Article
Biochemical Research Methods
Daniel Saska, Paul Pichler, Chen Qian, Christopher L. Buckley, Leon Lagnado
Summary: The mu SPIM Toolset is an open-source software built around the MicroManager platform that optimizes SPIM imaging, allowing high-frequency imaging of neural activity with relative independence from the microscope design. It provides a flexible solution for monitoring neural activity in the larval zebrafish brain.
JOURNAL OF NEUROSCIENCE METHODS
(2021)
Article
Biochemical Research Methods
Bingying Chen, Bo-Jui Chang, Philippe Roudot, Felix Zhou, Etai Sapoznik, Madeleine Marlar-Pavey, James B. Hayes, Peter T. Brown, Chih-Wei Zeng, Talley Lambert, Jonathan R. Friedman, Chun-Li Zhang, Dylan T. Burnette, Douglas P. Shepherd, Kevin M. Dean, Reto P. Fiolka
Summary: Structured illumination microscopy (SIM) improves the spatial resolution of fluorescence microscopy, while light-sheet fluorescence microscopy (LSFM) avoids exciting out-of-focus fluorescence. By combining SIM with LSFM using oblique plane microscopy, high-resolution three-dimensional imaging with low phototoxicity can be achieved.
Article
Optics
Pablo Roldan-Varona, Calum A. A. Ross, Luis Rodriguez-Cobo, Jose Miguel Lopez-Higuera, Erin Gaughan, Kevin Dhaliwal, Michael G. G. Tanner, Robert R. R. Thomson, Helen E. E. Parker
Summary: Imaging fibers are used to perform real-time fluorescence endomicroscopy, in vivo, in situ, with the goal of increasing diagnostic information for a plethora of organ systems and diseases. Widefield fiber endomicroscopy systems are simple, cost-effective, and come with fast image acquisition times. However, alternative approaches such as scanning systems produce higher contrast images with intrinsic optical sectioning, improving the visibility of histological features, albeit at the expense of simplicity, cost, and acquisition rate. We developed a selective plane illumination microscopy endoscopic fiber platform, consisting of an ultrafast laser fabricated end-cap, integrated with a polymer coherent fiber bundle, and an epifluorescence microscope. Polymer fibers are known to fluoresce when pumped with blue light, enhancing the background and noise in images. Our end-cap design circumvents this challenge. We demonstrate a reduction of out-of-focus features, along with improved contrast of in-focus features, in images of a tissue phantom. Moreover, we demonstrate the utility of our platform for endomicroscopy using a whole, ex vivo human lung model.
Article
Biochemical Research Methods
Caroline Bissardon, Xacier Mermet, Clement Quintard, Federico Sanjuan, Yves Fouillet, Frederic Bottausci, Marie Carriere, Florence Rivera, Pierre Blandin
Summary: In this article, the authors present an original selective plane illumination fluorescence microscope that is dedicated to imaging biostructures similar to organ-on-chips in microfluidic chips. The microscope compromises between a relatively large field of view and moderate resolution to allow morphological analysis of volumetric samples at the cellular scale inside microfluidic chambers. The setup is based on a simple design built around the chip and its microfluidic environment, enabling 3D imaging inside the chip.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Optics
Jialong Chen, Songyun Gu, Yunlong Meng, Zhiqiang Fu, Shih-Chi Chen
Summary: The letter introduces a holography-based structured light illumination method to enhance the resolution of widefield temporal focusing microscopy. By inducing temporal focusing and generating structured patterns, this method improves optical cross-sectioning capability and demonstrates enhanced axial confinement and improved suppression of out-of-focus fluorescence in imaging experiments.
Article
Optics
Jiajia Chen, Zhenhong Du, Chenhao Xu, Xiao Xiao, Wei Gong, Ke Si
Summary: Here we report an ultrafast 3D histological imaging scheme based on optimized selective plane illumination microscopy (mSPIM), a minutes-time scale clearing method (FOCM), and a deep learning-based image enhancement algorithm (SRACNet) to realize histological preparation and imaging of clinical tissues. Our scheme enables fast imaging at micron-level resolution and demonstrates detailed 3D morphological connections that are difficult to identify in conventional 2D histology.
