synchrotron x-ray facility. This system provides simultaneous measurements of pressure and x-ray diffraction in low and narrow pressure ranges. The EoSs of ice VI obtained from the RTEM and the x-ray diffraction data with the IRPM are consistent with each other. The complementarity of both RTEM and IRPM systems will provide a great opportunity to scrutinize the detailed kinetic pathways of phase transitions using dDAC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Versatile recognition of graphene layers from optical images under controlled illumination through green channel correlation method

In this study, a simple yet versatile method is proposed for identifying the number of exfoliated graphene layers transferred on an oxide substrate from optical images, utilizing a limited number of input images for training, paired with a more traditional number of a few thousand well-published Github images for testing and predicting. Two thresholding approaches, namely the standard deviation-based approach and the linear regression-based approach, were employed in this study. The method specifically leverages the red, green, and blue color channels of image pixels and creates a correlation between the green channel of the background and the green channel of the various layers of graphene. This method proves to be a feasible alternative to deep learning-based graphene recognition and traditional microscopic analysis. The proposed methodology performs well under conditions where the effect of surrounding light on the graphene-on-oxide sample is minimum and allows rapid identification of the various graphene layers. Here, the study additionally addresses the functionality of the proposed methodology with nonhomogeneous lighting conditions, showcasing successful prediction of graphene layers from images that are lower in quality compared to typically published in literature. In all, the proposed methodology opens up the possibility for the non-destructive identification of graphene layers from optical images by utilizing a new and versatile method that is quick, inexpensive, and works well with fewer images that are not necessarily of high quality.

36 MATERIALS SCIENCE↗

Optical image analysis of WSe 2 − thresholding for layer detection

The fast and reliable layer identification of two-dimensional transition metal dichalcogenide (TMD), such as WSe 2 , is essential to investigating their thickness-dependent electronic and optical properties. This article presents efficient optical image thresholding methodology designed to segment the mono, bi, and tri-layer regions of WSe 2 flakes mechanically exfoliated onto a SiO 2 /Si substrate. The optical images were first preprocessed to exclude the background effect and analyzed using the pixel medians and interquartile ranges for fundamental color channels—red, green, and blue (RGB). The analysis of red channel pixel intensities yielded three distinct ranges, serving as thresholds for layer segmentation: monolayer (111.0–118.0), bilayer (103.0–110.0), and tri-layer (93.0–103.0). Similarly, thresholds were established for each color channel, facilitating a comparative study of the segmentation performances. Further, the intersection-over-union ($IoU$) calculations revealed that the red and green channels demonstrated greater than 99 % and 90 % accuracy in differentiating each layer, respectively. This approach yields remarkable results without substantial data calibration that utilizes time-intensive heuristic techniques. Moreover, the proposed methodology offers the flexibility to compare performances across different color channels, expanding the applicability for other 2D material systems.

2D Materials↗

Multimodal nonlinear optical imaging via evanescent wave excitation

A system for multimodal nonlinear optical imaging is provided. Each mode uses a high NA objective to cause total internal reflection excitation at a sample-substrate interface. The system has a femtosecond oscillator to generate pulses used for two beams. The objective receives at least one beam, redirects the received at least one beam through a dielectric substrate to cause the TIR and produces corresponding evanescent waves in a portion of the sample adjacent to the sample-substrate interface, and collects a backward-propagating beam of pulses of responsive light. The portion of the sample illuminated by the evanescent waves emits responsive light. Different modes or combinations of the distinct modalities may be selected to access complementary chemical and structural information for various chemical species near the sample-substrate interface. Each mode may have mode-specific control such as selective beam blocking, power ratios and filtering.

