@misc{rosen_alford_allan_anand_arnon_arockiaraj_art_bai_balasubramaniam_birnbaum_et al._2024, title={Roadmap on computational methods in optical imaging and holography [invited]}, volume={130}, ISSN={["1432-0649"]}, DOI={10.1007/s00340-024-08280-3}, abstractNote={Computational methods have been established as cornerstones in optical imaging and holography in recent years. Every year, the dependence of optical imaging and holography on computational methods is increasing significantly to the extent that optical methods and components are being completely and efficiently replaced with computational methods at low cost. This roadmap reviews the current scenario in four major areas namely incoherent digital holography, quantitative phase imaging, imaging through scattering layers, and super-resolution imaging. In addition to registering the perspectives of the modern-day architects of the above research areas, the roadmap also reports some of the latest studies on the topic. Computational codes and pseudocodes are presented for computational methods in a plug-and-play fashion for readers to not only read and understand but also practice the latest algorithms with their data. We believe that this roadmap will be a valuable tool for analyzing the current trends in computational methods to predict and prepare the future of computational methods in optical imaging and holography.}, number={9}, journal={APPLIED PHYSICS B-LASERS AND OPTICS}, author={Rosen, Joseph and Alford, Simon and Allan, Blake and Anand, Vijayakumar and Arnon, Shlomi and Arockiaraj, Francis Gracy and Art, Jonathan and Bai, Bijie and Balasubramaniam, Ganesh M. and Birnbaum, Tobias and et al.}, year={2024}, month={Sep} } @article{ahmad_wrennall_goriounova_sekhri_iskarpatyoti_ghosh_abdelwahab_voeller_rai_mahida_et al._2024, title={Specific Inhibition of Orai1-mediated Calcium Signalling Resolves Inflammation and Clears Bacteria in an Acute Respiratory Distress Syndrome Model}, volume={209}, ISSN={["1535-4970"]}, DOI={10.1164/rccm.202308-1393OC}, abstractNote={Rationale: Acute respiratory distress syndrome (ARDS) has an unacceptably high mortality rate (35%) and is without effective therapy. Orai1 is a Ca2+ channel involved in store-operated Ca2+ entry (SOCE), a process that exquisitely regulates inflammation. Orai1 is considered a druggable target, but no Orai1-specific inhibitors exist to date. Objectives: To evaluate whether ELD607, a first-in-class Orai1 antagonist, can treat ARDS caused by bacterial pneumonia in preclinical models. Methods: ELD607 pharmacology was evaluated in HEK293T cells and freshly isolated immune cells from patients with ARDS. A murine acute lung injury model caused by bacterial pneumonia was then used: mice were infected with Pseudomonas aeruginosa, Staphylococcus aureus, methicillin-resistant S. aureus, or multidrug-resistant P. aeruginosa and then treated with ELD607 intranasally. Measurements and Main Results: ELD607 specifically inhibited SOCE in HEK293T cells with a half-maximal inhibitory concentration of 9 nM. ELD607 was stable in ARDS airway secretions and inhibited SOCE in ARDS immune cells. In vivo, inhaled ELD607 significantly reduced neutrophilia and improved survival. Surprisingly, Orai1 inhibition by ELD607 caused a significant reduction in lung bacteria, including methicillin-resistant S. aureus. ELD607 worked as an immunomodulator that reduced cytokine levels, reduced neutrophilia, and promoted macrophage-mediated resolution of inflammation and clearance of bacteria. Indeed, when alveolar macrophages were depleted with inhaled clodronate, ELD607 was no longer able to resolve inflammation or clear bacteria. Conclusions: These data indicate that specific Orai1 inhibition by ELD607 may be a novel approach to reduce multiorgan inflammation and treat antibiotic-resistant bacteria.}, number={6}, journal={AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE}, author={Ahmad, Saira and Wrennall, Joe A. and Goriounova, Alexandra S. and Sekhri, Malika and Iskarpatyoti, Jason A. and Ghosh, Arunava and Abdelwahab, Sabri H. and Voeller, Alexis and Rai, Mani and Mahida, Rahul Y. and et al.}, year={2024}, month={Mar}, pages={703–715} } @article{moatti_connard_de britto_dunn_rastogi_rai_schnabel_ligler_hutson_fitzpatrick_et al._2024, title={Surgical procedure of intratympanic injection and inner ear pharmacokinetics simulation in domestic pigs}, volume={15}, ISSN={["1663-9812"]}, DOI={10.3389/fphar.2024.1348172}, abstractNote={Introduction: One major obstacle in validating drugs for the treatment or prevention of hearing loss is the limited data available on the distribution and concentration of drugs in the human inner ear. Although small animal models offer some insights into inner ear pharmacokinetics, their smaller organ size and different barrier (round window membrane) permeabilities compared to humans can complicate study interpretation. Therefore, developing a reliable large animal model for inner ear drug delivery is crucial. The inner and middle ear anatomy of domestic pigs closely resembles that of humans, making them promising candidates for studying