Article
Optics
Dorian Bouchet, Jacob Seifert, Allard P. Mosk
Summary: This study presents a numerical framework to quantify the precision of estimating parameters from measured data using the Fisher information matrix as a benchmark for assessing CDI methods. By optimizing the Fisher information metric with deep learning libraries, the research identifies an optimal illumination scheme for minimizing estimation errors under specific experimental constraints, paving the way for efficient characterization of structured samples at the sub-wavelength scale.
Article
Multidisciplinary Sciences
Elena Goi, Steffen Schoenhardt, Min Gu
Summary: This article presents a compact optical-electronic module based on multi-layered diffractive neural networks that can directly retrieve pupil phase information from an imaging sensor. Compared to current phase retrieval schemes, this module has a smaller size and higher practical value.
NATURE COMMUNICATIONS
(2022)
Article
Optics
Deniz Mengu, Anika Tabassum, Mona Jarrahi, Aydogan Ozcan
Summary: Multispectral imaging has applications in various fields and a diffractive optical network-based system is proposed to create a virtual spectral filter array. This system performs coherent imaging over a large spectrum and routes specific spectral channels onto an array of pixels without filters or recovery algorithms. The system's compact design and polarization insensitivity make it transformative for imaging applications where high-density multispectral pixel arrays are not readily available.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Optics
Guoxuan Liu, Ning Xu, Huaidong Yang, Qiaofeng Tan, Guofan Jin
Summary: Structured illumination microscopy (SIM) is an advanced microscope system with superresolution capability and fast imaging speed. However, the bulky size has limited its wider application. We developed a miniaturized SIM system that greatly simplified the experimental setup and demonstrated its important applications in bio-imaging.
PHOTONICS RESEARCH
(2022)
Article
Nanoscience & Nanotechnology
Rajesh Menon, Nicole Brimhall
Summary: Flat optics, which have been used for focusing and imaging for many years, have experienced a recent resurgence due to advancements in computational electromagnetics and nanofabrication. In this perspective, the connections between flat lenses and holograms are summarized, the current state of diffractive flat lenses is described, an effective metric for comparing their performance is proposed (the generalized strehl ratio), and potential areas for future research are explored.
Article
Biochemical Research Methods
Sheng Xiao, Shuqi Zheng, Jerome Mertz
Summary: Conventional phase microscopy techniques are limited in thick sample applications, requiring large numbers of measurements for volumetric imaging. By combining new technologies, high-speed 3D phase imaging in thick, scattering tissues can be achieved.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Optics
Francesco Reda, Marcella Salvatore, Fabio Borbone, Pasqualino Maddalena, Antonio Ambrosio, Stefano Luigi Oscurato
Summary: This research demonstrates the realization of a fully reconfigurable flat varifocal diffractive lens, which can be directly manufactured, erased, and reshaped on the surface of an azopolymer film. Integrating the lens into the optical system allows for multi-depth object imaging. This approach provides an effective choice for integrating or substituting modern optical systems for advanced functionalities.
Article
Optics
Kartik Ayyer, P. Lourdu Xavier, Johan Bielecki, Zhou Shen, Benedikt J. Daurer, Amit K. Samanta, Salah Awel, Richard Bean, Anton Barty, Martin Bergemann, Tomas Ekeberg, Armando D. Estillore, Hans Fangohr, Klaus Giewekemeyer, Mark S. Hunter, Mikhail Karnevskiy, Richard A. Kirian, Henry Kirkwood, Yoonhee Kim, Jayanath Koliyadu, Holger Lange, Romain Letrun, Jannik Lubke, Thomas Michelat, Andrew J. Morgan, Nils Roth, Tokushi Sato, Margin Sikorski, Florian Schulz, John C. H. Spence, Patrik Vagovic, Tamme Wollweber, Lena Worbs, Oleksandr Yefanov, Yulong Zhuang, Filipe R. N. C. Maia, Daniel A. Horke, Jochen Kuepper, N. Duane Loh, Adrian P. Mancuso, Henry N. Chapman
Summary: Single particle imaging at XFELs has the potential to determine the structure and dynamics of single biomolecules at room temperature. By overcoming hurdles in collecting high-quality diffraction patterns and computational purification, researchers have successfully obtained sub-nano meter resolution 3D reconstructions for biomolecular imaging. These advancements in X-ray sources, detectors, sample delivery, and data analysis algorithms illuminate new possibilities for characterizing diverse ensembles at the structural level.