Doughty, Benjamin L.↗

All-optical image denoising using a diffractive visual processor

Abstract Image denoising, one of the essential inverse problems, targets to remove noise/artifacts from input images. In general, digital image denoising algorithms, executed on computers, present latency due to several iterations implemented in, e.g., graphics processing units (GPUs). While deep learning-enabled methods can operate non-iteratively, they also introduce latency and impose a significant computational burden, leading to increased power consumption. Here, we introduce an analog diffractive image denoiser to all-optically and non-iteratively clean various forms of noise and artifacts from input images – implemented at the speed of light propagation within a thin diffractive visual processor that axially spans <250 × λ, where λ is the wavelength of light. This all-optical image denoiser comprises passive transmissive layers optimized using deep learning to physically scatter the optical modes that represent various noise features, causing them to miss the output image Field-of-View (FoV) while retaining the object features of interest. Our results show that these diffractive denoisers can efficiently remove salt and pepper noise and image rendering-related spatial artifacts from input phase or intensity images while achieving an output power efficiency of ~30–40%. We experimentally demonstrated the effectiveness of this analog denoiser architecture using a 3D-printed diffractive visual processor operating at the terahertz spectrum. Owing to their speed, power-efficiency, and minimal computational overhead, all-optical diffractive denoisers can be transformative for various image display and projection systems, including, e.g., holographic displays.

36 MATERIALS SCIENCE↗

Plasmonics-Enhanced Optical Imaging Systems for Bioenergy Research

This final report summarizes the key accomplishments of the project entitled “Plasmonics-Enhanced Optical Imaging Systems for Bioenergy Research”. The goal of this project is aimed at developing innovative and improved imaging instrumentation for visualization and quantitative characterization of biomarkers related to molecular processes and cellular function in living plants. This project focused on three specific aims: 1) Development of Advanced Multimodal Optical Sensing And Imaging Combinatory (MOSAIC) System for SERS biosensing and bioimaging. 2) Evaluation of MOSAIC technologies for sensing and imaging gene expression in plant systems using plasmonic nanoprobes. 3) Application of MOSAIC techniques to bioenergy research.

47 OTHER INSTRUMENTATION↗

Accelerated Nano-Optical Imaging through Sparse Sampling

The integration time and signal-to-noise ratio are inextricably linked when performing scanning probe microscopy based on raster scanning. This often yields a large lower bound on the measurement time, for example, in nano-optical imaging experiments performed using a scanning near-field optical microscope (SNOM). Here, in this study, we utilize sparse scanning augmented with Gaussian process regression to bypass the time constraint. We apply this approach to image charge-transfer polaritons in graphene residing on ruthenium trichloride (α-RuCl 3 ) and obtain key features such as polariton damping and dispersion. Critically, nano-optical SNOM imaging data obtained via sparse sampling are in good agreement with those extracted from traditional raster scans but require 11 times fewer sampled points. As a result, Gaussian process-aided sparse spiral scans offer a major decrease in scanning time.

36 MATERIALS SCIENCE↗

Optical Imaging Methods for Volumetric Additive Manufacturing

Tomographic volumetric additive manufacturing (VAM) is a technique that enables light-induced curing of photoresins into complex 3D end use objects within a single step. This is made possible through projecting tomographically patterned light energy into a photo-curable resin volume within a rotating container. In order to monitor, quantify, and control curing during tomographic VAM, researchers need to visualize the curing parts in real-time. This may enable advancements toward dynamic, controlled and closedloop VAM methods in the future, as some researchers have shown. Herein we briefly review various optical imaging methods used to monitor printing in real-time, as well as provide some perspectives for future needs and considerations for imaging methods in VAM.

36 MATERIALS SCIENCE↗

Molecular homing and retention of muscle membrane stabilizing copolymers by non-invasive optical imaging in vivo

First-in-class membrane stabilizer Poloxamer 188 (P188) has been shown to confer membrane protection in an extensive range of clinical conditions; however, elements of the systemic distribution and localization of P188 at the organ, tissue, and muscle fiber levels in vivo have not yet been elucidated. Here we used non-invasive fluorescence imaging to directly visualize and track the distribution and localization of P188 in vivo. The results demonstrated that the Alx647 probe did not alter the fundamental properties of P188 to protect biological membranes. Distribution kinetics in mdx mice demonstrated that Alx647 did not interface with muscle membranes and had fast clearance kinetics. In contrast, the distribution kinetics for P188-Alx647 was significantly slower, indicating a dramatic depot and retention effect of P188. Results further demonstrated the significant retention of P188-Alx647 in the skeletal muscle of mdx mice, showing a significant genotype effect with a higher fluorescence signal in the mdx muscles over BL10 mice. High-resolution optical imaging provided direct evidence of P188 surrounding the sarcolemma of skeletal and cardiac muscle cells. Taken together, these findings provide direct evidence of muscle-disease-dependent molecular homing and retention of synthetic copolymers in striated muscles thereby facilitating advanced studies of copolymer-membrane association in health and disease.

