@article{fraher_watson_nguyen_moore_lewis_kudenov_yencho_gorny_2024, title={A Comparison of Three Automated Root-Knot Nematode Egg Counting Approaches Using Machine Learning, Image Analysis, and a Hybrid Model}, volume={9}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-01-24-0217-SR}, abstractNote={spp. (root-knot nematodes [RKNs]) are a major threat to a wide range of agricultural crops worldwide. Breeding crops for RKN resistance is an effective management strategy, yet assaying large numbers of breeding lines requires laborious bioassays that are time-consuming and require experienced researchers. In these bioassays, quantifying nematode eggs through manual counting is considered the current standard for quantifying establishing resistance in plant genotypes. Counting RKN eggs is highly laborious, and even experienced researchers are subject to fatigue or misclassification, leading to potential errors in phenotyping. Here, we present three automated egg counting models that rely on machine learning and image analysis to quantify RKN eggs extracted from tobacco and sweet potato plants. The first method relied on convolutional neural networks trained using annotated images to identify eggs (}, journal={PLANT DISEASE}, author={Fraher, Simon P. and Watson, Mark and Nguyen, Hoang and Moore, Savannah and Lewis, Ramsey S. and Kudenov, Michael and Yencho, G. Craig and Gorny, Adrienne M.}, year={2024}, month={Sep} }
 @article{ahmed_wijewardane_lu_jones_kudenov_williams_villordon_kamruzzaman_2024, title={Advancing sweetpotato quality assessment with hyperspectral imaging and explainable artificial intelligence}, volume={220}, ISSN={["1872-7107"]}, url={http://dx.doi.org/10.1016/j.compag.2024.108855}, DOI={10.1016/j.compag.2024.108855}, abstractNote={The quality evaluation of sweetpotatoes is of utmost importance during postharvest handling as it significantly impacts consumer satisfaction, nutritional value, and market competitiveness. This study presents an innovative approach that integrates explainable artificial intelligence (AI) with hyperspectral imaging to enhance the assessment of three important quality attributes in sweetpotatoes, i.e., dry matter content, soluble solid content, and firmness. Sweetpotato samples of three different varieties, including "Bayou Belle", "Murasaki", and "Orleans", were imaged using a portable visible near-infrared hyperspectral imaging (VNIR-HSI) camera, with a 400–1000 nm spectral range. The extracted spectral data were used to select key wavelengths, develop multivariate regression models, and utilize SHapley Additive exPlanations (SHAP) values to ascertain model effectiveness and interpretability. The regression models (dry matter: R2p = 0.92, RMSEP = 1.50 % and RPD = 5.58; soluble solid content: R2p = 0.66, RMSEP = 0.85obrix, and RPD = 1.72; firmness: R2p = 0.85; RMSEP = 1.66 N and RPD = 2.63) developed with key wavelengths were used to generate prediction maps to visualize the spatial distribution of response attributes, facilitating an improved evaluation of sweetpotato quality. The study demonstrated that the combination of HSI, variable selection, and explainable AI has the potential to enhance the quality assessment of sweetpotatoes, ensuring supplies of higher quality products to consumers.}, journal={COMPUTERS AND ELECTRONICS IN AGRICULTURE}, author={Ahmed, Toukir and Wijewardane, Nuwan K. and Lu, Yuzhen and Jones, Daniela S. and Kudenov, Michael and Williams, Cranos and Villordon, Arthur and Kamruzzaman, Mohammed}, year={2024}, month={May} }
 @article{martinez_kudenov_nguyen_jones_williams_2024, title={Evaluating two high-throughput phenotyping platforms at early stages of the post-harvest pipeline of sweetpotatoes}, volume={8}, ISSN={["2772-3755"]}, url={http://dx.doi.org/10.1016/j.atech.2024.100469}, DOI={10.1016/j.atech.2024.100469}, abstractNote={Recent advancements in artificial intelligence and big data analytics introduce new tools that can enhance the packing efficiency of sweetpotatoes (Ipomoea batatas) (SPs). In this study, we focused on the quantification of inventory as early in the packing process as possible to allow for effective storage planning, smarter inventory selection to fulfill orders, and ultimately reduce the need for refrigeration of excess packed SPs. We built and implemented two scanners to quantify phenotype distributions at different stages of the post-harvest pipeline. Testing and validation were conducted through a collaboration with an industry-partner's packing facility in North Carolina, gaining access to their packing methods, warehouse data, and resources. The first scanner imaged all SPs during the conveyance stage, immediately after they are washed but before they are sorted. The second scanner, positioned to view the top bins after harvest, scanned the top layer of bins on harvesting trucks as they entered the storage warehouse for receiving. We compared the output of our first scanner to the output of a commercial optical sorter under a controlled packing simulation, and then compared our two developed scanners against each other in an observational commercial packing operation. We evaluated millions of SPs, assessing length, width, length-to-width ratio (LW ratio), and weight. We computed a pairwise t-test for each phenotype across scanner pairs and evaluated the Cohen's d effect size to interpret our results. We observed no significant differences in the grade distributions across the scanners, except for the "Giant" weight class, which showed variation between the top bin and eliminator table scanners. In summary, both systems demonstrated promising outcomes, suggesting a potential enhancement in packing efficiency through the timely delivery of comprehensive inventory data.}, journal={SMART AGRICULTURAL TECHNOLOGY}, author={Martinez, Enrique E. Pena and Kudenov, Michael and Nguyen, Hoang and Jones, Daniela S. and Williams, Cranos}, year={2024}, month={Aug} }
 @article{schrickx_kashani_buck_ding_rech_flagg_li_kudenov_you_richter_et al._2024, title={Exceptional Alignment in a Donor-Acceptor Conjugated Polymer via a Previously Unobserved Liquid Crystal Mesophase}, volume={4}, ISSN={["1616-3028"]}, DOI={10.1002/adfm.202315183}, abstractNote={AbstractOrienting polymer semiconductors is desirable to optimize device characteristics, provide insight into microstructure, and magnify subtle phase behavior. Here, a combination of uniaxial strain and subsequent heating of the donor–acceptor (DA) polymer PBnDT‐FTAZ is discovered to lead to exceptional optical dichroic ratios of up to 38 (and close to 50 near the polymer's absorption edge). This alignment is achieved due to the existence of a previously undetected thermotropic liquid crystal (LC) mesophase. The LC transition, not discernable through calorimetry, is uncovered through a combination of in situ UV–vis spectroscopy, X‐ray scattering, and dynamic mechanical analysis (DMA). Comparing PBnDT‐FTAZ to the non‐fluorinated PBnDT‐HTAZ and the homo polymer PBnDT, all of which show similar thermal transitions, reveals that exceptional alignment is only found in PBnDT‐FTAZ. This is attributed to the PBnDT‐FTAZ film having two distinct liquid crystal populations, and the polymer templating to a highly aligned, high‐clearing temperature population when heated. The DMA thermal relaxation behavior observed here is also seen in other DA conjugated polymers suggesting that such thermotropic LC mesophases may be common in these materials. These findings demonstrate a polymer semiconductor with remarkable alignment and uncover phase behavior with broad implications for process‐structure‐property relationships in polymer semiconductors.}, journal={ADVANCED FUNCTIONAL MATERIALS}, author={Schrickx, Harry M. and Kashani, Somayeh and Buck, Lauren and Ding, Kan and Rech, Jeromy J. and Flagg, Lucas Q. and Li, Ruipeng and Kudenov, Michael W. and You, Wei and Richter, Lee J. and et al.}, year={2024}, month={Apr} }
 @article{schrickx_gyurek_moore_hernandez-pagan_doherty_kudenov_brendan t. o'connor_2024, title={Flexible Self-Powered Organic Photodetector with High Detectivity for Continuous On-Plant Sensing}, volume={2}, ISSN={["2195-1071"]}, DOI={10.1002/adom.202400005}, abstractNote={AbstractOrganic photodetectors (OPDs) exhibit performance on par with inorganic detectors (e.g., Si) but can be ultrathin, ultra‐lightweight, flexible, and mechanically resilient, opening up opportunities for novel applications including optical sensors for continuous human and plant health monitoring. Here, a high‐performance flexible self‐powered OPD designed for on‐plant optical sensing is developed. The OPD employs an electrode consisting of Ag nanowires (NWs) embedded in a UV‐curable resin to achieve a flexible and thin form factor. In addition, the OPD active layer consisting of D18‐Cl and Y6 is sequentially cast to reduce dark current. The flexible OPD is sensitive to 400–950 nm wavelengths and exhibits photodetector characteristics comparable to state‐of‐the‐art rigid OPDs. The responsivity reaches values of 0.47 A W−1 and specific detectivity exceeds 1012 Jones. Owing to the embedded Ag NW electrodes in a thin substrate (t = 20 µm) and sequentially cast active layers, the detector demonstrates excellent bending stability. The photocurrent remains steady across 4000 cycles with a bending radius of 2 mm. The flexible OPD is demonstrated to effectively detect plant uptake of the rare‐earth metal terbium and sense time‐dependent chlorophyll fluorescence. Thus, this work highlights the potential for OPDs as on‐plant sensors to advance precision agriculture.}, journal={ADVANCED OPTICAL MATERIALS}, author={Schrickx, Harry M. and Gyurek, Sydney and Moore, Caleb and Hernandez-Pagan, Edmaritz and Doherty, Colleen J. and Kudenov, Michael W. and Brendan T. O'Connor}, year={2024}, month={Feb} }
 @article{banah_balint-kurti_houdinet_hawkes_kudenov_2024, title={The quantification of southern corn leaf blight disease using deep UV fluorescence spectroscopy and autoencoder anomaly detection techniques}, volume={19}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0301779}, abstractNote={Southern leaf blight (SLB) is a foliar disease caused by the fungus Cochliobolus heterostrophus infecting maize plants in humid, warm weather conditions. SLB causes production losses to corn producers in different regions of the world such as Latin America, Europe, India, and Africa. In this paper, we demonstrate a non-destructive method to quantify the signs of fungal infection in SLB-infected corn plants using a deep UV (DUV) fluorescence spectrometer, with a 248.6 nm excitation wavelength, to acquire the emission spectra of healthy and SLB-infected corn leaves. Fluorescence emission spectra of healthy and diseased leaves were used to train an Autoencoder (AE) anomaly detection algorithm—an unsupervised machine learning model—to quantify the phenotype associated with SLB-infected leaves. For all samples, the signature of corn leaves consisted of two prominent peaks around 450 nm and 325 nm. However, SLB-infected leaves showed a higher response at 325 nm compared to healthy leaves, which was correlated to the presence of C. heterostrophus based on disease severity ratings from Visual Scores (VS). Specifically, we observed a linear inverse relationship between the AE error and the VS ( R 2 = 0.94 and RMSE = 0.935). With improved hardware, this method may enable improved quantification of SLB infection versus visual scoring based on e.g., fungal spore concentration per unit area and spatial localization.}, number={5}, journal={PLOS ONE}, author={Banah, Hashem and Balint-Kurti, Peter J. and Houdinet, Gabriella and Hawkes, Christine V. and Kudenov, Michael}, year={2024}, month={May} }
 @article{kudenov_krafft_scarboro_doherty_balint-kurti_2023, title={Hybrid spatial-temporal Mueller matrix imaging spectropolarimeter for high throughput plant phenotyping}, volume={62}, ISSN={["2155-3165"]}, DOI={10.1364/AO.483870}, abstractNote={Many correlations exist between
					spectral reflectance or transmission with various phenotypic responses
					from plants. Of interest to us are metabolic characteristics, namely,
					how the various polarimetric components of plants may correlate to
					underlying environmental, metabolic, and genotypic differences among
					different varieties within a given species, as conducted during large
					field experimental trials. In this paper, we overview a portable
					Mueller matrix imaging spectropolarimeter, optimized for field use, by
					combining a temporal and spatial modulation scheme. Key aspects of the
					design include minimizing the measurement time while maximizing the
					signal-to-noise ratio by mitigating systematic error. This was
					achieved while maintaining an imaging capability across multiple
					measurement wavelengths, spanning the blue to near-infrared spectral
					region (405–730 nm). To this end, we present our optimization
					procedure, simulations, and calibration methods. Validation results,
					which were taken in redundant and non-redundant measurement
					configurations, indicated that the polarimeter provides average
					absolute errors of (5.3±2.2)×10−3 and (7.1±3.1)×10−3, respectively. Finally, we provide
					preliminary field data (depolarization, retardance, and diattenuation)
					to establish baselines of barren and non-barren Zea maize hybrids (G90 variety), as captured from various
					leaf and canopy positions during our summer 2022 field experiments.
