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1. Real-time, deep-learning aided lensless microscope

   https://doi.org/10.1364/BOE.490199  

   Wu, Jimin; Boominathan, Vivek; Veeraraghavan, Ashok; Robinson, Jacob_T (July 2023, Biomedical Optics Express)

   Traditional miniaturized fluorescence microscopes are critical tools for modern biology. Invariably, they struggle to simultaneously image with a high spatial resolution and a large field of view (FOV). Lensless microscopes offer a solution to this limitation. However, real-time visualization of samples is not possible with lensless imaging, as image reconstruction can take minutes to complete. This poses a challenge for usability, as real-time visualization is a crucial feature that assists users in identifying and locating the imaging target. The issue is particularly pronounced in lensless microscopes that operate at close imaging distances. Imaging at close distances requires shift-varying deconvolution to account for the variation of the point spread function (PSF) across the FOV. Here, we present a lensless microscope that achieves real-time image reconstruction by eliminating the use of an iterative reconstruction algorithm. The neural network-based reconstruction method we show here, achieves more than 10000 times increase in reconstruction speed compared to iterative reconstruction. The increased reconstruction speed allows us to visualize the results of our lensless microscope at more than 25 frames per second (fps), while achieving better than 7 µm resolution over a FOV of 10 mm². This ability to reconstruct and visualize samples in real-time empowers a more user-friendly interaction with lensless microscopes. The users are able to use these microscopes much like they currently do with conventional microscopes. 

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2. Light Microscopy Outreach as an Introduction to Scientific Concepts for Students in Under-Resourced Schools Across the Globe

   Endow, Sharyn A.; Paul, Umika S. (January 2020, Microscopy and microanalysis)

   Light microscopy provides a window into another world that is not visible to the unaided eye. Because of this and its importance in biological discoveries, the light microscope is an essential tool for scientific studies. It can also be used with a variety of easily obtained specimens to provide dramatic demonstrations of previously unknown features of common plants and animals. Thus, one way to interest young people in science is to start with an introduction to light microscopy. This is an especially effective strategy for individuals who attend less advantaged or under-resourced schools, as they may not have been previously exposed to scientific concepts in their classes. However, introducing light microscopy lessons in the classroom can be challenging because of the high cost of light microscopes, even those that are relatively basic, in addition to their usual large size. Efforts are underway by our laboratory in collaboration with the Biophysical Society (BPS) to introduce young people to light microscopy using small, easy-to-assemble wooden microscopes developed by Echo Laboratories. The microscopes are available online as low-cost kits ($10 each with shipping), each consisting of 19 parts printed onto an 81⁄2 x 11 inch sheet of light-weight wood (Fig. 1). After punching out the pieces, they can be assembled into a microscope with a moveable stage and a low-power lens, also provided in the kit (Fig. 2). Photos taken with a cell phone through the microscope lens can give magnifications of ~16-18x, or higher. At these magnifications, features of specimens that are not visible to the unaided eye can be easily observed, e.g., small hairs on the margins of leaves or lichens [1]. As a member of the BPS Education Committee, one of us (SAE) wrote a Lesson Plan on Light Microscopy specifically for use with the wooden microscopes. SAE was also able to obtain a gift of 500 wooden microscope kits for the BPS from Echo Laboratories and Chroma Technology Corp in 2016. The wooden microscope kits, together with the lesson plan, have provided the materials for our present outreach efforts. Rather than giving out the wooden microscope kits to individuals, the BPS asked the Education Committee to maximize the impact of the gift by distributing the microscopes with the Lesson Plan on Light Microscopy to teachers, e.g., through teachers’ workshops or outreach sessions. This strategy was devised to enable the Society to reach a larger number of young people than by giving the microscopes to individuals. The Education Committee first evaluated the microscopes as a tool to introduce students to scientific concepts by providing microscopes to a BPS member at the National University of Colombia who conducted a workshop on Sept 19-24, 2016 in Tumaco, Columbia. During the workshop, which involved 120 high school girls and 80 minority students, including Afro-Colombian and older students, the students built the wooden microscopes and examined specimens, and compared the microscopes to a conventional light microscope. Assembling the wooden microscopes was found to be a useful procedure that was similar to a scientific protocol, and encouraged young girls and older students to participate in science. This was especially promising in Colombia, where there are few women in science and little effort to increase women in STEM fields. Another area of outreach emerged recently when one of us, USP, an undergraduate student at Duke University, who was taught by SAE how to assemble the wooden microscopes and how to use the lesson plan, took three wooden microscopes on a visit to her family in Bangalore, India in summer 2018 [2]. There she organized and led three sessions in state run, under-resourced government schools, involving classes of ~25-40 students each. This was very successful – the students enjoyed learning about the microscopes and building them, and the science teachers were interested in expanding the sessions to other government schools. USP taught the teachers how to assemble and use the microscopes and gave the teachers the microscopes and lesson plan, which is also available to the public at the BPS web site. She also met with a founder of the organization, Whitefield Rising, which is working to improve teaching in government schools, and taught her and several volunteers how to assemble the microscopes and conduct the sessions. The Whitefield Rising members have been able to conduct nine further sessions in Bangalore over the past ~18 months (Fig. 3), using microscope kits provided to them by the BPS. USP has continued to work with members of the Whitefield Rising group during her summer and winter breaks on visits to Bangalore. Recently she has been working with another volunteer group that has expanded the outreach efforts to New Delhi. The light microscopy outreach that our laboratory is conducting in India in collaboration with the BPS is having a positive impact because we have been able to develop a partnership with volunteers in Bangalore and New Delhi. The overall goal is to enhance science education globally, especially in less advantaged schools, by providing a low-cost microscope that can be used to introduce students to scientific concepts. 