Article
Optics
Li Song, Edmund Y. Lam
Summary: This paper proposes a fast and robust phase retrieval method for masked CDI based on the alternating direction method of multipliers (ADMM), which incorporates prior knowledge of the mask using a plug-and-play ADMM approach. The method utilizes a regularizer based on the structure tensor and Harris corner detector and achieves comparable reconstruction results with less time compared to conventional phase retrieval methods. Experimental validation on real in situ CDI data demonstrates the method's efficiency and robustness, making it suitable for imaging dynamic objects.
PHOTONICS RESEARCH
(2022)
Article
Optics
Gensen Yang, Jinjin Jin, Mingbo Pu, He Lin, Yingli Ha, Xiangang Luo
Summary: In this paper, a miniaturized diffractive/refractive hybrid system for solar-blind ultraviolet imaging is presented. The system uses a diffractive optical element and three refractive lenses to achieve high-resolution and excellent imaging capability. The experiments demonstrate that the system has the ability to distinguish the smallest line pair and a high modulation transfer function at the target maximum frequency. This strategy provides significant guidance for the mass production of miniaturized and lightweight solar-blind ultraviolet imaging systems.
Article
Environmental Sciences
Nikolay Ivliev, Viktoria Evdokimova, Vladimir Podlipnov, Maxim Petrov, Sofiya Ganchevskaya, Ivan Tkachenko, Dmitry Abrameshin, Yuri Yuzifovich, Artem Nikonorov, Roman Skidanov, Nikolay Kazanskiy, Victor Soifer
Summary: This study presents a nanosatellite using an ultra-lightweight harmonic diffractive lens for Earth remote sensing. The researchers described the CubeSat platform, lens synthesis, design, and manufacturing process, and the image post-processing with a convolutional neural network on Earth.
Article
Optics
Guo-Wei Wu, Liang-Chia Chen
Summary: A novel method utilizing artificial neural network (ANN) and diffractive image microscopy (DIM) was proposed in this study, achieving precise measurement of surface height, inclined angle, and tilted direction. This approach does not require prior knowledge of neighboring geometric information.
OPTICS AND LASERS IN ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Cheng Zheng, Jong Kang Park, Murat Yildirim, Josiah R. Boivin, Yi Xue, Mriganka Sur, Peter T. C. So, Dushan N. Wadduwage
Summary: Nonlinear optical microscopy allows deep tissue imaging at millimeter scale in vivo, but has limited throughput. The DEEP technique combines patterned excitation and computational imaging to improve image quality in thick scattering samples, enabling reconstruction of high-resolution structural features from multiple DEEP images.
Article
Multidisciplinary Sciences
Jeonghun Oh, Herve Hugonnet, YongKeun Park
Summary: The authors propose a holographic image sensor that can reconstruct the complex amplitude of scattered light from a single-intensity image using reciprocal diffractive imaging. This allows for holographic imaging of three-dimensional diffusive objects and potential applications in both static and dynamic conditions.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Applied
Xiaowen Shi, Jian Shi, Edwin Fohtung
Summary: The rapid development in the field of ferroelectric and magnetic materials has attracted significant attention. Bragg coherent x-ray diffractive imaging (CXDI) is a non-destructive imaging technique that provides high-resolution and refraction sensitivities, playing a crucial role in the characterization of nano-scale crystals and electronic devices.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Biotechnology & Applied Microbiology
Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J. Madigan, Rachel Oshiro, Kira S. Makarova, Eugene Koonin, Feng Zhang
Summary: CRISPR-Cas13 systems have been developed for precise RNA editing, and a new ultrasmall family of Cas13b proteins called Cas13bt has been identified, which can facilitate mammalian transcript knockdown. By engineering compact variants of RNA editors using Cas13bt, researchers have demonstrated successful packaging within a single adeno-associated virus, with potential therapeutic applications.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hui-Lan Hu, Kalanghad P. Srinivas, Shuoshuo Wang, Moses Chao, Timothee Lionnet, Ian Mohr, Angus C. Wilson, Daniel P. Depledge, Tony T. Huang
Summary: Single-cell RNA sequencing is a powerful tool for understanding cell diversity and phenotypic states in tissues. In this study, scRNA-seq and smFISH were used to investigate host transcriptome changes upon the reactivation of HSV-1. Gadd45b was identified as a critical factor regulating HSV-1 reactivation, with different subcellular localization correlating with viral gene expression.