					Results indicate that subtle variations in retardance and
					diattenuation versus leaf canopy position may be present before they
					are clearly visible in the spectral transmission.}, number={8}, journal={APPLIED OPTICS}, author={Kudenov, Michael W. and Krafft, Danny and Scarboro, Clifton G. and Doherty, Colleen J. and Balint-Kurti, Peter}, year={2023}, month={Mar}, pages={2078–2091} }
 @article{altaqui_schrickx_gyurek_sen_escuti_brendan t. o'connor_kudenov_2022, title={Cephalopod-inspired snapshot multispectral sensor based on geometric phase lens and stacked organic photodetectors}, volume={61}, ISSN={["1560-2303"]}, DOI={10.1117/1.OE.61.7.077104}, abstractNote={Abstract. Multispectral imaging (MSI) is a valuable sensing modality for applications that require detecting a scene’s chemical characteristics. Existing MSI techniques utilize a filter wheel or color filter arrays, which are subject to reduced temporal or spatial resolution. In this work, we present a cephalopod-inspired multispectral organic sensor (CiMOS) based on geometric phase lenses (GPLs) and organic photovoltaics (OPVs) to enable aberration-based color sensing. We mimic the approach by which animals with single-type photoreceptors perceive colors via chromatic aberration. The intrinsic chromatic aberration of GPLs allows for multispectral sensing by stacking precisely patterned OPVs within specific spectrally dependent focal lengths. We provide simulations and a proof of concept of the CiMOS and highlight its advantages, including its simple design and snapshot multi-color detection using only a single axial position. Experimental results demonstrate the sensor’s ability to detect four colors with full width at half maximum spectral resolution as low as 35 nm.}, number={7}, journal={OPTICAL ENGINEERING}, author={Altaqui, Ali and Schrickx, Harry and Gyurek, Sydney and Sen, Pratik and Escuti, Michael and Brendan T. O'Connor and Kudenov, Michael}, year={2022}, month={Jul} }
 @article{larsen_austin_dunne_kudenov_2022, title={Drone-based polarization imaging for phenotyping peanut in response to leaf spot disease}, volume={12112}, ISBN={["978-1-5106-5100-5"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.2623073}, abstractNote={Polarization imaging has been used extensively in applications related to atmospheric monitoring, remote sensing, and quality control. However, it has been used less extensively in agricultural applications, where color sensing - either red, green, and blue (RGB) imaging, multispectral, and/or hyperspectral cameras are more common. In this paper, we discuss our preliminary results related to the use of polarization imaging to quantify defoliation in peanut plants in response to leaf spot disease. A key metric for breeding resistant peanut varieties involves identifying the point at which defoliation occurs. Since defoliation is a geometrical property of the plant canopy, we investigated whether polarization imaging can provide a better-automated score when compared to conventional visual scoring. Initial results are presented, as well as a discussion of our drone-based platform and our experimental trials conducted during the 2021 North Carolina growing season.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XV}, author={Larsen, Joshua C. and Austin, Robert and Dunne, Jeffrey and Kudenov, Michael W.}, year={2022} }
 @article{hetzler_wang_krafft_jamalzadegan_overton_kudenov_ligler_wei_2022, title={Flexible sensor patch for continuous carbon dioxide monitoring}, volume={10}, ISSN={["2296-2646"]}, DOI={10.3389/fchem.2022.983523}, abstractNote={Monitoring and measurement of carbon dioxide (CO2) is critical for many fields. The gold standard CO2 sensor, the Severinghaus electrode, has remained unchanged for decades. In recent years, many other CO2 sensor formats, such as detection based upon pH-sensitive dyes, have been demonstrated, opening the door for relatively simple optical detection schemes. However, a majority of these optochemical sensors require complex sensor preparation steps and are difficult to control and repeatably execute. Here, we report a facile CO2 sensor generation method that suffers from none of the typical fabrication issues. The method described here utilizes polydimethylsiloxane (PDMS) as the flexible sensor matrix and 1-hydroxypyrene-3,6,8-trisulfonate (HPTS), a pH-sensitive dye, as the sensing material. HPTS, a base (NaOH), and glycerol are loaded as dense droplets into a thin PDMS layer which is subsequently cured around the droplet. The fabrication process does not require prior knowledge in chemistry or device fabrication and can be completed as quickly as PDMS cures (∼2 h). We demonstrate the application of this thin-patch sensor for in-line CO2 quantification in cell culture media. To this end, we optimized the sensing composition and quantified CO2 in the range of 0–20 kPa. A standard curve was generated with high fidelity (R2 = 0.998) along with an analytical resolution of 0.5 kPa (3.7 mm Hg). Additionally, the sensor is fully autoclavable for applications requiring sterility and has a long working lifetime. This flexible, simple-to-manufacture sensor has a myriad of potential applications and represents a new, straightforward means for optical carbon dioxide measurement.}, journal={FRONTIERS IN CHEMISTRY}, author={Hetzler, Zach and Wang, Yan and Krafft, Danny and Jamalzadegan, Sina and Overton, Laurie and Kudenov, Michael W. and Ligler, Frances S. and Wei, Qingshan}, year={2022}, month={Sep} }
 @article{scarboro_doherty_balint-kurti_kudenov_2022, title={Multistatic fiber-based system for measuring the Mueller matrix bidirectional reflectance distribution function}, volume={61}, ISSN={["2155-3165"]}, DOI={10.1364/AO.470608}, abstractNote={Bidirectionality effects can be a significant confounding factor when
					measuring hyperspectral reflectance data. The bidirectional
					reflectance distribution function (BRDF) can effectively characterize
					the reflectivity of surfaces to correct remote sensing measurements.
					However, measuring BRDFs can be time-consuming, especially when
					collecting Mueller matrix BRDF (mmBRDF) measurements of a surface via
					conventional goniometric techniques. In this paper, we present a
					system for collecting mmBRDF measurements using static optical fiber
					detectors that sample the hemisphere surrounding an object. The
					entrance to each fiber contains a polarization state analyzer
					configuration, allowing for the simultaneous acquisition of the Stokes
					vector intensity components at many altitudinal and azimuthal viewing
					positions. We describe the setup, calibration, and data processing
					used for this system and present its performance as applied to mmBRDF
					measurements of a ground glass diffuser.}, number={33}, journal={APPLIED OPTICS}, author={Scarboro, Clifton G. and Doherty, Colleen J. and Balint-Kurti, Peter J. and Kudenov, Michael W.}, year={2022}, month={Nov}, pages={9832–9842} }
 @article{kudenov_altaqui_williams_2022, title={Practical spectral photography II: snapshot spectral imaging using linear retarders and microgrid polarization cameras}, volume={30}, ISSN={["1094-4087"]}, DOI={10.1364/OE.453538}, abstractNote={Despite recent advances, customized multispectral cameras can be challenging or costly to deploy in some use cases. Complexities span electronic synchronization, multi-camera calibration, parallax and spatial co-registration, and data acquisition from multiple cameras, all of which can hamper their ease of use. This paper discusses a generalized procedure for multispectral sensing using a pixelated polarization camera and anisotropic polymer film retarders to create multivariate optical filters. We then describe the calibration procedure, which leverages neural networks to convert measured data into calibrated spectra (intensity versus wavelength). Experimental results are presented for a multivariate and channeled optical filter. Finally, imaging results taken using a red, green, and blue microgrid polarization camera and the channeled optical filter are presented. Imaging experiments indicated that the calculated spectra’s root mean square error is highest in the region where the camera’s red, green, and blue filter responses overlap. The average error of the spectral reflectance, measured of our spectralon tiles, was 6.5% for wavelengths spanning 425-675 nm. This technique demonstrates that 12 spectral channels can be obtained with a relatively simple and robust optical setup, and at minimal cost beyond the purchase of the camera.}, number={8}, journal={OPTICS EXPRESS}, author={Kudenov, Michael W. and Altaqui, Ali and Williams, Cranos}, year={2022}, month={Apr}, pages={12337–12352} }
 @article{mckee_nguyen_kudenov_christian_2022, title={StarNAV with a wide field-of-view optical sensor}, volume={197}, ISSN={["1879-2030"]}, DOI={10.1016/j.actaastro.2022.04.027}, abstractNote={StarNAV is a method for inferring an observer's velocity from measurements of starlight that have been perturbed by stellar aberration. This usually takes the form of measuring changes in inter-star angles as compared to a reference. Usable velocity estimates require either the measurement of (1) a few inter-star angles with high accuracy or (2) a great many inter-star angles with lower accuracy. This work explores the efficacy of a hypothetical sensor following the latter approach through the use of wide field-of-view (FOV) optical cameras. Key algorithmic considerations for processing large star fields are discussed and an exploration of the design space is performed. A feasible point design with proof-of-concept performance is developed and is shown to fit within a 3U CubeSat form factor.}, journal={ACTA ASTRONAUTICA}, author={McKee, Paul and Nguyen, Hoang and Kudenov, Michael W. and Christian, John A.}, year={2022}, month={Aug}, pages={220–234} }
 @article{altaqui_schrickx_sen_li_rech_lee_balar_you_kim_escuti_et al._2021, title={Bio-inspired spectropolarimetric sensor based on tandem organic photodetectors and multi-twist liquid crystals}, volume={29}, ISSN={["1094-4087"]}, url={https://doi.org/10.1364/OE.431858}, DOI={10.1364/OE.431858}, abstractNote={Simultaneous spectral and polarimetric imaging enables versatile detection and multimodal characterization of targets of interest. Current architectures incorporate a 2×2 pixel arrangement to acquire the full linear polarimetric information causing spatial sampling artifacts. Additionally, they suffer from limited spectral selectivity and high color crosstalk. Here, we demonstrate a bio-inspired spectral and polarization sensor structure based on integrating semitransparent polarization-sensitive organic photovoltaics (P-OPVs) and liquid crystal polymer (LCP) retarders in a tandem configuration. Color tuning is realized by leveraging the dynamic chromatic retardation control of LCP films, while polarization sensitivity is realized by exploiting the flexible anisotropic properties of P-OPVs. The structure is marked by its ultra-thin design and its ability to detect spectral and polarimetric contents along the same optical axis, thereby overcoming the inherent limitations associated with conventional division-of-focal plane sensors.}, number={26}, journal={OPTICS EXPRESS}, publisher={The Optical Society}, author={Altaqui, Ali and Schrickx, Harry and Sen, Pratik and Li, Lingshan and Rech, Jeromy and Lee, Jin-Woo and Balar, Nrup and You, Wei and Kim, Bumjoon J. and Escuti, Michael and et al.}, year={2021}, month={Dec}, pages={43953–43969} }
 @article{haque_lobaton_nelson_yencho_pecota_mierop_kudenov_boyette_williams_2021, title={Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery}, volume={182}, ISSN={0168-1699}, url={http://dx.doi.org/10.1016/j.compag.2021.106011}, DOI={10.1016/j.compag.2021.106011}, abstractNote={For many horticultural crops, variation in quality (e.g., shape and size) contributes significantly to the crop's market value. Metrics characterizing less subjective harvest quantities (e.g., yield and total biomass) are routinely monitored. In contrast, metrics quantifying more subjective crop quality characteristics such as ideal size and shape remain difficult to characterize objectively at the production-scale due to the lack of modular technologies for high-throughput sensing and computation. Several horticultural crops are sent to packing facilities after having been harvested, where they are sorted into boxes and containers using high-throughput scanners. These scanners capture images of each fruit or vegetable being sorted and packed, but the images are typically used solely for sorting purposes and promptly discarded. With further analysis, these images could offer unparalleled insight on how crop quality metrics vary at the industrial production-scale and provide further insight into how these characteristics translate to overall market value. At present, methods for extracting and quantifying quality characteristics of crops using images generated by existing industrial infrastructure have not been developed. Furthermore, prior studies that investigated horticultural crop quality metrics, specifically of size and shape, used a limited number of samples, did not incorporate deformed or non-marketable samples, and did not use images captured from high-throughput systems. In this work, using sweetpotato (SP) as a use case, we introduce a computer vision algorithm for quantifying shape and size characteristics in a high-throughput manner. This approach generates 3D model of SPs from two 2D images captured by an industrial sorter 90 degrees apart and extracts 3D shape features in a few hundred milliseconds. We applied the 3D reconstruction and feature extraction method to thousands of image samples to demonstrate how variations in shape features across SP cultivars can be quantified. We created a SP shape dataset containing SP images, extracted shape features, and qualitative shape types (U.S. No. 1 or Cull). We used this dataset to develop a neural network-based shape classifier that was able to predict Cull vs. U.S. No. 1 SPs with 84.59% accuracy. In addition, using univariate Chi-squared tests and random forest, we identified the most important features for determining qualitative shape type (U.S. No. 1 or Cull) of the SPs. Our study serves as a key step towards enabling big data analytics for industrial SP agriculture. The methodological framework is readily transferable to other horticultural crops, particularly those that are sorted using commercial imaging equipment.}, journal={Computers and Electronics in Agriculture}, publisher={Elsevier BV}, author={Haque, Samiul and Lobaton, Edgar and Nelson, Natalie and Yencho, G. Craig and Pecota, Kenneth V. and Mierop, Russell and Kudenov, Michael W. and Boyette, Mike and Williams, Cranos M.}, year={2021}, month={Mar}, pages={106011} }
 @article{dorman_kudenov_lytle_griffith_huseth_2021, title={Computer vision for detecting field‐evolved lepidopteran resistance to
            <i>Bt