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3. In-Situ Investigation of Electron Beam-Induced Gas-Phase Polymerization Using Closed-Cell Transmission Electron Microscopy

   https://doi.org/10.1093/mam/ozaf048.939  

   Cai, Zizhen; Koo, Kunmo; Hu, Xiaobing; Dravid, Vinayak P (July 2025, Microscopy and Microanalysis)

   Electron beam-induced polymerization (EBIP) has been widely explored in coatings, adhesives, and nanostructure fabrication, relying on electron irradiation to generate reactive species that initiate polymerization via radical pathways [1]. While its efficiency in solid and thin-film systems is well established [2], real-time observation of gas-phase polymerization at the nanoscale remains challenging due to the lack of suitable experimental platforms. In this study, we employ a custom-built ultrathin (UT) membrane gas-cell chip for in-situ closed-cell environmental transmission electron microscopy (ETEM). This platform offers enhanced reciprocal and spectral visibility, enabling precise tracking of crystallinity through diffraction patterns and gas composition through electron energy loss spectroscopy (EELS) [3-5]. By allowing real-time observation of polymerization kinetics under controlled electron irradiation, this work aims to elucidate the fundamental mechanisms governing EBIP in the gas phase, addressing a critical knowledge gap in electron beam-driven chemical reactions. 

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4. Optical coherence tomography-based design for a real-time motion corrected scanning microscope

   https://doi.org/10.1364/OL.490087  

   Tucker, Stephen_S; Giblin, John_T; Kiliç, Kivilcim; Chen, Anderson; Tang, Jianbo; Boas, David_A (July 2023, Optics Letters)

   While two-photon fluorescence microscopy is a powerful platform for the study of functional dynamics in living cells and tissues, the bulk motion inherent to these applications causes distortions. We have designed a motion tracking module based on spectral domain optical coherence tomography which compliments a laser scanning two-photon microscope with real-time corrective feedback. The module can be added to fluorescent imaging microscopes using a single dichroic and without additional contrast agents. We demonstrate that the system can track lateral displacements as large as 10μm at 5 Hz with latency under 14 ms and propose a scheme to extend the system to 3D correction with the addition of a remote focusing module. We also propose several ways to improve the module’s performance by reducing the feedback latency. We anticipate that this design can be adapted to other imaging modalities, enabling the study of samples subject to motion artifacts at higher resolution. 

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5. LED array reflectance microscopy for scattering-based multi-contrast imaging

   https://doi.org/10.1364/OL.387434  

   Song, Weiye; Matlock, Alex; Fu, Sipei; Qin, Xiaodan; Feng, Hui; Gabel, Christopher_V; Tian, Lei; Yi, Ji (March 2020, Optics Letters)

   LED array microscopy is an emerging platform for computational imaging with significant utility for biological imaging. Existing LED array systems often exploit transmission imaging geometries of standard brightfield microscopes that leave the rich backscattered field undetected. This backscattered signal contains high-resolution sample information with superb sensitivity to subtle structural features that make it ideal for biological sensing and detection. Here, we develop an LED array reflectance microscope capturing the sample’s backscattered signal. In particular, we demonstrate multimodal brightfield, darkfield, and differential phase contrast imaging on fixed and living biological specimens includingCaenorhabditis elegans (C. elegans), zebrafish embryos, and live cell cultures. Video-rate multimodal imaging at 20 Hz records real time features of freely movingC. elegansand the fast beating heart of zebrafish embryos. Our new reflectance mode is a valuable addition to the LED array microscopic toolbox. 

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