Article
Nanoscience & Nanotechnology
Feifei Wang, Fuqiang Ren, Zhuoran Ma, Liangqiong Qu, Ronan Gourgues, Chun Xu, Ani Baghdasaryan, Jiachen Li, Iman Esmaeil Zadeh, Johannes W. N. Los, Andreas Fognini, Jessie Qin-Dregely, Hongjie Dai
Summary: By studying light scattering and utilizing new materials technology, the imaging depth of high-resolution optical microscopy in live mammals can be improved. This study demonstrates single-photon excitation fluorescence imaging in the NIR-IIc range, achieving the longest single-photon excitation and emission wavelengths to date for in vivo imaging of mice.
NATURE NANOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Giovanni Barbera, Rachel Jun, Yan Zhang, Bo Liang, Yun Li, Da-Ting Lin
Summary: In this work, a lightweight one-photon microscope capable of imaging at different focal depths is presented. The focal plane can be dynamically changed by modulating the pulse width of the control signal, enabling the switching of focal plane between frames. Experimental results showed an increase in the number of imaged neurons compared to single plane imaging.
SCIENTIFIC REPORTS
(2022)
Article
Optics
Stephan Daetwyler, Bo-jui Chang, Bingying Chen, Fabian f. Voigt, Divya Rajendran, Felix Zhou, Reto Fiolka
Summary: Understanding the intricate interplay and inter-connectivity of biological processes across an entire organism is crucial in various fields of biology. The mesoscopic oblique plane microscope (OPM) presented here allows high-speed whole organism imaging with fine details revealed. By utilizing a microprism, the axial resolution and optical sectioning are enhanced through total internal reflection. The imaging depth is extended up to threefold while maintaining constant axial resolution through rapid refocusing of the light sheet. The mesoscopic OPM enables in vivo and in toto whole organism imaging, demonstrating quantitative mapping of blood flow dynamics in zebrafish vasculature and endothelial nuclei at a 12 Hz acquisition rate.
Article
Chemistry, Analytical
Clara Gomez-Cruz, Sonia Laguna, Ariadna Bachiller-Pulido, Cristina Quilez, Marina Canadas-Ortega, Ignacio Albert-Smet, Jorge Ripoll, Arrate Munoz-Barrutia
Summary: This manuscript presents a novel architecture of a single-plane illumination microscopy (SPIM) for high-resolution imaging of live processes at a cellular level. The custom-made microscope overcomes limitations of existing techniques, achieving high-speed acquisition capabilities, low phototoxicity, and low mechanical disturbances, and demonstrating excellent imaging performance in microfluidic devices.
Article
Optics
S. R. Rinsa, Kripa Chitre, Aditya Kurup, Upendra Nongthomba, Srinivasa Murty Srinivasula, Mayanglambam Suheshkumar Singh
Summary: We present a novel optical-based microscopy imaging technology called simultaneous multiple-level magnification selective plane illumination microscopy (sMx-SPIM) imaging system. This system overcomes the longstanding challenge of non-destructively obtaining images of biological samples at different field of views and spatial resolutions simultaneously in real-time. The unique feature of independently controlling the magnification powers of individual images enables simultaneous observation of sub-microscopic details and entire structure, as well as spatio-temporal dynamics of functional activities of biological specimens. Experimental results demonstrate the significant impacts of this system in both technological implication and biological applications.
Article
Chemistry, Applied
Jingshuo Gao, Xu Jia, Zhenbo Guo, Shuhan Yang, Lingyu Wei, Pingzhu Zhang, Chao Wei, Guofeng Chen, Xiaoliu Li
Summary: This study successfully designed and synthesized a novel two-photon ratiometric fluorescent probe (BCD) for imaging endogenous H2S in living cells and zebrafish, showing large emission separation, excellent selectivity, and high sensitivity.
Article
Biochemical Research Methods
Carlas S. Smith, Johan A. Slotman, Lothar Schermelleh, Nadya Chakrova, Sangeetha Hari, Yoram Vos, Cornelis W. Hagen, Marcel Mueller, Wiggert van Cappellen, Adriaan B. Houtsmuller, Jacob P. Hoogenboom, Sjoerd Stallinga
Summary: This study presents a physically realistic noise model explaining structured noise artifacts and proposes new complementary reconstruction approaches to eliminate them. By utilizing True-Wiener-filtered SIM and flat-noise SIM methods, contrast optimization and resolution maintenance are achieved while overcoming structured noise artifacts. These techniques enhance the objective representation of imaged objects without the need for adjustable parameters.