            maize}, volume={77}, ISSN={1526-498X 1526-4998}, url={http://dx.doi.org/10.1002/ps.6566}, DOI={10.1002/ps.6566}, abstractNote={AbstractBACKGROUNDResistance evolution of lepidopteran pests to Bacillus thuringiensis (Bt) toxins produced in maize and cotton is a significant issue worldwide. Effective toxin stewardship requires reliable detection of field‐evolved resistance to enable the implementation of mitigation strategies. Currently, visual estimates of maize injury are used to document changing susceptibility. In this study, we evaluated an existing maize injury monitoring protocol used to estimate Bt resistance levels in Helicoverpa zea (Lepidoptera: Noctuidae).RESULTSWe detected high interobserver variability across multiple injury metrics, suggesting that the precision and accuracy of maize injury detection could be improved. To do this, we developed a computer vision‐based algorithm to measure H. zea injury. Algorithm estimates were more accurate and precise than a sample of human observers. Moreover, observer estimates tended to overpredict H. zea injury, which may increase the false‐positive rate, leading to prophylactic insecticide application and unnecessary regulatory action.CONCLUSIONSAutomated detection and tracking of lepidopteran resistance evolution to Bt toxins are critical for genetically engineered crop stewardship to prevent the use of additional insecticides to combat resistant pests. Advantages of this computerized screening are: (i) standardized Bt injury metrics in space and time, (ii) preservation of digital data for cross‐referencing when thresholds are reached, and (iii) the ability to increase sample sizes significantly. This technological solution represents a significant step toward improving confidence in resistance monitoring efforts among researchers, regulators and the agricultural biotechnology industry.}, number={11}, journal={Pest Management Science}, publisher={Wiley}, author={Dorman, Seth J and Kudenov, Michael W and Lytle, Amanda J and Griffith, Emily H and Huseth, Anders S}, year={2021}, month={Aug}, pages={5236–5245} }
 @article{kudenov_krafft_scarboro_doherty_balint-kurti_2021, title={Fieldable Mueller matrix imaging spectropolarimeter using a hybrid spatial and temporal modulation scheme}, volume={11833}, ISSN={["1996-756X"]}, DOI={10.1117/12.2593970}, abstractNote={Many correlations exist between spectral reflectance and various phenotypic responses from plants. Of interest to us are structural characteristics; namely, how the various spectral and polarimetric components may correlate to underlying environmental, metabolic, and genotypic differences among plant varieties within a given species. In this paper, we overview a portable Mueller matrix imaging spectropolarimeter that has been optimized for field use. Key aspects to the design included minimizing the measurement time while maximizing signal-to-noise ratio with low systematic errors. These goals must be achieved while maintaining an imaging capability across multiple measurement wavelengths, spanning the blue to near-infrared spectral region. To this end, we will review our optimization procedure, simulations, and experimental results, including preliminary field data taken from our summer 2021 field trials.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING X}, author={Kudenov, Michael W. and Krafft, Danny and Scarboro, Clifton G. and Doherty, Colleen J. and Balint-Kurti, Peter}, year={2021} }
 @article{kudenov_scarboro_altaqui_boyette_yencho_williams_2021, title={Internal defect scanning of sweetpotatoes using interactance spectroscopy}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0246872}, abstractNote={While standard visible-light imaging offers a fast and inexpensive means of quality analysis of horticultural products, it is generally limited to measuring superficial (surface) defects. Using light at longer (near-infrared) or shorter (X-ray) wavelengths enables the detection of superficial tissue bruising and density defects, respectively; however, it does not enable the optical absorption and scattering properties of sub-dermal tissue to be quantified. This paper applies visible and near-infrared interactance spectroscopy to detect internal necrosis in sweetpotatoes and develops a Zemax scattering simulation that models the measured optical signatures for both healthy and necrotic tissue. This study demonstrates that interactance spectroscopy can detect the unique near-infrared optical signatures of necrotic tissues in sweetpotatoes down to a depth of approximately 5±0.5 mm. We anticipate that light scattering measurement methods will represent a significant improvement over the current destructive analysis methods used to assay for internal defects in sweetpotatoes.}, number={2}, journal={PLOS ONE}, author={Kudenov, Michael W. and Scarboro, Clifton G. and Altaqui, Ali and Boyette, Mike and Yencho, G. Craig and Williams, Cranos M.}, year={2021}, month={Feb} }
 @article{altaqui_sen_schrickx_rech_lee_escuti_you_kim_kolbas_brendan t. o'connor_et al._2021, title={Mantis shrimp-inspired organic photodetector for simultaneous hyperspectral and polarimetric imaging}, volume={7}, ISSN={["2375-2548"]}, url={https://doi.org/10.1126/sciadv.abe3196}, DOI={10.1126/sciadv.abe3196}, abstractNote={Semitransparent polarization-sensitive organic detectors reveal unprecedented degrees of freedom for multidimensional imaging.}, number={10}, journal={SCIENCE ADVANCES}, publisher={American Association for the Advancement of Science (AAAS)}, author={Altaqui, Ali and Sen, Pratik and Schrickx, Harry and Rech, Jeromy and Lee, Jin-Woo and Escuti, Michael and You, Wei and Kim, Bumjoon J. and Kolbas, Robert and Brendan T. O'Connor and et al.}, year={2021}, month={Mar} }
 @article{altaqui_kolbas_escuti_brendan t. o'connor_kudenov_2021, title={Organic-based photodetectors for multiband spectral imaging}, volume={60}, ISSN={["2155-3165"]}, DOI={10.1364/AO.417069}, abstractNote={Using organic photodetectors for multispectral sensing is attractive due to their unique capabilities to tune spectral response, transmittance, and polarization sensitivity. Existing methods lack tandem multicolor detection and exhibit high spectral cross talk. We exploit the polarization sensitivity of organic photodetectors, together with birefringent optical filters to design single-pixel multispectral detectors that achieve high spectral selectivity and good radiometric performance. Two different architectures are explored and optimized, including the Solc-based and multitwist-retarder-based organic photodetectors. Although the former demonstrated a higher spectral resolution, the latter enables a more compact sensor as well as greater flexibility in device fabrication.}, number={8}, journal={APPLIED OPTICS}, author={Altaqui, Ali and Kolbas, Robert M. and Escuti, Michael J. and Brendan T. O'Connor and Kudenov, Michael W.}, year={2021}, month={Mar}, pages={2314–2323} }
 @article{scarboro_ruzsa_doherty_kudenov_2021, title={Quantification of gray mold infection in lettuce using a bispectral imaging system under laboratory conditions}, volume={5}, ISSN={["2475-4455"]}, url={https://doi.org/10.1002/pld3.317}, DOI={10.1002/pld3.317}, abstractNote={AbstractGray mold disease caused by the fungus Botrytis cinerea damages many crop hosts worldwide and is responsible for heavy economic losses. Early diagnosis and detection of the disease would allow for more effective crop management practices to prevent outbreaks in field or greenhouse settings. Furthermore, having a simple, non‐invasive way to quantify the extent of gray mold disease is important for plant pathologists interested in measuring infection rates. In this paper, we design and build a bispectral imaging system for discriminating between leaf regions infected with gray mold and those that remain unharmed on a lettuce (Lactuca spp.) host. First, we describe a method to select two optimal (high contrast) spectral bands from continuous hyperspectral imagery (450–800 nm). We then explain the process of building a system based on these two spectral bands, located at 540 and 670 nm. The resultant system uses two cameras, with a narrow band‐pass spectral filter mounted on each, to measure the bispectral reflectance of a lettuce leaf. The two resulting images are combined using a normalized difference calculation that produces a single image with high contrast between the leaves’ infected and healthy regions. A classifier was then created based on the thresholding of single pixel values. We demonstrate that this simple classification produces a true‐positive rate of 95.25% with a false‐positive rate of 9.316% in laboratory conditions.}, number={3}, journal={PLANT DIRECT}, publisher={Wiley}, author={Scarboro, Clifton G. and Ruzsa, Stephanie M. and Doherty, Colleen J. and Kudenov, Michael W.}, year={2021}, month={Mar} }
 @article{kudenov_altaqui_williams_2021, title={Snapshot spectral imaging using Solc-based multivariate optical filters and pixelated polarization cameras}, volume={11833}, ISSN={["1996-756X"]}, DOI={10.1117/12.2596580}, abstractNote={Despite recent advances, customized multispectral cameras can be challenging or costly to deploy in some use cases. Complexities span electronic synchronization, multi-camera calibration, parallax and spatial coregistration, and data acquisition from multiple cameras, all of which can hamper their ease of use. This paper discusses a generalized procedure for multispectral sensing using a pixelated polarization camera and Solc stages to create multivariate optical filters. We then describe some preliminary experimental results of a fabricated filtered camera system. Finally, classification of the imagery is achieved using either shallow or deep neural networks. We also discuss the potential of using a color red, green, and blue microgrid polarization camera to detect upwards of 12 spectral channels using readily available standard off-the-shelf components.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING X}, author={Kudenov, Michael W. and Altaqui, Ali and Williams, Cranos}, year={2021} }
 @article{schrickx_sen_booth_altaqui_burleson_rech_lee_biliroglu_gundogdu_kim_et al._2021, title={Ultra-High Alignment of Polymer Semiconductor Blends Enabling Photodetectors with Exceptional Polarization Sensitivity}, volume={10}, ISSN={["1616-3028"]}, DOI={10.1002/adfm.202105820}, abstractNote={AbstractPhotodetectors that can sense not only light intensity but also light's polarization state add valuable information that is beneficial in a wide array of applications. Polymer semiconductors are an attractive material system to achieve intrinsic polarization sensitivity due to their anisotropic optoelectronic properties. In this report, the thermomechanical properties of the polymer semiconductors PBnDT‐FTAZ and P(NDI2OD‐T2) are leveraged to realize bulk heterojunction (BHJ) films with record in‐plane alignment. Two polymer blends with distinct weight average molar masses (Mw) are considered and either a strain‐ or rub‐alignment process is applied to align the polymer blend films. Optimized processing yields films with dichroic ratios (DR) of over 11 for the high Mw system and nearly 17 for the low Mw system. Incorporating the aligned films into photodetectors results in a polarized photocurrent ratio of 15.25 with corresponding anisotropy ratio of 0.88 at a wavelength of 530 nm, representing the highest reported photocurrent ratio for photodiodes that can operate in a self‐powered regime. The demonstrated performance showcases the ability of polymer semiconductors to achieve BHJ films with exceptional in‐plane polymer alignment, enabling high performance polarization sensitive photodetectors for incorporation into novel device architectures.}, journal={ADVANCED FUNCTIONAL MATERIALS}, author={Schrickx, Harry M. and Sen, Pratik and Booth, Ronald E. and Altaqui, Ali and Burleson, Jacob and Rech, Jeromy J. and Lee, Jin-Woo and Biliroglu, Melike and Gundogdu, Kenan and Kim, Bumjoon J. and et al.}, year={2021}, month={Oct} }
 @article{kudenov_pantalone_yang_2020, title={Dual-beam potassium Voigt filter for atomic line imaging}, volume={59}, ISSN={["2155-3165"]}, DOI={10.1364/AO.393649}, abstractNote={Spectrally narrowband imaging in remote sensing applications can be advantageous for detecting atomic emission features. This is especially useful in detecting specific constituents within rocket plumes, which are challenging to discern from naturally occurring sunglints. In this paper, we demonstrate a dual-beam technique, implemented with a Wollaston prism, for calibrating a Voigt magneto-optical filter for a linear polarizer’s finite extinction ratio, as well as optical misalignment between the linear polarizers’ transmission axes. Such a strategy would be key towards expanding the filter’s field of view while maintaining its classification capabilities. Validation of the potassium Voigt filter is demonstrated using the simulation tool ElecSus in combination with a potassium hollow cathode lamp. RMS error between the filter’s temperature response and that of the simulation was approximately 2%. We then demonstrate the detection of a potassium model rocket motor outdoors alongside a sunglint. Results indicate a 20-fold increase in contrast when using our dual-beam calibration strategy.}, number={17}, journal={APPLIED OPTICS}, author={Kudenov, Michael W. and Pantalone, Brett and Yang, Ruonan}, year={2020}, month={Jun}, pages={5282–5289} }
 @article{yang_sen_o'connor_kudenov_2020, title={Optimization of an intrinsic coincident polarimeter and quantitative architectural comparison of different polarimeter techniques}, volume={59}, ISSN={["1560-2303"]}, DOI={10.1117/1.OE.59.2.024111}, abstractNote={Abstract. Polarimeters have broad applications in remote sensing, astronomy, and biomedical imaging to measure a scene’s polarization state. An intrinsic coincident (IC) full-Stokes polarimeter was previously demonstrated and optimized to achieve high temporal and spatial resolution. We optimized the IC polarimeter by introducing additional waveplates or measurement channels and compared it with existing polarimeter architectures under signal-independent Gaussian noise and signal-dependent Poisson noise. The quantitative comparison of noise variances showed that the IC and division-of-amplitude polarimeters have the lowest noise variances due to their higher signal collection ability. Both polarimeters have a factor of 2 and 2 improved signal-to-noise ratio, in the S0 component, for Gaussian and Poisson noises, respectively, as compared to division of time, division of focal plane, and division of aperture polarimeters. While the division of amplitude and IC polarimeters outperforms other approaches, the IC polarimeter has a significantly simpler design, potentially allowing for cost-effective, high-performance polarimetric imaging.}, number={2}, journal={OPTICAL ENGINEERING}, author={Yang, Ruonan and Sen, Pratik and O'Connor, Brendan and Kudenov, Michael}, year={2020}, month={Feb} }
 @article{kudenov_pantalone_2019, title={Direct correlation spectrometer using polarized light}, volume={11132}, ISSN={["1996-756X"]}, DOI={10.1117/12.2530056}, abstractNote={Measuring a target’s radial velocity is usually achieved using high-resolution spectroscopy; however, higher signal to noise ratios can be obtained using direct correlation spectrometers (DCSs). In our system, a liquid crystal spatial light modulator serves as the mask against which the incident spectrum is correlated, and the polarization is controlled to enable both in- and out-of-band light to be captured simultaneously. This offers enhanced performance against atmospheric scintillation and may also enable single-shot radial velocity measurements. In this paper, we describe the design and implementation of our polarization-DCS and experimental validation is performed by acquiring radial velocity measurements of Venus.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING IX}, author={Kudenov, Michael W. and Pantalone, Brett}, year={2019} }