Article
Multidisciplinary Sciences
Hao Li, Praneeth Namburi, Jacob M. Olson, Matilde Borio, Mackenzie E. Lemieux, Anna Beyeler, Gwendolyn G. Calhoon, Natsuko Hitora-Imamura, Austin A. Coley, Avraham Libster, Aneesh Bal, Xin Jin, Huan Wang, Caroline Jia, Sourav R. Choudhury, Xi Shi, Ada C. Felix-Ortiz, Veronica de la Fuente, Vanessa P. Barth, Hunter O. King, Ehsan M. Izadmehr, Jasmin S. Revanna, Kanha Batra, Kyle B. Fischer, Laurel R. Keyes, Nancy Padilla-Coreano, Cody A. Siciliano, Kenneth M. McCullough, Romy Wichmann, Kerry J. Ressler, Ila R. Fiete, Feng Zhang, Yulong Li, Kay M. Tye
Summary: The study demonstrates that neurotensin-expressing neurons in the paraventricular nucleus of the thalamus (PVT) play a role in assigning positive or negative valence during associative learning through modulation of the basolateral amygdala (BLA). The study also shows that reward learning enhances calcium dynamics within the PVT-BLA:NT projection and increases NT concentrations in the BLA, while punishment learning reduces these dynamics and concentrations.
Article
Biochemistry & Molecular Biology
Ana Uzquiano, Amanda J. Kedaigle, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim, Tyler Faits, Surya Nagaraja, Noelia Anton-Bolanos, Chiara Gerhardinger, Ashley Tucewicz, Evan Murray, Xin Jin, Jason Buenrostro, Fei Chen, Silvia Velasco, Aviv Regev, Joshua Z. Levin, Paola Arlotta
Summary: A comprehensive atlas of human cortical organoid development provides a valuable resource for studying cellular diversification and fate specification mechanisms, independent of metabolic states.
Article
Biology
Thomas G. W. Graham, John Joseph Ferrie, Gina M. Dailey, Robert Tjian, Xavier Darzacq
Summary: Single-molecule imaging is a powerful tool for studying biochemical processes in live cells, but tracking single molecules and detecting their interactions simultaneously remains challenging. This study describes a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which allows the detection of protein-protein interactions in live cells using two different labeled protein complexes in proximity.
Article
Biology
Alec Heckert, Liza Dahal, Robert Tijan, Xavier Darzacq
Summary: Single-particle tracking (SPT) is a powerful tool for studying molecular mechanisms of cellular regulation. However, there are technical limitations in interpreting SPT data for fast-diffusing proteins. Researchers have proposed methods based on Bayesian nonparametrics to address these limitations.
Article
Biology
Yu Chen, Claudia Cattoglio, Gina M. Dailey, Qiulin Zhu, Robert Tjian, Xavier Darzacq
Summary: The study has revealed the important role of intrinsically disordered regions (IDRs) in regulating the binding and diffusion behavior of transcription factors, providing insights into the mechanism of functional target site selectivity on chromatin.
Article
Genetics & Heredity
Tsung-Han S. Hsieh, Claudia Cattoglio, Elena Slobodyanyuk, Anders S. Hansen, Xavier Darzacq, Robert Tjian
Summary: Short-term maintenance of most gene expression and enhancer-promoter interactions does not require CTCF, Cohesin, WAPL, or YY1, but Cohesin may facilitate transcription factor binding to targets more efficiently.
Article
Biochemical Research Methods
Ella Bahry, Laura Breimann, Marwan Zouinkhi, Leo Epstein, Klim Kolyvanov, Nicholas Mamrak, Benjamin King, Xi Long, Kyle I. S. Harrington, Timothee Lionnet, Stephan Preibisch
Summary: Fluorescent in-situ hybridization (FISH) is a method to extract spatially resolved genetic and epigenetic information from biological samples. We present a new software, RS-FISH, for accurate and fast spot detection in microscopy images. RS-FISH offers interactive parameter tuning, scalability to large datasets and image volumes, and maintains high detection accuracy and low localization error across different signal-to-noise ratios.