60 APPLIED LIFE SCIENCES↗

Optical imaging of flavor order in flat band graphene

Abstract Spin- and valley flavor polarization plays a central role in the many-body physics of flat band graphene, with Fermi surface reconstruction — often accompanied by quantized anomalous Hall and superconducting state — observed in a variety of experimental systems. Here we describe an optical technique that sensitively and selectively detects flavor textures via the exciton response of a proximal transition metal dichalcogenide layer. Through a systematic study of rhombohedral and rotationally faulted graphene bilayers and trilayers, we show that when the semiconducting dichalcogenide is in direct contact with the graphene, the exciton response is most sensitive to the large momentum rearrangement of the Fermi surface, providing information that is distinct from and complementary to electrical compressibility measurements. The wide-field imaging capability of optical probes allows us to obtain spatial maps of flavor order with high throughput, and with broad temperature and device compatibility. Our work helps pave the way for optical probing and imaging of flavor orders in flat band graphene systems.

Science & Technology - Other Topics↗

Optical Imaging for Machine Vision [Slides]

This slide deck is intended for proper specification and procurement of cameras and (thin) lenses for machine vision applications. This will include equations that allow one to calculate image size, field of view, depth of field, and length of extension tubes required to focus the image. This requires knowledge of the camera sensor, lens, distance to imaged object, and visual acuity.

42 ENGINEERING↗

Optical Imaging for Understanding of Thermal Barrier Coated Piston Engine Performance

Thermal barrier coatings (TBC) applied to pistons have been a recently renewed research topic in the field of internal combustion engines. Single cylinder testing of a conventional C15™ Tier 4 final pro-duction steel piston and a TBC coated piston showed that the Yttrium stabilized Zirconia (YSZ) TBC did not significantly alter engine performance, with the TBC piston having slower combustion rates and higher criteria emissions. For deeper understanding, research continued by studying 3D-piston sections optically in a constant pressure vessel using photodiodes, four high-speed cameras (natural luminosity, CH*, and OH*), and visualization of the flame from two orthogonal directions. Particle Im-aging Velocimetry (PIV) algorithms were adapted to perform Combustion Imaging Velocimetry (CIV) to aid in quantification of the observed visual combustion flow field differences. The optical work showed that the TBC piston flame development is slower, spatially different, with lower mixing energy for the TBC variant. Geometric profiles of engine pistons and optical vessel 3D-piston sections were measured using a Coordinate Measurement Machine (CMM), and surface roughness was measured with a stylus surface profilometer. CMM results showed that the TBC piston bowl had reasonable macroscopic accuracy, but the rim had a larger radius with less reentrancy. A discussion of the results and analyses in relation to future TBC effort and direction concludes the work.

33 ADVANCED PROPULSION SYSTEMS↗

Deep optical imaging of star-forming blue early-type galaxies: Color map structures and faint features indicative of recent mergers

Blue early-type galaxies with galaxy-scale ongoing star formation are interesting targets in order to understand the stellar mass buildup in elliptical and S0 galaxies in the local Universe. We study the star-forming population of blue early-type galaxies to understand the origin of star formation in these otherwise red and dead stellar systems. The legacy survey imaging data taken with the dark energy camera in the g, r, and z bands for 55 star-forming blue early-type galaxies were examined, and g – r color maps were created. We identified low surface brightness features near 37 galaxies, faint-level interaction signatures near 15 galaxies, and structures indicative of recent merger activity in the optical color maps of all 55 galaxies. These features are not visible in the shallow Sloan Digital Sky Survey imaging data in which these galaxies were originally identified. Low surface brightness features found around galaxies could be remnants of recent merger events. The star-forming population of blue early-type galaxies could be post-merger systems that are expected to be the pathway for the formation of elliptical galaxies. We hypothesize that the star-forming population of blue early-type galaxies is a stage in the evolution of early-type galaxies. The merger features will eventually disappear, fuel for star formation will cease, and the galaxy will move to the passive population of normal early-type galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