 @article{kudenov_pantalone_2019, title={Dual-beam cross-correlation spectrometer for radial velocity measurements}, volume={58}, ISSN={["2155-3165"]}, DOI={10.1364/AO.58.009310}, abstractNote={Measuring the radial velocity of an object can be achieved by quantifying the Doppler shift of Fraunhofer lines. Measurements are typically made using high-resolution conventional spectroscopy, in which the Doppler shift is calculated numerically on a computer. An alternative technique includes cross-correlation spectroscopy, which performs an optical correlation of the incident spectrum against a reference spectrum embedded in the instrument. Many existing correlation spectrometers leverage a chrome mask and obtain a single beam measurement, making the sensors more sensitive to atmospheric turbulence without moving parts. In this paper, we present a static dual-beam polarization-based technique for acquiring cross-correlation spectra that is insensitive to atmospheric turbulence and contains no moving parts. The instrument is based on acquiring light both inside and outside of the solar Fraunhofer lines using a twisted nematic liquid-crystal spatial light modulator. Correlation spectra can be calculated as a ratio of these two components. A model of the dual-beam cross-correlation spectrometer is presented and subsequently validated with experimental observations of Venus. Radial velocity accuracies, as calculated against reference ephemerides, yielded an absolute error less than 0.24%.}, number={33}, journal={APPLIED OPTICS}, author={Kudenov, Michael W. and Pantalone, Brett}, year={2019}, month={Nov}, pages={9310–9317} }
 @article{maione_baldridge_kudenov_2019, title={Microbolometer with a multi-aperture polymer thin-film array for neural-network-based target identification}, volume={58}, ISSN={["2155-3165"]}, DOI={10.1364/AO.58.007285}, abstractNote={Infrared imaging spectrometers are frequently used for detecting chemicals at standoff distances. Cost, size, and sensitivity are common tradeoffs in this regime, particularly when deploying infrared imaging arrays. In this work, we develop and characterize an infrared snapshot computational imaging spectrometer that leverages a multi-aperture filtered design. A theoretical model is developed, describing the multiplexed encoding technique. The experimental system is then described, including filter optimization and fabrication. Finally, the performance of the system is tested, leveraging a neural-network-based calibration approach, for various indoor and outdoor detection scenarios involving liquid contaminants. The results of our testing demonstrate that the system can detect room-temperature liquid contaminants under cold sky downwelling radiance conditions. We achieve a false positive rate (FPR) of 0.12% at a true positive rate (TPR) of 95% for silicon oil on sand at 18°C and a FPR of 2% at a TPR of 95% for silicon oil on various substrates at 23°C. Results support the efficacy of using uncooled polymer absorption filters for infrared imaging liquid contaminant detectors.}, number={27}, journal={APPLIED OPTICS}, author={Maione, Bryan D. and Baldridge, Christopher and Kudenov, Michael W.}, year={2019}, month={Sep}, pages={7285–7297} }
 @article{yang_sen_brendan t. o'connor_kudenov_2020, title={Optical crosstalk and off-axis modeling of an intrinsic coincident polarimeter}, volume={59}, ISSN={["2155-3165"]}, DOI={10.1364/AO.59.000156}, abstractNote={Polarimeters have broad applications in remote sensing, astronomy, and biomedical imaging to measure the emitted, reflected, or transmitted state of polarization. An intrinsic coincident (IC) full-Stokes polarimeter was previously demonstrated by our group, in a free space configuration, by using stain-aligned polymer-based organic photovoltaics. To minimize the model’s complexity, these were tilted to avoid crosstalk from back-reflections. We present a theoretical model of a monolithic IC polarimeter that considers the back-reflection’s influence for on-axis light. The model was validated using a monolithic four-detector polarimeter, which achieved an error of less than 3%. Additionally, an off-axis model was produced and validated for a simpler two detector polarimeter, demonstrating an error between the TM and TE polarized components of less than 3% for angles spanning an 18° incidence cone.}, number={1}, journal={APPLIED OPTICS}, author={Yang, Ruonan and Sen, Pratik and Brendan T. O'Connor and Kudenov, Michael W.}, year={2020}, month={Jan}, pages={156–164} }
 @article{altaqui_kudenov_2019, title={Phase-shifting interferometry in fiber-based channeled spectropolarimeter}, volume={11132}, ISSN={["1996-756X"]}, DOI={10.1117/12.2529975}, abstractNote={Channeled spectropolarimetry measures the spectral dependence of the polarization states of light. This technique is marked by its snapshot feature, in that the complete polarization states can be determined simultaneously from a single intensity spectrum. However, without athermalization, it suffers from high sensitivity to temperature, which in turn, degrades the polarimetric reconstruction accuracy. In this paper, we present a calibration technique for a fiber-based channeled spectropolarimetry that leverages phase-shifting interferometry to accurately demodulate the retarders' phase, thereby improving the accuracy of the acquired Stokes parameters. Additionally, it enables robust spectropolarimetric performance that is insensitive to environmental perturbations. Experimental results demonstrate that calibrations using phase-shifting interferometry improve the Stokes reconstruction results by approximately a factor of 3 when compared to the reference beam calibration method.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING IX}, author={Altaqui, Ali and Kudenov, M. W.}, year={2019} }
 @article{altaqui_kudenov_2019, title={Phase-shiftinginterferometry-based Fourier transform channeled spectropolarimeter}, volume={58}, ISSN={["2155-3165"]}, DOI={10.1364/AO.58.001830}, abstractNote={Channeled spectropolarimetry is a snapshot technique for measuring the spectral dependence of the state of polarization of light. However, it suffers from two major limitations, namely, its high sensitivity to environmental perturbations and its susceptibility to channel crosstalk. These limitations reduce the polarimetric reconstruction accuracy of the spectropolarimeter. A new calibration technique for channeled spectropolarimetry is presented that utilizes the concept of phase-shifting interferometry to accurately acquire and demodulate the retardation phase factors, thereby improving the accuracy of the Stokes data reconstruction as well as enabling more robust performance. The new technique also enables the acquisition of high-resolution intensity spectrum by adopting a dual-scan measurement technique for reducing crosstalk. Experimental results show that calibrations using phase-shifting interferometry yield higher data reconstruction accuracy as compared to the self-calibration technique.}, number={7}, journal={APPLIED OPTICS}, author={Altaqui, Ali and Kudenov, M. W.}, year={2019}, month={Mar}, pages={1830–1840} }
 @article{chenault_goldstein_kudenov_kupinski_pezzaniti_shaw_snik_tyo_bradley_2019, title={Polarization: Systems, Measurement, Analysis, and Remote Sensing}, volume={58}, ISSN={["1560-2303"]}, DOI={10.1117/1.OE.58.8.082401}, abstractNote={This guest editorial introduces the Special Section on Polarization: Systems, Measurement, Analysis, and Remote Sensing.}, number={8}, journal={OPTICAL ENGINEERING}, author={Chenault, David B. and Goldstein, Dennis H. and Kudenov, Michael W. and Kupinski, Meredith and Pezzaniti, J. Larry and Shaw, Joseph A. and Snik, Frans and Tyo, J. Scott and Bradley, Christine L.}, year={2019}, month={Aug} }
 @article{wang_escuti_kudenov_2019, title={Snapshot channeled imaging spectrometer using geometric phase holograms}, volume={27}, ISSN={["1094-4087"]}, DOI={10.1364/OE.27.015444}, abstractNote={In this paper, we present the design and experimental demonstration of a snapshot imaging spectrometer based on channeled imaging spectrometry (CIS) and channeled imaging polarimetry (CIP). Using a geometric phase microlens array (GPMLA) with multiple focal lengths, the proposed spectrometer selects wavelength components within its designed operating waveband of 450-700 nm. Compared to other snapshot spectral imagers, its key components are especially suitable for roll-to-roll (R2R) rapid fabrication, which gives the spectrometer potential for low-cost mass production. The principles and proof-of-concept experimental system of the sensor are described in detail, followed by lab validation and outdoor measurement results which demonstrate the sensor's ability to resolve spectral and spatial contents under both experimental and natural illumination conditions.}, number={11}, journal={OPTICS EXPRESS}, author={Wang, Yifan and Escuti, Michael J. and Kudenov, Michael W.}, year={2019}, month={May}, pages={15444–15455} }
 @article{altaqui_kudenov_2019, title={Thermal stabilization of a fiber-based channeled spectropolarimetry}, volume={58}, ISSN={["1560-2303"]}, DOI={10.1117/1.OE.58.12.124102}, abstractNote={Abstract. Channeled spectropolarimetry (CSP) is a spectral modulation technique that furnishes snapshot polarimetric measurements. Among the different spectropolarimetric methods, fiber-based techniques are fundamental requirements in specific biomedical procedures, such as endoscopy. However, the optical fiber exhibits high sensitivity to temperature changes, which subsequently incurs errors in the polarimetric reconstructions. We present a calibration technique for fiber-based CSP that leverages phase-shifting interferometry (PSI) to acquire and demodulate the fiber’s retardation phase accurately. This technique provides high robustness against temperature variations and improved polarimetric reconstruction performance. Experimental results demonstrated that the PSI calibrations offer higher stability and accuracy, at different optical fiber temperatures, as compared to reference-beam calibrations.}, number={12}, journal={OPTICAL ENGINEERING}, author={Altaqui, Ali and Kudenov, Michael W.}, year={2019}, month={Dec} }
 @article{luo_barraza_kudenov_2018, title={Aircraft skin defect localization using imaging polarimetry}, volume={57}, ISSN={["1560-2303"]}, DOI={10.1117/1.OE.57.8.084101}, abstractNote={Abstract. Aircraft coatings are critical for protecting the substrate material from corrosion, and in some cases, serve to reduce the aircraft’s RADAR cross section. A coating system is generally formed from three layers: a topcoat, primer, and substrate. Exposed substrate or primer, from defects in the topcoat, poses an operational hazard to the aircraft and can shorten a component’s lifetime. Conventional computer vision techniques require intensive image processing algorithms to detect such defects across a wide range of observation angles, variations in incident illumination, and nondefect markings. We introduce a polarimetric imaging technique that can classify topcoat defects that penetrate to the primer or substrate versus superficial surface markings. Results demonstrate that circular and linear polarization can discriminate metallic and carbon fiber substrates from the dielectric paint and low observable topcoats. To this end, we demonstrate that the technique of using polarimetric imaging may be viable for in-situ robotic inspection of aircraft topcoats. This is followed by our experimental results, which demonstrate material identification on the single-pixel level.}, number={8}, journal={OPTICAL ENGINEERING}, author={Luo, David A. and Barraza, Enrique Tomas and Kudenov, Michael W.}, year={2018}, month={Aug} }
 @article{woodard_kudenov_2018, title={Channeled polarimetry using spectrally resolved longitudinal spatial coherence interferometry}, volume={10655}, ISSN={["1996-756X"]}, DOI={10.1117/12.2302676}, abstractNote={We present an alternative technique for channeled polarimetry which uses longitudinal spatial coherence interferometry to encode a scene’s angularly dependent polarization information onto the source’s power spectrum. By spectrally resolving the output using a spectrometer, a channeled spectrum is measured. Fourier transformation of the channeled spectrum in combination with reference beam calibration techniques yields a reconstruction of the incident scene’s angular Stokes parameters. Experimental validation of the technique is demonstrated, using a Fabry-Perot etalon, for the recovery of one-dimensional linearly polarized scenes.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XIII}, author={Woodard, Ethan R. and Kudenov, Michael W.}, year={2018} }
 @article{hornburg_xiang_kim_kudenov_escuti_2018, title={Design and fabrication of an aspheric geometric-phase lens doublet}, volume={10735}, ISSN={["1996-756X"]}, DOI={10.1117/12.2322327}, abstractNote={A prior simulation-only study of aspherical phase profiles [Hornburg et al, Proc SPIE 10743, 10743-4 (2018)] in geometric-phase lenses (GPLs) indicated that aspherical doublet lens systems should provide substantially improved off-axis performance than those using spherical phase profiles. In this work, we fabricate a liquid crystal GPL doublet (24.5 mm diameter, 40 mm back focal length at 633 nm) and compare it to with a reference spherical GPL singlet. We characterized the liquid crystal alignment quality, efficiencies, and spot performance. With these compact GP lens systems, we realize improved performance for wider fields of view, while maintaining low loss.}, journal={LIQUID CRYSTALS XXII}, author={Hornburg, Kathryn J. and Xiang, Xiao and Kim, Jihwan and Kudenov, Michael W. and Escuti, Michael J.}, year={2018} }
 @article{patty_luo_snik_ariese_buma_kate_spanning_sparks_germer_garab_et al._2018, title={Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry}, volume={1862}, ISSN={["1872-8006"]}, DOI={10.1016/j.bbagen.2018.03.005}, abstractNote={Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650 nm to 710 nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization.}, number={6}, journal={BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS}, author={Patty, C. H. Lucas and Luo, David A. and Snik, Frans and Ariese, Freek and Buma, Wybren Jan and Kate, Inge Loes and Spanning, Rob J. M. and Sparks, William B. and Germer, Thomas A. and Garab, Gyoz and et al.}, year={2018}, month={Jun}, pages={1350–1363} }
 @article{pantalone_kudenov_2018, title={Initial orbit determination using Doppler shift of Fraunhofer lines}, volume={130}, ISSN={["1572-9478"]}, DOI={10.1007/s10569-018-9878-9}, number={12}, journal={CELESTIAL MECHANICS & DYNAMICAL ASTRONOMY}, author={Pantalone, Brett and Kudenov, Michael W.}, year={2018}, month={Dec} }