Review
Biochemistry & Molecular Biology
Liza Dahal, Nike Walther, Robert Tjian, Xavier Darzacq, Thomas G. W. Graham
Summary: The interactions between molecules determine their movement. Single-molecule tracking (SMT) provides a unique means to observe the dynamic interactions of biomolecules within live cells. This article discusses the working principle of SMT, its implications in molecular biology, and how it has revolutionized our understanding of nuclear processes. The article also highlights the current limitations of SMT and explores new technical advancements that aim to overcome these limitations.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Biophysics
Robert F. DeJaco, Jacob M. Majikes, J. Alexander Liddle, Anthony J. Kearsley
Summary: We propose a method to determine the temperature-dependent properties of the SYTO-13 dye bound to DNA using fluorescence measurements. Through mathematical modeling, control experiments, and optimization, we can separate the dye binding strength, brightness, and experimental noise. By focusing on low-dye coverage, the model avoids bias and simplifies quantification. Utilizing the temperature-cycling capabilities of a real-time PCR machine increases throughput. The computed properties for single-stranded DNA and double-stranded DNA are consistent with intuition and explain the enhanced fluorescence of the dye in the presence of double-stranded DNA compared to single-stranded DNA.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Samuel Collombet, Isabell Rall, Claire Dugast-Darzacq, Alec Heckert, Aliaksandr Halavatyi, Agnes Le Saux, Gina Dailey, Xavier Darzacq, Edith Heard
Summary: The authors demonstrate that the disappearance of RNA polymerase II (RNAPII) from the inactive X chromosome territory is not caused by biophysical compartmentalization, but rather due to the loss of RNAPII bound fraction on chromatin. They show that RNAPII freely accesses the Xist territory during the initiation of X chromosome inactivation (XCI), indicating that the exclusion of RNAPII is not a consequence of physical compartmentalization. These findings highlight the importance of actively transcribing RNAPII in the regulation of gene silencing during XCI.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Martina Pigoni, Ana Uzquiano, Bruna Paulsen, Amanda J. Kedaigle, Sung Min Yang, Panagiotis Symvoulidis, Xian Adiconis, Silvia Velasco, Rafaela Sartore, Kwanho Kim, Ashley Tucewicz, Sarah Yoshimi Tropp, Kalliopi Tsafou, Xin Jin, Lindy Barrett, Fei Chen, Edward S. Boyden, Aviv Regev, Joshua Z. Levin, Paola Arlotta
Summary: De novo heterozygous loss-of-function mutations in the PTEN gene have been found to affect specific cell types during human brain development and contribute to the occurrence of autism spectrum disorders. Using human cortical organoids from different donors, this study identified cell-type specific developmental events affected by PTEN mutations. The findings showed variations in developmental timing and abnormal neuronal activity caused by PTEN heterozygosity, which were influenced by the genetic background of the donors.
HUMAN MOLECULAR GENETICS
(2023)
Review
Chemistry, Multidisciplinary
Jacob M. Majikes, J. Alexander Liddle
Summary: Nucleic Acid Nanotechnology (NAN) has matured over the past 40 years and is finding commercial applications. To compete with incumbent technologies, NAN should seek collaboration with adjacent technologies, and explore new application areas by creating a bridge between biology and semiconductor technology.
Article
Mathematical & Computational Biology
Corentin Guerinot, Valentin Marcon, Charlotte Godard, Thomas Blanc, Hippolyte Verdier, Guillaume Planchon, Francesca Raimondi, Nathalie Boddaert, Mariana Alonso, Kurt Sailor, Pierre-Marie Lledo, Bassam Hajj, Mohamed El Beheiry, Jean-Baptiste Masson
Summary: Combining virtual reality with cloud computing allows for natural interaction, annotation, and analysis of three-dimensional data, addressing issues with traditional methods and showing promising applications.
FRONTIERS IN BIOINFORMATICS
(2022)