Article
Chemistry, Physical
Xin Gao, Xuemeng Li, Wei Min
Summary: Stimulated Raman scattering (SRS) is a fundamental optical process that has been known for over 60 years. While SRS microscopy has advanced biological imaging, there is still a lack of understanding of the molecular response under SRS. This study introduces a new framework to determine the molecule-intrinsic SRS cross sections and challenges the conventional belief that Raman spectroscopy is always a weak process. The findings provide a comprehensive foundation for future advancements in SRS spectroscopy and microscopy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Yanquan Mo, Fan Feng, Heng Mao, Junchao Fan, Liangyi Chen
Summary: Despite the wide application of structured illumination microscopy (SIM) in live-cell super-resolution imaging, aberrations caused by various sources remain a challenge. This study focused on investigating the impact of sample thickness on aberrations due to scattering of excitation light in SIM imaging, finding that thicker samples led to more severe aberrant interference light and degraded image reconstruction. The findings can guide future algorithm development to suppress SIM artefacts caused by scattering in thick samples.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Optics
Ali Mohebi, Aymeric Le Gratiet, Riccardo Marongiu, Fabio Callegari, Paolo Bianchini, Alberto Diaspro
Summary: The combination of CIDS microscopy with a phasor map approach provides an intuitive view of sample organization and the presence of different molecular species in the illumination volume. The phasor map method has the potential to pave the way for the analysis of large data sets.
Article
Biochemical Research Methods
Aymeric Le Gratiet, Artemi Bendandi, Colin J. R. Sheppard, Alberto Diaspro
Summary: Many significant improvements in resolution in optical microscopy techniques are achieved by reducing scattering effects. Polarimetry-based imaging allows discrimination between scattering phenomena and experimental noise, providing additional structural information of a sample. The use of coherency matrix and related decompositions leads to improved imaging contrast without requiring complicated algebraic operations or prior knowledge of the sample.
JOURNAL OF BIOPHOTONICS
(2021)
Review
Chemistry, Analytical
Salvatore Surdo, Marti Duocastella, Alberto Diaspro
Summary: This review discusses the physics and engineering strategies of photonic nanojets and their recent implementations for generating arbitrary nanopatterns. The potential impact of nanopatterning technologies based on photonic nanojets in various biomedical areas is also highlighted.
Review
Chemistry, Multidisciplinary
Aymeric Le Gratiet, Ali Mohebi, Fabio Callegari, Paolo Bianchini, Alberto Diaspro
Summary: Optical scanning microscopy techniques based on polarization control of light offer non-invasive label-free contrast by comparing polarization states and utilizing Mueller matrix. The main challenge lies in encoding and decoding polarized light pixel-by-pixel and calibrating for polarimetric artifacts. This review discusses various approaches to implement such techniques in optical scanning microscopes, requiring high-speed polarization control, and explores recent technological advancements from industrial to medical applications.
APPLIED SCIENCES-BASEL
(2021)
Article
Optics
Muhammad Waseem Ashraf, Rajeev Ranjan, Alberto Diaspro
Summary: Angle-resolved circularly polarized light scattering calculations can be used to distinguish virus particles from nonvirus particles, with the scattering signature sensitive to chiral parameters that reveal information about the particles. Different electromagnetic models and parameters, such as RNA polymer changes and packaging, can influence the scattering calculations and provide insights into the interaction of virus particles with light.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS
(2021)
Article
Optics
Colin J. R. Sheppard, Marco Castello, Giorgio Tortarolo, Eli Slenders, Takahiro Deguchi, Sami Koho, Paolo Bianchini, Giuseppe Vicidomini, Alberto Diaspro
Summary: In image scanning microscopy, a detector array is used instead of a pinhole in a confocal microscope, allowing for maximum likelihood restoration and compensation for aberrations. Illumination with a vortex doughnut beam is investigated as an example of aberration, leading to a more compact point spread function, higher resolution, and signal level compared to conventional microscopy.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION
(2021)
Article
Optics
Colin J. R. Sheppard, Artemi Bendandi, Aymeric Le Gratiet, Alberto Diaspro
Summary: This article reexamines the measures of purity for 3D partially polarized fields, focusing on the separation of circularly and linearly polarized contributions and introducing a new degree of total linear polarization. Explicit expressions for the characteristic decomposition based on coherency matrix elements are presented, including the special case of an intrinsic coherency matrix. The parameterization of the coherency matrix in terms of ellipticity, and the directions of the ellipse normal and major axis are investigated. The discussion also includes phase consistency and provides a comprehensive collection of results regarding intrinsic polarization properties.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION
(2022)
Article
Multidisciplinary Sciences
Elena Cerutti, Morgana D'Amico, Isotta Cainero, Gaetano Ivan Dellino, Mario Faretta, Giuseppe Vicidomini, Pier Giuseppe Pelicci, Paolo Bianchini, Alberto Diaspro, Luca Lanzano
Summary: Quantifying imaging performances in an unbiased way is crucial in super-resolution microscopy. An algorithm based on image correlation spectroscopy is described to assess super-resolution image quality by calculating autocorrelation function parameters related to resolution, brightness, and noise variance. Evaluating STED images shows that increasing depletion power improves resolution but may reduce contrast, while increasing line averages improves signal-to-noise ratio but may lead to photobleaching. SPLIT approaches, such as tunable STED depletion power and Leica Tau-STED, efficiently improve resolution and contrast in STED microscopy.