 @article{yang_sen_brendan t. o'connor_kudenov_2018, title={Monolithic Intrinsic Coincident Polarimeter using Organic Photovoltaics}, volume={10655}, ISSN={["1996-756X"]}, DOI={10.1117/12.2500476}, abstractNote={Polarimeters have broad applications in remote sensing, astronomy, and biomedical imaging to measure the emitted, reflected, or transmitted state of polarization (SOP). An Intrinsic Coincident full-Stokes Polarimeter (ICP) was previously demonstrated by our group, in a free space configuration, by using stain-aligned polymer-based organic photovoltaics (OPVs). These were tilted to avoid back-reflection cross-talk. In this paper, we present a theoretical model of a monolithic ICP which considers the back-reflection’s influence. This includes a comparison between the free space model to the new monolithic model. Experimental demonstrations yield less than 3% error between our model and the experiment data.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XIII}, author={Yang, Ruonan and Sen, Pratik and Brendan T. O'Connor and Kudenov, Michael W.}, year={2018} }
 @article{hornburg_xiang_kudenov_escuti_2018, title={Optimization of aspheric geometric-phase lenses for improved field-of-view}, volume={10743}, ISSN={["1996-756X"]}, DOI={10.1117/12.2322326}, abstractNote={In optical thin-films and surfaces, geometric phase is utilized to control the phase beyond that possible through optical path differences. Geometric-phase lenses, which are significantly thinner than refractive lenses for the same numerical aperture (NA), most commonly use a spherical phase profile. This is especially effective for normally incident light, but like other thin lenses, the performance degrades noticeably for off-axis incidence and wider fields-of-view. In this study, we investigate whether or not various aspheric designs provide better off-axis performance. We simulate aspheric singlet and doublet liquid crystal geometric-phase lenses (24.5 mm diameter, 40 mm back focal length at 633 nm), aiming to optimize spot size performance at 0, 3, and 7 degrees field angles, using Zemax OpticStudio 16.5. By using Zernike fringe phase expansions, we find conditions which provide improved off-axis performance. We demonstrate improved performance of a compact lens system utilizing these polarization-dependent optics.}, journal={OPTICAL MODELING AND PERFORMANCE PREDICTIONS X}, author={Hornburg, Kathryn J. and Xiang, Xiao and Kudenov, Michael W. and Escuti, Michael J.}, year={2018} }
 @article{sen_yang_rech_feng_ho_huang_so_kline_you_kudenov_et al._2019, title={Panchromatic All-Polymer Photodetector with Tunable Polarization Sensitivity}, volume={7}, ISSN={["2195-1071"]}, DOI={10.1002/adom.201801346}, abstractNote={AbstractIn this report, a high‐performance all‐polymer organic photodetector that is sensitive to linearly polarized light throughout the visible spectrum is demonstrated. The active layer is a bulk heterojunction composed of an electron donor polymer PBnDT‐FTAZ and acceptor polymer P(NDI2OD‐T2) that have complementary spectral absorption resulting in efficient detection from 350 to 800 nm. The blend film exhibits good ductility with the ability to accommodate large strains of over 60% without fracture. This allows the film to undergo large uniaxial strain resulting in in‐plane alignment of both polymers making the film optically anisotropic and intrinsically polarization sensitive. The films are characterized by UV–vis spectroscopy and grazing incidence wide‐angle X‐ray scattering showing that both polymers have similar in‐plane backbone alignment and maintain packing order after being strained. The films are integrated into devices and characterized under linear polarized light. The strain‐oriented detectors have maximum photocurrent anisotropies of 1.4 under transverse polarized light while maintaining peak responsivities of 0.21 A W−1 and a 3 dB cutoff frequency of ≈1 kHz. The demonstrated performance is comparable to the current state of the art all‐polymer photodetectors with the added capability of polarization sensitivity enabling new application opportunities.}, number={4}, journal={ADVANCED OPTICAL MATERIALS}, author={Sen, Pratik and Yang, Ruonan and Rech, Jeromy J. and Feng, Yuanxiang and Ho, Carr Hoi Yi and Huang, Jinsong and So, Franky and Kline, R. Joseph and You, Wei and Kudenov, Michael W. and et al.}, year={2019}, month={Feb} }
 @article{sen_xiong_zhang_park_you_ade_kudenov_brendan t. o'connor_2018, title={Shear-Enhanced Transfer Printing of Conducting Polymer Thin Films}, volume={10}, ISSN={["1944-8244"]}, DOI={10.1021/acsami.8b09968}, abstractNote={Polymer conductors that are solution-processable provide an opportunity to realize low-cost organic electronics. However, coating sequential layers can be hindered by poor surface wetting or dissolution of underlying layers. This has led to the use of transfer printing where solid film inks are transferred from a donor substrate to partially fabricated devices using a stamp. This approach typically requires favorable adhesion differences between the stamp, ink, and receiving substrate. Here, we present a shear-assisted organic printing (SHARP) technique that employs a shear load on a post-less polydimethylsiloxane (PDMS) elastomer stamp to print large-area polymer films that can overcome large unfavorable adhesion differences between the stamp and receiving substrate. We explore the limits of this process by transfer printing poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) films with varied formulation that tune the adhesive fracture energy. Using this platform, we show that the SHARP process is able to overcome a 10-fold unfavorable adhesion differential without the use of a patterned PDMS stamp, enabling large-area printing. The SHARP approach is then used to print PEDOT:PSS films in the fabrication of high-performance semitransparent organic solar cells.}, number={37}, journal={ACS APPLIED MATERIALS & INTERFACES}, author={Sen, Pratik and Xiong, Yuan and Zhang, Qanqian and Park, Sungjune and You, Wei and Ade, Harald and Kudenov, Michael W. and Brendan T. O'Connor}, year={2018}, month={Sep}, pages={31560–31567} }
 @article{kudenov_scarboro_2018, title={Synthetic neural network calibration of a hyperspectral imaging camera}, volume={10656}, ISSN={["1996-756X"]}, DOI={10.1117/12.2305521}, abstractNote={The use of machine learning algorithms is used extensively when analyzing and labeling image data. However, these techniques also offer additional post-processing advantages when they are used to calibrate sensor data. In this paper, a new calibration strategy for a Snapshot Hyperspectral Imaging Fourier Transform (SHIFT) spectrometer is discussed. The method, which is based on use of artificial neural networks, offers greater accuracy in both space and frequency when compared to conventional post-processing techniques. A theoretical model for the calibration procedure is presented, the laboratory data collection protocol is provided, and validation is conducted by measuring NIST-traceable spectral reflectance standards.}, journal={IMAGE SENSING TECHNOLOGIES: MATERIALS, DEVICES, SYSTEMS, AND APPLICATIONS V}, author={Kudenov, Michael W. and Scarboro, Clifton G.}, year={2018} }
 @article{wu_kudenov_2017, title={A reconstruction algorithm for three-dimensional object-space data using Spatial-Spectral Multiplexing}, volume={10198}, ISBN={["978-1-5106-0898-6"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.2264643}, abstractNote={This paper presents a reconstruction algorithm for the Spatial-Spectral Multiplexing (SSM) optical system. The goal of this algorithm is to recover the three-dimensional spatial and spectral information of a scene, given that a one-dimensional spectrometer array is used to sample the pupil of the spatial-spectral modulator. The challenge of the reconstruction is that the non-parametric representation of the three-dimensional spatial and spectral object requires a large number of variables, thus leading to an underdetermined linear system that is hard to uniquely recover. We propose to reparameterize the spectrum using B-spline functions to reduce the number of unknown variables. Our reconstruction algorithm then solves the improved linear system via a least- square optimization of such B-spline coefficients with additional spatial smoothness regularization. The ground truth object and the optical model for the measurement matrix are simulated with both spatial and spectral assumptions according to a realistic field of view. In order to test the robustness of the algorithm, we add Poisson noise to the measurement and test on both two-dimensional and three-dimensional spatial and spectral scenes. Our analysis shows that the root mean square error of the recovered results can be achieved within 5.15%.}, journal={ALGORITHMS AND TECHNOLOGIES FOR MULTISPECTRAL, HYPERSPECTRAL, AND ULTRASPECTRAL IMAGERY XXIII}, author={Wu, Zhejun and Kudenov, Michael W.}, year={2017} }
 @article{kudenov_lowenstern_craven_lacasse_2017, title={Field deployable pushbroom hyperspectral imaging polarimeter}, volume={56}, ISSN={["1560-2303"]}, DOI={10.1117/1.oe.56.10.103107}, abstractNote={Abstract. Hyperspectral imaging polarimetry enables both the spectrum and its spectrally resolved state of polarization to be measured. This information is important for identifying material properties for various applications in remote sensing and agricultural monitoring. We describe the design and performance of a ruggedized, field deployable hyperspectral imaging polarimeter, designed for wavelengths spanning the visible to near-infrared (450 to 800 nm). An entrance slit was used to sample the scene in a pushbroom scanning mode across a 30 deg vertical by 110 deg horizontal field-of-view. Furthermore, athermalized achromatic retarders were implemented in a channel spectrum generator to measure the linear Stokes parameters. The mechanical and optical layout of the system and its peripherals, in addition to the results of the sensor’s spectral and polarimetric calibration, are provided. Finally, field measurements are also provided and an error analysis is conducted. With its present calibration, the sensor has an absolute polarimetric error of 2.5% RMS and a relative spectral error of 2.3% RMS.}, number={10}, journal={OPTICAL ENGINEERING}, author={Kudenov, Michael W. and Lowenstern, Mariano E. and Craven, Julia M. and LaCasse, Charles F.}, year={2017}, month={Oct} }
 @article{pantalone_kudenov_2017, title={Fraunhofer line optical correlator for improvement of initial orbit determination}, volume={10407}, ISBN={["978-1-5106-1271-6"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.2274804}, abstractNote={The design of a Fraunhofer line optical correlator is detailed. The instrument described herein correlates a reflected solar spectrum against multiple Fraunhofer absorption lines to estimate the radial velocity of the reflecting body. By using a spatial light modulator (SLM) as a photomask for known solar absorption lines in the visible spectrum, the ratio of Doppler shifted solar energy to the total received energy can be calculated. Although the reflected light from targets in high orbit is weak, signal-to-noise ratio (SNR) is enhanced by the measurement of multiple Fraunhofer lines in a single snapshot image. Simulations indicate that prediction of orbital parameters is improved by incorporation of this velocity information, and in some cases the number of line-of-sight measurements can be reduced from three to two.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING VIII}, author={Pantalone, Brett A. and Kudenov, Michael W.}, year={2017} }
 @article{yang_sen_o'connor_kudenov_2017, title={Intrinsic coincident full-Stokes polarimeter using stacked organic photovoltaics}, volume={56}, ISSN={["2155-3165"]}, DOI={10.1364/ao.56.001768}, abstractNote={An intrinsic coincident full-Stokes polarimeter is demonstrated by using strain-aligned polymer-based organic photovoltaics (OPVs) that can preferentially absorb certain polarized states of incident light. The photovoltaic-based polarimeter is capable of measuring four Stokes parameters by cascading four semitransparent OPVs in series along the same optical axis. This in-line polarimeter concept potentially ensures high temporal and spatial resolution with higher radiometric efficiency as compared to the existing polarimeter architecture. Two wave plates were incorporated into the system to modulate the S3 Stokes parameter so as to reduce the condition number of the measurement matrix and maximize the measured signal-to-noise ratio. Radiometric calibration was carried out to determine the measurement matrix. The polarimeter presented in this paper demonstrated an average RMS error of 0.84% for reconstructed Stokes vectors after normalized to S0. A theoretical analysis of the minimum condition number of the four-cell OPV design showed that for individually optimized OPV cells, a condition number of 2.4 is possible.}, number={6}, journal={APPLIED OPTICS}, author={Yang, Ruonan and Sen, Pratik and O'Connor, B. T. and Kudenov, M. W.}, year={2017}, month={Feb}, pages={1768–1774} }
 @article{yang_sen_o'connor_kudenov_2017, title={Intrinsic coincident full-Stokes polarimeter using stacked organic photovoltaics and architectural comparison of polarimeter techniques}, volume={10407}, ISBN={["978-1-5106-1271-6"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.2273885}, abstractNote={An intrinsic coincident full-Stokes polarimeter is demonstrated by using stain-aligned polymer-based organic photovoltaics (OPVs) which can preferentially absorb certain polarized states of incident light. The photovoltaic-based polarimeter is capable of measuring four stokes parameters by cascading four semitransparent OPVs in series along the same optical axis. Two wave plates were incorporated into the system to modulate the S3 stokes parameter so as to reduce the condition number of the measurement matrix. The model for the full-Stokes polarimeter was established and validated, demonstrating an average RMS error of 0.84%. The optimization, based on minimizing the condition number of the 4-cell OPV design, showed that a condition number of 2.4 is possible. Performance of this in-line polarimeter concept was compared to other polarimeter architectures, including Division of Time (DoT), Division of Amplitude (DoAm), Division of Focal Plane (DoFP), and Division of Aperture (DoA) from signal-to-noise ratio (SNR) perspective. This in-line polarimeter concept has the potential to enable both high temporal (as compared with a DoT polarimeter) and high spatial resolution (as compared with DoFP and DoA polarimeters). We conclude that the intrinsic design has the same ~√2 SNR advantage as the DoAm polarimeter, but with greater compactness.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING VIII}, author={Yang, Ruonan and Sen, Pratik and O'Connor, B. T. and Kudenov, M. W.}, year={2017} }