inner ear pharmacokinetics. However, unlike humans, the anatomical orientation and tortuosity of the porcine external ear canal frustrates local drug delivery to the inner ear.Methods: In this study, we developed a surgical technique to access the tympanic membrane of pigs. To assess hearing pre- and post-surgery, auditory brainstem responses to click and pure tones were measured. Additionally, we performed 3D segmentation of the porcine inner ear images and used this data to simulate the diffusion of dexamethasone within the inner ear through fluid simulation software (FluidSim).Results: We have successfully delivered dexamethasone and dexamethasone sodium phosphate to the porcine inner ear via the intratympanic injection. The recorded auditory brainstem measurements revealed no adverse effects on hearing thresholds attributable to the surgery. We have also simulated the diffusion rates for dexamethasone and dexamethasone sodium phosphate into the porcine inner ear and confirmed the accuracy of the simulations using in-vivo data.Discussion: We have developed and characterized a method for conducting pharmacokinetic studies of the inner ear using pigs. This animal model closely mirrors the size of the human cochlea and the thickness of its barriers. The diffusion time and drug concentrations we reported align closely with the limited data available from human studies. Therefore, we have demonstrated the potential of using pigs as a large animal model for studying inner ear pharmacokinetics.}, journal={FRONTIERS IN PHARMACOLOGY}, author={Moatti, Adele and Connard, Shannon and De Britto, Novietta and Dunn, William A. and Rastogi, Srishti and Rai, Mani and Schnabel, Lauren V. and Ligler, Frances S. and Hutson, Kendall A. and Fitzpatrick, Douglas C. and et al.}, year={2024}, month={Jan} } @article{rai_li_ghashghaei_greenbaum_2023, title={Deep learning-based adaptive optics for light sheet fluorescence microscopy}, volume={14}, ISSN={["2156-7085"]}, DOI={10.1364/BOE.488995}, abstractNote={Light sheet fluorescence microscopy (LSFM) is a high-speed imaging technique that is often used to image intact tissue-cleared specimens with cellular or subcellular resolution. Like other optical imaging systems, LSFM suffers from sample-induced optical aberrations that decrement imaging quality. Optical aberrations become more severe when imaging a few millimeters deep into tissue-cleared specimens, complicating subsequent analyses. Adaptive optics are commonly used to correct sample-induced aberrations using a deformable mirror. However, routinely used sensorless adaptive optics techniques are slow, as they require multiple images of the same region of interest to iteratively estimate the aberrations. In addition to the fading of fluorescent signal, this is a major limitation as thousands of images are required to image a single intact organ even without adaptive optics. Thus, a fast and accurate aberration estimation method is needed. Here, we used deep-learning techniques to estimate sample-induced aberrations from only two images of the same region of interest in cleared tissues. We show that the application of correction using a deformable mirror greatly improves image quality. We also introduce a sampling technique that requires a minimum number of images to train the network. Two conceptually different network architectures are compared; one that shares convolutional features and another that estimates each aberration independently. Overall, we have presented an efficient way to correct aberrations in LSFM and to improve image quality.}, number={6}, journal={BIOMEDICAL OPTICS EXPRESS}, author={Rai, Mani Ratnam and Li, Chen and Ghashghaei, H. Troy and Greenbaum, Alon}, year={2023}, month={Jun}, pages={2905–2919} } @article{li_rai_ghashghaei_greenbaum_2022, title={Illumination angle correction during image acquisition in light-sheet fluorescence microscopy using deep learning}, volume={13}, ISSN={["2156-7085"]}, DOI={10.1364/BOE.447392}, abstractNote={Light-sheet fluorescence microscopy (LSFM) is a high-speed imaging technique that provides optical sectioning with reduced photodamage. LSFM is routinely used in life sciences for live cell imaging and for capturing large volumes of cleared tissues. LSFM has a unique configuration, in which the illumination and detection paths are separated and perpendicular to each other. As such, the image quality, especially at high resolution, largely depends on the degree of overlap between the detection focal plane and the illuminating beam. However, spatial heterogeneity within the sample, curved specimen boundaries, and mismatch of refractive index between tissues and immersion media can refract the well-aligned illumination beam. This refraction can cause extensive blur and non-uniform image quality over the imaged field-of-view. To address these issues, we tested a deep learning-based approach to estimate the angular error of the illumination beam relative to the detection focal plane. The illumination beam was then corrected using a pair of galvo scanners, and the correction significantly improved the image quality across the entire field-of-view. The angular estimation was based on calculating the defocus level on a pixel level within the image using two defocused images. Overall, our study provides a framework that can correct the angle of the light-sheet and improve the overall image quality in high-resolution LSFM 3D image acquisition.