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  1. We have designed and implemented an approach for three-dimensional (3D) structured illumination (SI) microscopy (SIM) based on a quasi-monochromatic extended source illuminating a Wollaston prism to improve robustness, light efficiency and flexibility over our previous design. We show through analytical and experimental verification of the presented theoretical framework for our proposed tunable structured illumination microscopy (TSIM) system, that a simple and accurate determination of the axial modulation of the SI pattern is achieved, enabling a realistic characterization of the system’s effective optical transfer function (OTF). System performance as a function of the extended source size is investigated with simulations. Results from a comparative performance analysis of the proposed TSIM system and traditional SIM systems show some advantages over the traditional two-wave and three-wave interference SIM systems. We show that by controlling the source size and thereby the axial modulation of the 3D SI pattern, the TSIM scheme offers increased OTF compact support and improved optical sectioning capability, quantified by the integrated intensity, under certain conditions, which may be desirable when imaging optically thick samples. The additional tunability of the 3D SI pattern, provides a unique opportunity for OTF engineering in our TSIM system.

     
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  2. Underproduction, low retention, and lack of diversity in STEM disciplines, especially engineering, are significant challenges nationally, but are particularly acute in regions, both urban and rural, where educational access is limited. Leveraging our institutional location at a public urban research university in a city marked by its connection to its rural surroundings, we seek to address these challenges by implementing the Vertically Integrated Projects (VIP) model at our university with the support of an NSF IUSE grant. The VIP model is based on active learning and enables tiered mentoring from students at all academic years, thereby providing the opportunity of role modeling from upper-level undergraduate and graduate students as well as faculty. In addition, programs based on the VIP model are accessible to all students (not just high performing students) and provide a meaningful networking environment. We use our implementation of the VIP model to foster STEM identity growth and a sense of belonging, while increasing and celebrating diversity in engineering and other STEM disciplines. Our VIP program leverages best practices from the well-established VIP model and adapts it to address unique aspects of our university’s community and interests. Specifically, the program includes freshmen and will also serve as a recruitment tool for local community college students. It employs a tiered mentoring approach and activities that prepare students for research and foster networking. The long-term goal of the VIP experience is to create a research culture and community in engineering and eventually across STEM disciplines that is inclusive and supportive of students from diverse backgrounds. An additional focus is to showcase the value of diversity in research and innovation through the program. Both the research culture and increased acknowledgement of the value of diversity are designed to enhance students’ STEM identity, which is important for retention in the major and career. The purpose of this paper is to report on the planning and launch of our VIP program in Fall 2022, focusing on the PIs’ experiences implementing the program and on our first cohort’s (N = 12; 7 women; 4 Black/African American; 2 Hispanic) experiences participating in the program during their first semester. Specifically, this paper will describe the challenges and opportunities of implementing the VIP program and how the VIP model has been adapted to align with unique aspects of our institution and student body. We will also report preliminary analyses of student journal data collected from the first cohort throughout the Fall semester, where students described their initial expectations/hopes and concerns for the semester; their activities and emotional responses during the semester; and finally, their reflections on their experiences, positive or negative, throughout the semester. The paper will conclude by offering lessons learned from the first year of this project as well as directions for moving forward. 
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    Free, publicly-accessible full text available June 25, 2024
  3. The performance of structured illumination microscopy (SIM) systems depends on the computational method used to process the raw data. In this paper, we present a regularized three-dimensional (3D) model-based (MB) restoration method with positivity constraint (PC) for 3D processing of data from 3D-SIM (or 3-beam interference SIM), in which the structured illumination pattern varies laterally and axially. The proposed 3D-MBPC method introduces positivity in the solution through the reconstruction of an auxiliary function using a conjugate-gradient method that minimizes the mean squared error between the data and the 3D imaging model. The 3D-MBPC method providesaxial super resolution, which is not the same as improved optical sectioning demonstrated with model-based approaches based on the 2D-SIM (or 2-beam interference SIM) imaging model, for either 2D or 3D processing of a single plane from a 3D-SIM dataset. Results obtained with our 3D-MBPC method show improved 3D resolution over what is achieved by the standard generalized Wiener filter method, the first known method that performs 3D processing of 3D-SIM data. Noisy simulation results quantify the achieved 3D resolution, which is shown to match theoretical predictions. Experimental verification of the 3D-MBPC method with biological data demonstrates successful application to data volumes of different sizes.

     
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