 @article{youngs_kudenov_2017, title={Snapshot Hyperspectral Imaging Fourier Transform Spectropolarimeter}, volume={10407}, ISBN={["978-1-5106-1271-6"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.2273866}, abstractNote={The design and experimental results of a snapshot spatially heterodyned imaging Fourier transform (SHIFT) spectropolarimeter are presented. The sensor utilizes common-path interferometry, which lends improved compactness and ruggedness over free-space interferometric techniques. The polarization-dependency of the optical instrument can also be leveraged to obtain both spectral and polarimetric measurements. In this paper, calibration procedures and the SHIFT data processing algorithms are described. A data-reduction matrix is utilized to transform the measured per-pixel interferograms into corresponding Stokes parameters. Using this matrix, neural networks are trained to automate the transformation process from measurement to Stokes parameters. Finally, preliminary experimental results of the SHIFT’s ability to distinguish certain spectral signatures are demonstrated.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING VIII}, author={Youngs, E. J. and Kudenov, M. W.}, year={2017} }
 @article{maione_brickson_escuti_kudenov_2017, title={Snapshot imaging spectrometry with a heterodyned Savart plate interferometer}, volume={56}, ISSN={["1560-2303"]}, DOI={10.1117/1.oe.56.8.081806}, abstractNote={Imaging spectrometers are frequently used in remote sensing for their increased target discrimination capabilities over conventional imaging. Increasing the spectral resolution of these sensors further enables the system’s ability to discriminate certain targets and adds the potential for monitoring narrow-line spectral features. We describe a high spectral resolution (Δλ=1.1  nm full-width at half maximum) snapshot imaging spectrometer capable of distinguishing two narrowly separated bands in the red-visible spectrum. A theoretical model is provided to detail the first polarization grating-based spatial heterodyning of a Savart plate interferometer. Following this discussion, the experimental conditions of the narrow-line imaging spectrometer (NLIS) are provided. Finally, calibration and target identification methods are applied and quantified. Ultimately it is demonstrated that in a full spectral acquisition the NLIS sensor is capable of less than 3.5% error in reconstruction. Additionally, it is demonstrated that neural networks provide greater than 99% reduction in crosstalk when compared to pseudoinversion and expectation maximization in single target identification.}, number={8}, journal={OPTICAL ENGINEERING}, author={Maione, Bryan and Brickson, Leandra and Escuti, Michael and Kudenov, Michael}, year={2017}, month={Aug} }
 @article{woodard_kudenov_2017, title={Snapshot spectrally resolved longitudinal spatial coherence interferometry}, volume={56}, ISSN={["1560-2303"]}, DOI={10.1117/1.oe.56.6.064104}, abstractNote={Abstract. We present a one-dimensional (1-D) imaging technique that uses longitudinal spatial coherence interferometry to encode a scene’s spatial information onto the source’s power spectrum. By spectrally resolving the output using a spectrometer, a channeled spectrum is measured. Fourier transformation of the channeled spectrum yields a measurement of the incident scene’s angular spectrum. The theory is presented to exhibit analogies to conventional Fourier transform spectroscopy of the power spectrum. Experimental validation of the technique is demonstrated, using a Fabry–Perot etalon, for the reconstruction of 1-D sinusoidal and randomly generated angular spectra. Root mean square error between the input and output angular spectra is demonstrated, on average, to be 12.7% and 13.6% for single-frequency and random spectra, respectively.}, number={6}, journal={OPTICAL ENGINEERING}, author={Woodard, Ethan R. and Kudenov, Michael W.}, year={2017}, month={Jun} }
 @article{woodard_kudenov_2017, title={Spectrally Resolved Longitudinal Spatial Coherence Interferometry}, volume={10198}, ISBN={["978-1-5106-0898-6"]}, ISSN={["0277-786X"]}, DOI={10.1117/12.2264324}, abstractNote={We present an alternative imaging technique using spectrally resolved longitudinal spatial coherence interferometry to encode a scene’s angular information onto the source’s power spectrum. Fourier transformation of the spectrally resolved channeled spectrum output yields a measurement of the incident scene’s angular spectrum. Theory for the spectrally resolved interferometric technique is detailed, demonstrating analogies to conventional Fourier transform spectroscopy. An experimental proof of concept system and results are presented using an angularly-dependent Fabry-Perot interferometer-based optical design for successful reconstruction of one-dimensional sinusoidal angular spectra. Discussion for a potential future application of the technique, in which polarization information is encoded onto the source’s power spectrum is also given.}, journal={ALGORITHMS AND TECHNOLOGIES FOR MULTISPECTRAL, HYPERSPECTRAL, AND ULTRASPECTRAL IMAGERY XXIII}, author={Woodard, Ethan R. and Kudenov, Michael W.}, year={2017} }
 @article{anderson_bapst_coon_pung_kudenov_2017, title={Supervised non-negative tensor factorization for automatic hyperspectral feature extraction and target discrimination}, volume={10198}, ISBN={["978-1-5106-0898-6"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.2267730}, abstractNote={Hyperspectral imaging provides a highly discriminative and powerful signature for target detection and discrimination. Recent literature has shown that considering additional target characteristics, such as spatial or temporal profiles, simultaneously with spectral content can greatly increase classifier performance. Considering these additional characteristics in a traditional discriminative algorithm requires a feature extraction step be performed first. An example of such a pipeline is computing a filter bank response to extract spatial features followed by a support vector machine (SVM) to discriminate between targets. This decoupling between feature extraction and target discrimination yields features that are suboptimal for discrimination, reducing performance. This performance reduction is especially pronounced when the number of features or available data is limited. In this paper, we propose the use of Supervised Nonnegative Tensor Factorization (SNTF) to jointly perform feature extraction and target discrimination over hyperspectral data products. SNTF learns a tensor factorization and a classification boundary from labeled training data simultaneously. This ensures that the features learned via tensor factorization are optimal for both summarizing the input data and separating the targets of interest. Practical considerations for applying SNTF to hyperspectral data are presented, and results from this framework are compared to decoupled feature extraction/target discrimination pipelines.}, journal={ALGORITHMS AND TECHNOLOGIES FOR MULTISPECTRAL, HYPERSPECTRAL, AND ULTRASPECTRAL IMAGERY XXIII}, author={Anderson, Dylan and Bapst, Aleksander and Coon, Joshua and Pung, Aaron and Kudenov, Michael}, year={2017} }
 @article{kudenov_miskiewicz_sanders_escuti_2016, title={Achromatic Wollaston prism beam splitter using polarization gratings}, volume={41}, ISSN={["1539-4794"]}, DOI={10.1364/ol.41.004461}, abstractNote={We describe a method to achromatize a Wollaston prism beam splitter by combining it with a polarization grating. The advantage of this technique, compared to refractive methods of correction, is that only one type of birefringent crystal is needed. Additionally, the assembly can be made thinner while remaining achromatized. In this Letter, a model for the achromatized grating prism is formulated. Experimental validation is conducted by achromatizing a calcite Wollaston prism (apex angle of 5.35°) using a polarization grating with a spatial period of 253 μm. We found that the primary dispersion was reduced by approximately 6.5 times for wavelengths spanning the conventional F, d, and C Fraunhofer lines (486 to 656 nm).}, number={19}, journal={OPTICS LETTERS}, author={Kudenov, Michael W. and Miskiewicz, Matthew and Sanders, Nathan and Escuti, Michael J.}, year={2016}, month={Oct}, pages={4461–4463} }
 @article{huang_li_gurarslan_yu_kirste_guo_zhao_collazo_sitar_parsons_et al._2016, title={Atomically Thin MoS2 Narrowband and Broadband Light Superabsorbers}, volume={10}, ISSN={["1936-086X"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000381959100030&KeyUID=WOS:000381959100030}, DOI={10.1021/acsnano.6b02195}, abstractNote={We present a combined theoretical and experimental effort to enable strong light absorption (>70%) in atomically thin MoS2 films (≤4 layers) for either narrowband incidence with arbitrarily prespecified wavelengths or broadband incidence like solar radiation. This is achieved by integrating the films with resonant photonic structures that are deterministically designed using a unique reverse design approach based on leaky mode coupling. The design starts with identifying the properties of leaky modes necessary for the targeted strong absorption, followed by searching for the geometrical features of nanostructures to support the desired modes. This process is very intuitive and only involves a minimal amount of computation, thanks to the straightforward correlations between optical functionality and leaky modes as well as between leaky modes and the geometrical feature of nanostructures. The result may provide useful guidance for the development of high-performance atomic-scale photonic devices, such as solar cells, modulators, photodetectors, and photocatalysts.}, number={8}, journal={ACS NANO}, author={Huang, Lujun and Li, Guoqing and Gurarslan, Alper and Yu, Yiling and Kirste, Ronny and Guo, Wei and Zhao, Junjie and Collazo, Ramon and Sitar, Zlatko and Parsons, Gregory N. and et al.}, year={2016}, month={Aug}, pages={7493–7499} }
 @article{lowenstern_kudenov_2016, title={Field Deployable Pushbroom Hyperspectral Imagining Polarimeter}, volume={9853}, ISSN={["0277-786X"]}, DOI={10.1117/12.2224212}, abstractNote={Hyperspectral polarimetry is demonstrated to measure the spectrum and polarization state of a scene. This information is important to identify material properties for applications such as remote sensing and agricultural monitoring, among others. We report the design and performance of a ruggedized, field deployable Hyperspectral Polarimeter Imaging (HPI) system over the VIS to NIR range (450-800 nm). An entrance slit was used to sample a scene in a pushbroom scanning mode, sampling over a 30 degree vertical by 110 degree horizontal field of view. Furthermore, athermalized achromatic retarders were implemented in a channel spectrum generator to measure the linear Stoke vectors. This paper reports the mechanical and optical layout of the system and its peripherals. We present preliminary spectral and polarimetry calibration techniques as well as testing results in field environments.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XII}, author={Lowenstern, Mariano and Kudenov, Michael W.}, year={2016} }
 @article{evans_kudenov_sassenrath_dereniak_yalkowsky_2016, title={Imaging of in vitro parenteral drug precipitation}, volume={512}, ISSN={["1873-3476"]}, DOI={10.1016/j.ijpharm.2016.08.030}, abstractNote={Solid particulate matter introduced into the bloodstream as a result of parenteral drug administration can produce serious pathological conditions. Particulate matter that cannot be eliminated by pre-infusion filtration is often the result of drug precipitation that occurs when certain parenteral formulations are mixed with blood. A new device is designed to model the mixing of drug formulations with flowing blood utilizing a uniquely designed flow cell and a CCD camera to view the formulation as it is mixed with a blood surrogate in real time. The performance of the proposed device is measured using 3 commercially available parenteral formulations previously tested using a validated in vitro model.}, number={1}, journal={INTERNATIONAL JOURNAL OF PHARMACEUTICS}, author={Evans, Daniel C. and Kudenov, Michael W. and Sassenrath, Kimberly C. and Dereniak, Eustace L. and Yalkowsky, Samuel H.}, year={2016}, month={Oct}, pages={219–223} }
 @article{roy_awartani_sen_o'connor_kudenov_2016, title={Intrinsic coincident linear polarimetry using stacked organic photovoltaics}, volume={24}, ISSN={["1094-4087"]}, DOI={10.1364/oe.24.014737}, abstractNote={Polarimetry has widespread applications within atmospheric sensing, telecommunications, biomedical imaging, and target detection. Several existing methods of imaging polarimetry trade off the sensor's spatial resolution for polarimetric resolution, and often have some form of spatial registration error. To mitigate these issues, we have developed a system using oriented polymer-based organic photovoltaics (OPVs) that can preferentially absorb linearly polarized light. Additionally, the OPV cells can be made semitransparent, enabling multiple detectors to be cascaded along the same optical axis. Since each device performs a partial polarization measurement of the same incident beam, high temporal resolution is maintained with the potential for inherent spatial registration. In this paper, a Mueller matrix model of the stacked OPV design is provided. Based on this model, a calibration technique is developed and presented. This calibration technique and model are validated with experimental data, taken with a cascaded three cell OPV Stokes polarimeter, capable of measuring incident linear polarization states. Our results indicate polarization measurement error of 1.2% RMS and an average absolute radiometric accuracy of 2.2% for the demonstrated polarimeter.}, number={13}, journal={OPTICS EXPRESS}, author={Roy, S. Gupta and Awartani, O. M. and Sen, P. and O'Connor, B. T. and Kudenov, M. W.}, year={2016}, month={Jun}, pages={14737–14747} }
 @article{lacasse_redman_kudenov_craven_2016, title={Maximum bandwidth snapshot channeled imaging polarimeter with polarization gratings}, volume={9853}, ISSN={["0277-786X"]}, DOI={10.1117/12.2228561}, abstractNote={Compact snapshot imaging polarimeters have been demonstrated in literature to provide Stokes parameter estimations for spatially varying scenes using polarization gratings. However, the demonstrated system does not employ aggressive modulation frequencies to take full advantage of the bandwidth available to the focal plane array. A snapshot imaging Stokes polarimeter is described and demonstrated through results. The simulation studies the challenges of using a maximum bandwidth configuration for a snapshot polarization grating based polarimeter, such as the fringe contrast attenuation that results from higher modulation frequencies. Similar simulation results are generated and compared for a microgrid polarimeter. Microgrid polarimeters are instruments where pixelated polarizers are superimposed onto a focal plan array, and this is another type of spatially modulated polarimeter, and the most common design uses a 2x2 super pixel of polarizers which maximally uses the available bandwidth of the focal plane array.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XII}, author={LaCasse, Charles F. and Redman, Brian J. and Kudenov, Michael W. and Craven, Julia M.}, year={2016} }