}, number={2}, journal={BIOMEDICAL OPTICS EXPRESS}, author={Li, Chen and Rai, Mani Ratnam and Ghashghaei, H. Troy and Greenbaum, Alon}, year={2022}, month={Feb}, pages={888–901} } @article{newell_kapps_cai_rai_st armour_horman_rock_witchey_greenbaum_patisaul_2023, title={Maternal organophosphate flame retardant exposure alters the developing mesencephalic dopamine system in fetal rat}, volume={191}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfac137}, abstractNote={AbstractOrganophosphate flame retardants (OPFRs) have become the predominant substitution for legacy brominated flame retardants but there is concern about their potential developmental neurotoxicity (DNT). OPFRs readily dissociate from the fireproofed substrate to the environment, and they (or their metabolites) have been detected in diverse matrices including air, water, soil, and biota, including human urine and breastmilk. Given this ubiquitous contamination, it becomes increasingly important to understand the potential effects of OPFRs on the developing nervous system. We have previously shown that maternal exposure to OPFRs results in neuroendocrine disruption, alterations to developmental metabolism of serotonin (5-HT) and axonal extension in male fetal rats, and potentiates adult anxiety-like behaviors. The development of the serotonin and dopamine systems occur in parallel and interact, therefore, we first sought to enhance our prior 5-HT work by first examining the ascending 5-HT system on embryonic day 14 using whole mount clearing of fetal heads and 3-dimensional (3D) brain imaging. We also investigated the effects of maternal OPFR exposure on the development of the mesocortical dopamine system in the same animals through 2-dimensional and 3D analysis following immunohistochemistry for tyrosine hydroxylase (TH). Maternal OPFR exposure induced morphological changes to the putative ventral tegmental area and substantia nigra in both sexes and reduced the overall volume of this structure in males, whereas 5-HT nuclei were unchanged. Additionally, dopaminergic axogenesis was disrupted in OPFR exposed animals, as the dorsoventral spread of ventral telencephalic TH afferents were greater at embryonic day 14, while sparing 5-HT fibers. These results indicate maternal exposure to OPFRs alters the development trajectory of the embryonic dopaminergic system and adds to growing evidence of OPFR DNT.}, number={2}, journal={TOXICOLOGICAL SCIENCES}, author={Newell, Andrew J. and Kapps, Victoria A. and Cai, Yuheng and Rai, Mani Ratnam and St Armour, Genevieve and Horman, Brian M. and Rock, Kylie D. and Witchey, Shannah K. and Greenbaum, Alon and Patisaul, Heather B.}, year={2023}, month={Feb}, pages={357–373} } @article{rai_li_greenbaum_2022, title={Quantitative analysis of illumination and detection corrections in adaptive light sheet fluorescence microscopy}, volume={13}, ISSN={["2156-7085"]}, DOI={10.1364/BOE.454561}, abstractNote={Light-sheet fluorescence microscopy (LSFM) is a high-speed, high-resolution and minimally phototoxic technique for 3D imaging of in vivo and in vitro specimens. LSFM exhibits optical sectioning and when combined with tissue clearing techniques, it facilitates imaging of centimeter scale specimens with micrometer resolution. Although LSFM is ubiquitous, it still faces two main challenges that effect image quality especially when imaging large volumes with high-resolution. First, the light-sheet illumination plane and detection lens focal plane need to be coplanar, however sample-induced aberrations can violate this requirement and degrade image quality. Second, introduction of sample-induced optical aberrations in the detection path. These challenges intensify when imaging whole organisms or structurally complex specimens like cochleae and bones that exhibit many transitions from soft to hard tissue or when imaging deep (> 2 mm). To resolve these challenges, various illumination and aberration correction methods have been developed, yet no adaptive correction in both the illumination and the detection path have been applied to improve LSFM imaging. Here, we bridge this gap, by implementing the two correction techniques on a custom built adaptive LSFM. The illumination beam angular properties are controlled by two galvanometer scanners, while a deformable mirror is positioned in the detection path to correct for aberrations. By imaging whole porcine cochlea, we compare and contrast these correction methods and their influence on the image quality. This knowledge will greatly contribute to the field of adaptive LSFM, and imaging of large volumes of tissue cleared specimens.}, number={5}, journal={BIOMEDICAL OPTICS EXPRESS}, author={Rai, Mani Ratnam and Li, Chen and Greenbaum, Alon}, year={2022}, month={May}, pages={2960–2974} }