 @article{maione_brickson_kudenov_escuti_2016, title={Narrowband emission line imaging spectrometry using Savart plates}, volume={9853}, ISSN={["0277-786X"]}, DOI={10.1117/12.2224275}, abstractNote={Polarization spatial heterodyne interferometry (PSHI) allows for the development of compact, vibration insensitive, high spectral resolution sensors. Introducing the imaging qualities of a lenslet array extends the advantages of PSHI to imaging interferometers. The use of Savart plates enables a birefringent interferometer that obtains higher spectral resolution with fewer optical aberrations when compared to alternative designs. In this paper, we describe the design, construction, calibration and validation of a narrowband emission line imaging spectrometer (NELIS), based on Savart plates and liquid crystal polarization gratings, along with its associated theoretical model. This sensor is advantageous for spectral imaging in the areas of remote sensing, biomedical imaging and machine vision.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XII}, author={Maione, Bryan and Brickson, Leandra and Kudenov, Michael and Escuti, Michael}, year={2016} }
 @article{luo_kudenov_2016, title={Neural network calibration of a snapshot birefringent Fourier transform spectrometer with periodic phase errors}, volume={24}, ISSN={["1094-4087"]}, DOI={10.1364/oe.24.011266}, abstractNote={Systematic phase errors in Fourier transform spectroscopy can severely degrade the calculated spectra. Compensation of these errors is typically accomplished using post-processing techniques, such as Fourier deconvolution, linear unmixing, or iterative solvers. This results in increased computational complexity when reconstructing and calibrating many parallel interference patterns. In this paper, we describe a new method of calibrating a Fourier transform spectrometer based on the use of artificial neural networks (ANNs). In this way, it is demonstrated that a simpler and more straightforward reconstruction process can be achieved at the cost of additional calibration equipment. To this end, we provide a theoretical model for general systematic phase errors in a polarization birefringent interferometer. This is followed by a discussion of our experimental setup and a demonstration of our technique, as applied to data with and without phase error. The technique's utility is then supported by comparison to alternative reconstruction techniques using fast Fourier transforms (FFTs) and linear unmixing.}, number={10}, journal={OPTICS EXPRESS}, author={Luo, David and Kudenov, Michael W.}, year={2016}, month={May} }
 @article{maione_luo_miskiewicz_escuti_kudenov_2016, title={Spatially heterodyned snapshot imaging spectrometer}, volume={55}, ISSN={["2155-3165"]}, DOI={10.1364/ao.55.008667}, abstractNote={Snapshot hyperspectral imaging Fourier transform (SHIFT) spectrometers are a promising technology in optical detection and target identification. For any imaging spectrometer, spatial, spectral, and temporal resolution, along with form factor, power consumption, and computational complexity are often the design considerations for a desired application. Motivated by the need for high spectral resolution systems, capable of real-time implementation, we demonstrate improvements to the spectral resolution and computation trade-space. In this paper, we discuss the implementation of spatial heterodyning, using polarization gratings, to improve the spectral resolution trade space of a SHIFT spectrometer. Additionally, we employ neural networks to reduce the computational complexity required for data reduction, as appropriate for real-time imaging applications. Ultimately, with this method we demonstrate an 87% decrease in processing steps when compared to Fourier techniques. Additionally, we show an 80% reduction in spectral reconstruction error and a 30% increase in spatial fidelity when compared to linear operator techniques.}, number={31}, journal={APPLIED OPTICS}, author={Maione, Bryan D. and Luo, David and Miskiewicz, Matthew and Escuti, Michael and Kudenov, Michael W.}, year={2016}, month={Nov}, pages={8667–8675} }
 @article{stirman_smith_kudenov_smith_2016, title={Wide field-of-view, multi-region, two-photon imaging of neuronal activity in the mammalian brain}, volume={34}, ISSN={["1546-1696"]}, DOI={10.1038/nbt.3594}, abstractNote={Two-photon calcium imaging provides an optical readout of neuronal activity in populations of neurons with subcellular resolution. However, conventional two-photon imaging systems are limited in their field of view to ∼1 mm(2), precluding the visualization of multiple cortical areas simultaneously. Here, we demonstrate a two-photon microscope with an expanded field of view (>9.5 mm(2)) for rapidly reconfigurable simultaneous scanning of widely separated populations of neurons. We custom designed and assembled an optimized scan engine, objective, and two independently positionable, temporally multiplexed excitation pathways. We used this new microscope to measure activity correlations between two cortical visual areas in mice during visual processing.}, number={8}, journal={NATURE BIOTECHNOLOGY}, author={Stirman, Jeffrey N. and Smith, Ikuko T. and Kudenov, Michael W. and Smith, Spencer L.}, year={2016}, month={Aug}, pages={857-+} }
 @article{roy_awartani_sen_o'connor_kudenov_2015, title={Complete Intrinsic Coincident Polarimetry using Stacked Organic Photovoltaics}, volume={9613}, ISSN={["0277-786X"]}, DOI={10.1117/12.2188972}, abstractNote={Measuring the 2 dimensional Stokes vector, to determine the polarization state of light, finds application in multiple areas, including the characterization of aerosol size distributions, target identification, quality control by evaluating the distribution of stress birefringence, resolving data channels in telecommunications, and for evaluating biological tissues in medical imaging. Conventional methods, such as channeled and division of focal plane polarimeters, usually limit spatial resolution, while others, like division of aperture or division of amplitude polarimeters, have higher complexity and less compactness. To help solve these issues, we have developed a system that uses semitransparent organic photovoltaics (OPVs) as photodetectors. The active area of the devices consist of biaxially oriented polymer films, which enables the device to preferentially absorb certain polarized states of incident light, depending on the orientation of the polymer chains. Taking advantage of the cells’ transparency and ease of processing, compared to inorganic materials, enables multiple devices to be “stacked” along the optical axis. Presently, experiments have been conducted to detect linear polarization states of light. We use three stacked OPVs, where each device can measure one of the first three Stokes parameters simultaneously, thereby ensuring high spatial and temporal resolution with inherent spatial registration. In this paper, the fabrication of the OPVs and the design and calibration technique is documented, along with experimental data, supporting the hypothesis.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING VII}, author={Roy, S. Gupta and Awartani, O. M. and Sen, P. and O'Connor, B. T. and Kudenov, M. W.}, year={2015} }
 @article{kim_li_miskiewicz_oh_kudenov_escuti_2015, title={Fabrication of ideal geometric-phase holograms with arbitrary wavefronts}, volume={2}, ISSN={["2334-2536"]}, DOI={10.1364/optica.2.000958}, abstractNote={Throughout optics and photonics, phase is normally controlled via an optical path difference. Although much less common, an alternative means for phase control exists: a geometric phase (GP) shift occurring when a light wave is transformed through one parameter space, e.g., polarization, in such a way as to create a change in a second parameter, e.g., phase. In thin films and surfaces where only the GP varies spatially—which may be called GP holograms (GPHs)—the phase profile of nearly any (physical or virtual) object can in principle be embodied as an inhomogeneous anisotropy manifesting exceptional diffraction and polarization behavior. Pure GP elements have had poor efficiency and utility up to now, except in isolated cases, due to the lack of fabrication techniques producing elements with an arbitrary spatially varying GP shift at visible and near-infrared wavelengths. Here, we describe two methods to create high-fidelity GPHs, one interferometric and another direct-write, capable of recording the wavefront of nearly any physical or virtual object. We employ photoaligned liquid crystals to record the patterns as an inhomogeneous optical axis profile in thin films with a few μm thickness. We report on eight representative examples, including a GP lens with F/2.3 (at 633 nm) and 99% diffraction efficiency across visible wavelengths, and several GP vortex phase plates with excellent modal purity and remarkably small central defect size (e.g., 0.7 and 7 μm for topological charges of 1 and 8, respectively). We also report on a GP Fourier hologram, a fan-out grid with dozens of far-field spots, and an elaborate phase profile, which showed excellent fidelity and very low leakage wave transmittance and haze. Together, these techniques are the first practical bases for arbitrary GPHs with essentially no loss, high phase gradients (∼rad/μm), novel polarization functionality, and broadband behavior.}, number={11}, journal={OPTICA}, author={Kim, Jihwan and Li, Yanming and Miskiewicz, Matthew N. and Oh, Chulwoo and Kudenov, Michael W. and Escuti, Michael J.}, year={2015}, month={Nov}, pages={958–964} }
 @article{awartani_kudenov_kline_brendan t. o'connor_2015, title={In-Plane Alignment in Organic Solar Cells to Probe the Morphological Dependence of Charge Recombination}, volume={25}, ISSN={["1616-3028"]}, DOI={10.1002/adfm.201403377}, abstractNote={Bulk heterojunction (BHJ) organic solar cells are fabricated with the polymer semiconductor aligned in the plane of the film to probe charge recombination losses associated with aggregates characterized by varying degrees of local order. 100% uniaxial strain is applied on ductile poly(3‐hexylthiophene):phenyl‐C61‐butyric acid methyl ester (P3HT:PCBM) BHJ films and characterize the resulting morphology with ultraviolet‐visible absorption spectroscopy and grazing incidence X‐ray diffraction. It is found that the strained films result in strong alignment of the highly ordered polymer aggregates. Polymer aggregates with lower order and amorphous regions also align but with a much broader orientation distribution. The solar cells are then tested under linearly polarized light where the light is selectively absorbed by the appropriately oriented polymer, while maintaining a common local environment for the sweep out of photogenerated charge carriers. Results show that charge collection losses associated with a disordered BHJ film are circumvented, and the internal quantum efficiency is independent of P3HT local aggregate order near the heterojunction interface. Uniquely, this experimental approach allows for selective excitation of distinct morphological features of a conjugated polymer within a single BHJ film, providing insight into the morphological origin of recombination losses.}, number={8}, journal={ADVANCED FUNCTIONAL MATERIALS}, author={Awartani, Omar and Kudenov, Michael W. and Kline, R. Joseph and Brendan T. O'Connor}, year={2015}, month={Feb}, pages={1296–1303} }
 @article{woodard_kudenov_2015, title={Passive Standoff Imaging using Spatial-Spectral Multiplexing}, volume={9472}, ISSN={["1996-756X"]}, DOI={10.1117/12.2177272}, abstractNote={The concept of a passive far-field imaging system, using a unique spatial-spectral multiplexing (SSM) technique, is presented. The described SSM technique uses spectrally resolved interferometry to multiplex a scene’s angular spectrum onto the power spectrum, while dispersion characteristics are implemented to heterodyne the channeled spectrum into the spectral range of visible light. In this paper, the theory of the design is detailed and an analysis of the spatial and spectral tradespace of the system are discussed. Applications for this imaging technique are primarily focused in remote sensing and far-field target identification.}, journal={ALGORITHMS AND TECHNOLOGIES FOR MULTISPECTRAL, HYPERSPECTRAL, AND ULTRASPECTRAL IMAGERY XXI}, author={Woodard, Ethan R. and Kudenov, Michael W.}, year={2015} }
 @article{roy_kudenov_2015, title={Snapshot Imaging Fraunhofer Line Discriminator for Detection of Plant Fluorescence}, volume={9472}, ISSN={["1996-756X"]}, DOI={10.1117/12.2176906}, abstractNote={Non-invasive quantification of plant health is traditionally accomplished using reflectance based metrics, such as the normalized difference vegetative index (NDVI). However, measuring plant fluorescence (both active and passive) to determine photochemistry of plants has gained importance. Due to better cost efficiency, lower power requirements, and simpler scanning synchronization, detecting passive fluorescence is preferred over active fluorescence. In this paper, we propose a high speed imaging approach for measuring passive plant fluorescence, within the hydrogen alpha Fraunhofer line at ~656 nm, using a Snapshot Imaging Fraunhofer Line Discriminator (SIFOLD). For the first time, the advantage of snapshot imaging for high throughput Fraunhofer Line Discrimination (FLD) is cultivated by our system, which is based on a multiple-image Fourier transform spectrometer and a spatial heterodyne interferometer (SHI). The SHI is a Sagnac interferometer, which is dispersion compensated using blazed diffraction gratings. We present data and techniques for calibrating the SIFOLD to any particular wavelength. This technique can be applied to quantify plant fluorescence at low cost and reduced complexity of data collection.}, journal={ALGORITHMS AND TECHNOLOGIES FOR MULTISPECTRAL, HYPERSPECTRAL, AND ULTRASPECTRAL IMAGERY XXI}, author={Roy, S. Gupta and Kudenov, M. W.}, year={2015} }
 @article{wang_kudenov_kashani_schwiegerling_escuti_2015, title={Snapshot retinal imaging Mueller matrix polarimeter}, volume={9613}, ISSN={["0277-786X"]}, DOI={10.1117/12.2188480}, abstractNote={Early diagnosis of glaucoma, which is a leading cause for visual impairment, is critical for successful treatment. It has been shown that Imaging polarimetry has advantages in early detection of structural changes in the retina. Here, we theoretically and experimentally present a snapshot Mueller Matrix Polarimeter fundus camera, which has the potential to record the polarization-altering characteristics of retina with a single snapshot. It is made by incorporating polarization gratings into a fundus camera design. Complete Mueller Matrix data sets can be obtained by analyzing the polarization fringes projected onto the image plane. In this paper, we describe the experimental implementation of the snapshot retinal imaging Mueller matrix polarimeter (SRIMMP), highlight issues related to calibration, and provide preliminary images acquired from the camera.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING VII}, author={Wang, Yifan and Kudenov, Michael and Kashani, Amir H. and Schwiegerling, Jim and Escuti, Michael}, year={2015} }
 @article{kudenov_roy_pantalone_maione_2015, title={Ultraspectral Imaging and the Snapshot Advantage}, volume={9467}, ISSN={["1996-756X"]}, DOI={10.1117/12.2176980}, abstractNote={Ultraspectral sensing has been investigated as a way to resolve terrestrial chemical fluorescence within solar Fraunhofer lines. Referred to as Fraunhofer Line Discriminators (FLDs), these sensors attempt to measure "band filling" of terrestrial fluorescence within these naturally dark regions of the spectrum. However, the method has challenging signal to noise ratio limitations due to the low fluorescence emission signal of the target, which is exacerbated by the high spectral resolution required by the sensor (<0.1 nm). To now, many Fraunhofer line discriminators have been scanning sensors; either pushbroom or whiskbroom, which require temporal and/or spatial scanning to acquire an image. In this paper, we attempt to quantify the snapshot throughput advantage in ultraspectral imaging for FLD. This is followed by preliminary results of our snapshot FLD sensor. The system has a spatial resolution of 280x280 pixels and a spectral resolving power of approximately 10,000 at a 658 nm operating wavelength.}, journal={MICRO- AND NANOTECHNOLOGY SENSORS, SYSTEMS, AND APPLICATIONS VII}, author={Kudenov, Michael W. and Roy, Subharup Gupta and Pantalone, Brett and Maione, Bryan}, year={2015} }
 @article{maione_luo_kudenov_escuti_miskiewicz_2014, title={Birefringent snapshot imaging spatial heterodyne spectrometer}, volume={9099}, ISSN={["1996-756X"]}, DOI={10.1117/12.2049726}, abstractNote={High speed spectral imaging is useful for a variety of tasks spanning industrial monitoring, target detection, and chemical identification. To better meet these needs, compact hyperspectral imaging instrumentation, capable of high spectral resolution and real-time data acquisition and processing, are required. In this paper, we describe the first snapshot imaging spatial heterodyne Fourier transform spectrometer based on birefringent crystals and polarization gratings. This includes details about its architecture, as well as our preliminary proof of concept. Finally, we discuss details related to the calibration of the sensor, including our preliminary investigations into high speed data reconstruction and calibration using neural networks. With such an approach, it may be feasible to reconstruct and calibrate an entire interferogram cube in one step with minimal Fast Fourier Transform (FFT) processing.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XI}, author={Maione, Bryan D. and Luo, David A. and Kudenov, Michael W. and Escuti, Michael J. and Miskiewicz, Matthew N.}, year={2014} }
 @article{trail_kudenov_dereniak_2014, title={In situ fringe projector development for thermal coating deposition}, volume={53}, ISSN={["1560-2303"]}, DOI={10.1117/1.oe.53.7.074105}, abstractNote={Abstract. Thermal barrier coatings (TBCs) and plasma spray coatings, in general, require fine control over the deposited thickness to achieve a reliable coating performance. Currently, the plasma spray industry quantifies thickness by sampling the part before and after TBC deposition. Approximate thickness is inferred from previous runs; however, process variability can cause errors in these approximations that result in wasted time and resources that can ultimately lead to nonreliant coatings. To this end, we present an in situ optical fringe projector technology that enables coating thickness measurements across a two-dimensional surface. The sensor is capable of achieving micron scale resolution in the harsh environment of a thermal spray booth. Furthermore, unlike the existing approaches, this technique is extendable to parts with complex geometries. The underlying background of the fringe projection method, including a differential measurement technique, is presented. Current results on production equipment and cylindrical parts are also discussed, showing good correlation and agreement with physical measurements captured in an industrial setting.}, number={7}, journal={OPTICAL ENGINEERING}, author={Trail, Nicholas D. and Kudenov, Michael W. and Dereniak, Eustace L.}, year={2014}, month={Jul} }
 @article{awartani_kudenov_brendan t. o'connor_2014, title={Organic photovoltaic cells with controlled polarization sensitivity}, volume={104}, ISSN={["1077-3118"]}, DOI={10.1063/1.4868041}, abstractNote={In this study, we demonstrate linearly polarized organic photovoltaic cells with a well-controlled level of polarization sensitivity. The polarized devices were created through the application of a large uniaxial strain to the bulk heterojunction poly(3-hexylthiophene):Phenyl-C61-butyric acid methyl ester (P3HT:PCBM) film and printing the plastically deformed active layer onto a PEDOT:PSS and indium tin oxide coated glass substrate. The P3HT:PCBM layer is processed such that it is able to accommodate high strains (over 100%) without fracture. After printing the strained films, thermal annealing is used to optimize solar cell performance while maintaining polarization sensitivity. A dichroic ratio and short circuit current ratio of ≈6.1 and ≈1.6 were achieved, respectively.}, number={9}, journal={APPLIED PHYSICS LETTERS}, author={Awartani, Omar and Kudenov, Michael W. and Brendan T. O'Connor}, year={2014}, month={Mar} }
 @article{wang_kudenov_craven-jones_2014, title={Phase error in Fourier transform spectrometers employing polarization interferometers}, volume={9099}, ISSN={["1996-756X"]}, DOI={10.1117/12.2051037}, abstractNote={Phase error is common in reflective interferometers, such as the Michelson. This yields highly asymmetric interferograms that complicate the post-processing of single-sided interference data. Common methods of compensating for phase errors include the Mertz, Forman, and Cannes phase correction techniques. However, birefringent interferometers often have highly symmetric interferograms; thus, compensating for phase errors may represent an unnecessary and/or detrimental step in post processing. In this paper, an analysis of the phase error generated by the Infrared Hyperspectral Imaging Polarimeter (IHIP) is conducted. First, a model of the IHIP is presented that quantifies the phase error in the system. The error associated with calculating spectra from single-sided interferograms, using Mertz phase correction and simple singlesided to double-sided mirroring, is then investigated and compared to "true" double-sided Cannes phase corrected spectra. These error calculations are set within the context of measurements taken from a Michelson interferometer-based Fourier transform spectrometer. Results demonstrate that the phase error of the IHIP is comparatively small and that Mertz phase correction may not be necessary to minimize error in the spectral calculation.}, journal={POLARIZATION: MEASUREMENT, ANALYSIS, AND REMOTE SENSING XI}, author={Wang, Yifan and Kudenov, Michael W. and Craven-Jones, Julia}, year={2014} }
 @article{kudenov_miskiewicz_escuti_coward_2014, title={Polarization spatial heterodyne interferometer: model and calibration}, volume={53}, ISSN={["1560-2303"]}, DOI={10.1117/1.oe.53.4.044104}, abstractNote={Abstract. Spatial heterodyne interferometry (SHI) is a technique based on Fourier transform spectroscopy. As such, many of the benefits, such as high spectral resolving power, can be realized. Furthermore, unlike a Fourier transform spectrometer, an SHI is able to minimize the number of required samples for a given resolving power and spectral range. The calibration and detailed modeling of a polarization spatial heterodyne interferometer (PSHI) are detailed. Unlike our original first-order ray tracing model, the new model is based on the Jones matrix formalism. Using this improved model, we explore the nonideal aspects of the PSHI, including interference effects caused by retardance errors in the polarization grating and quarter wave plate. To minimize the influence of these errors, a calibration procedure is described based on a linear operator theory. Finally, the Jones matrix model and calibration procedure are validated through a series of simulations and experiments.}, number={4}, journal={OPTICAL ENGINEERING}, author={Kudenov, Michael W. and Miskiewicz, Matthew N. and Escuti, Michael J. and Coward, James F.}, year={2014}, month={Apr} }
 @article{craven-jones_way_kudenov_mercier_2013, title={Athermalized channeled spectropolarimetry using a biaxial potassium titanyl phosphate crystal}, volume={38}, ISSN={["0146-9592"]}, DOI={10.1364/ol.38.001657}, abstractNote={Channeled spectropolarimeters measure the polarization state of light as a function of wavelength. Typically, a channeled spectropolarimeter uses high-order retarders made of uniaxial crystal to amplitude modulate the measured spectrum with the Stokes polarization information. A primary limitation of these instruments is the thermal variability of the retarders, which necessitates frequent system recalibration. Past work has addressed this issue by implementing an athermalized retarder produced from two uniaxial crystals. However, reducing the complexity of an athermalized retarder is advantageous for minimizing size and weight requirements. In this Letter, a technique for producing a thermally stable channeled spectropolarimeter using biaxial retarders is presented. This technique preserves a constant phase over an appreciable temperature range. Proof-of-concept results from a KTP-based athermal partial channeled spectropolarimeter are presented from 500 to 750 nm for temperature changes up to 26°C. Spectropolarimetric reconstructions produced from this system vary by <=2.6% RMS when the retarder experiences a 13°C increase in temperature above 21°C ambient, <=5.2% for a 20°C increase, and <=6.7% for a 26°C increase.}, number={10}, journal={OPTICS LETTERS}, author={Craven-Jones, Julia and Way, Brandyn M. and Kudenov, Michael W. and Mercier, Jeffrey A.}, year={2013}, month={May}, pages={1657–1659} }
 @article{kudenov_miskiewicz_escuti_coward_2013, title={Compact spatial heterodyne interferometer using polarization gratings}, volume={8873}, ISSN={["1996-756X"]}, DOI={10.1117/12.2024104}, abstractNote={Spatial heterodyne interferometry (SHI) is a spectral measurement technique based on Fourier Transform Spectroscopy (FTS). One main benefit of an FTS lies in its higher spectral resolving power over direct measurement (dispersive) systems; however, accessing this higher resolving power can result in longer measurement times without heterodyning techniques. In this paper, the calibration and modeling of a polarization SHI is detailed, based on the Jones matrix formalism. With this, we explore non-ideal aspects of the polarization grating, such as zero-order light leakage. This light leakage causes crosstalk that can introduce errors in the spectral calibration. To minimize error, a calibration procedure is introduced based on a linear operator theory. Finally, the Jones matrix model and calibration procedure are validated through a series of experiments.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING VI}, author={Kudenov, Michael W. and Miskiewicz, Matthew N. and Escuti, Michael J. and Coward, Jim}, year={2013} }
 @misc{hagen_kudenov_2013, title={Review of snapshot spectral imaging technologies}, volume={52}, ISSN={["1560-2303"]}, DOI={10.1117/1.oe.52.9.090901}, abstractNote={Abstract. Within the field of spectral imaging, the vast majority of instruments used are scanning devices. Recently, several snapshot spectral imaging systems have become commercially available, providing new functionality for users and opening up the field to a wide array of new applications. A comprehensive survey of the available snapshot technologies is provided, and an attempt has been made to show how the new capabilities of snapshot approaches can be fully utilized.}, number={9}, journal={OPTICAL ENGINEERING}, author={Hagen, Nathan and Kudenov, Michael W.}, year={2013}, month={Sep} }
 @article{kudenov_mallik_escuti_hagen_oka_dereniak_2013, title={Snapshot Imaging Mueller Matrix Instrument}, volume={8897}, ISSN={["1996-756X"]}, DOI={10.1117/12.2028546}, abstractNote={A novel way to measure the Mueller matrix image enables a sample's diattenuation, retardance, and depolarization to be measured within a single camera integration period. Since the Mueller matrix components are modulated onto coincident carrier frequencies, the described technique provides unique solutions to image registration problems for moving objects. In this paper, a snapshot imaging Mueller matrix polarimeter is theoretically described, and preliminary results shows it to be a viable approach for use in surface characterization of moving objects.}, journal={ELECTRO-OPTICAL REMOTE SENSING, PHOTONIC TECHNOLOGIES, AND APPLICATIONS VII; AND MILITARY APPLICATIONS IN HYPERSPECTRAL IMAGING AND HIGH SPATIAL RESOLUTION SENSING}, author={Kudenov, Michael W. and Mallik, Sushmit and Escuti, Michael J. and Hagen, Nathan and Oka, Kazuhiko and Dereniak, Eustace L.}, year={2013} }
 @article{kudenov_banerjee_chan_dereniak_2012, title={Compact snapshot birefringent imaging Fourier transform spectrometer for remote sensing and endoscopy}, volume={8542}, ISSN={["0277-786X"]}, DOI={10.1117/12.945873}, abstractNote={The design and implementation of a compact multiple-image Fourier transform spectrometer (FTS) is presented. Based on the multiple-image FTS originally developed by A. Hirai, the presented device offers significant advantages over his original implementation. Namely, its birefringent nature results in a common-path interferometer which makes the spectrometer insensitive to vibration. Furthermore, it enables the potential of making the instrument ultra-compact, thereby improving the portability of the sensor. The theory of the birefringent FTS is provided, followed by details of its specific embodiment. A laboratory proof of concept of the sensor, designed and developed at the Optical Detection Lab, is also presented. Spectral measurements of laboratory sources are provided, including measurements of light-emitting diodes and gas-discharge lamps. These spectra are verified against a calibrated Ocean Optics USB2000 spectrometer. Other data were collected outdoors and of a rat esophagus, demonstrating the sensor’s ability to resolve spectral signatures in both standard outdoor lighting and environmental conditions, as well as in fluorescence spectroscopy.}, journal={ELECTRO-OPTICAL REMOTE SENSING, PHOTONIC TECHNOLOGIES, AND APPLICATIONS VI}, author={Kudenov, Michael W. and Banerjee, Bhaskar and Chan, Victoria C. and Dereniak, Eustace L.}, year={2012} }
 @article{kudenov_miskiewicz_escuti_dereniak_2012, title={Spatial heterodyne interferometry with polarization gratings}, volume={37}, ISSN={["1539-4794"]}, DOI={10.1364/ol.37.004413}, abstractNote={The implementation of a polarization-based spatial heterodyne interferometer (SHI) is described. While a conventional SHI uses a Michelson interferometer and diffraction gratings, our SHI exploits mechanically robust Wollaston prisms and polarization gratings. A theoretical model for the polarization SHI is provided and validated with data from our proof of concept experiments. This device is expected to provide a compact monolithic sensor for subangstrom resolution spectroscopy in remote sensing, biomedical imaging, and machine vision applications.}, number={21}, journal={OPTICS LETTERS}, author={Kudenov, Michael W. and Miskiewicz, Matthew N. and Escuti, Michael J. and Dereniak, Eustace L.}, year={2012}, month={Nov}, pages={4413–4415} }