SCIENTIFIC REPORTS
(2021)
Article
Polymer Science
Muhammad Waseem Ashraf, Aymeric Le Gratiet, Alberto Diaspro
Summary: Understanding the structural organization of chromatin is crucial for comprehending gene functions, with changes in chromatin organization being investigated through simulated solenoid models. Scattering signals demonstrate sensitivity to changes in solenoid parameters, suggesting potential applications for label-free polarized-light approaches at the nanoscale level.
Article
Biochemistry & Molecular Biology
Silvia Scalisi, Francesca Pennacchietti, Sandeep Keshavan, Nathan D. Derr, Alberto Diaspro, Dario Pisignano, Agnieszka Pierzynska-Mach, Silvia Dante, Francesca Cella Zanacchi
Summary: Single layer graphene (SLG) is an important nanomaterial with unique optical and electrical properties, making it a potential candidate for biomedical applications, biosensors, and tissue engineering. Studies have shown high cellular affinity for graphene, but the molecular mechanisms driving/regulating cellular adhesion and migration on SLG surfaces are not well understood. Research using super-resolution microscopy and cluster analysis has provided insights into the molecular distribution of adhesion proteins on SLG and revealed substrate-dependent interactions in different cell types.
Article
Optics
Colin J. R. Sheppard, Artemi Bendandi, Aymeric Le Gratiet, Alberto Diaspro
Summary: Depolarization is an important contrast mechanism in biological and medical imaging. This paper presents a historical review on polarization algebra, measures of depolarization, and purity spaces, and discusses their connections with the eigenvalues of the coherency matrix. The advantages of a barycentric eigenvalue space are outlined, and a new parameter called diattenuation-corrected purity is introduced. The use of a combination of eigenvalues of coherency matrices to specify the depolarization condition is proposed. The relationships between optical and polarimetric radar formalisms are also reviewed.
Article
Biochemistry & Molecular Biology
Barbara Storti, Benedetta Carlotti, Grazia Chiellini, Martina Ruglioni, Tiziano Salvadori, Marco Scotto, Fausto Elisei, Alberto Diaspro, Paolo Bianchini, Ranieri Bizzarri
Summary: By combining steady-state and ultrafast spectroscopy with gated STED imaging, this study demonstrates that F99S/M153T/V163A GFP is an efficient genetic reporter for STED imaging, with no excited state absorption at depletion wavelengths <600 nm and a long emission lifetime. This makes c3GFP a valuable alternative to more common, but less photostable, EGFP and YFP/Citrine mutants for STED imaging studies targeting the green-yellow region of the optical spectrum.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Anatomy & Morphology
Silvia Scalisi, Dario Pisignano, Francesca Cella Zanacchi
Summary: In recent years, single-molecule localization techniques have been used for biological research, and super-resolution has been proposed as a quantitative tool for quantifying protein copy numbers at the nanoscale. Quantitative approaches, including stepwise photobleaching and quantitative SMLM, offer a precise tool for investigating protein complexes.
MICROSCOPY RESEARCH AND TECHNIQUE
(2023)
Article
Materials Science, Biomaterials
Federica Viti, Francesca Micaela Pramotton, Michela Martufi, Raffaella Magrassi, Nicoletta Pedemonte, Mario Nizzari, Francesca Cella Zanacchi, Benedetta De Michele, Manuela Alampi, Martina Zambito, Giuseppe Santamaria, Adriana Bajetto, Sabah Sardar, Valeria Tomati, Paolo Gandullia, Costanza Giampietro, Tullio Florio, Francesco Beltrame, Massimo Vassalli, Isabella Ceccherini
Summary: This study analyzed the morpho-mechanical phenotype of human dermal fibroblasts from patients with VSCM and found that they retained a clear signature of the disease compared to different control groups. The measurement of cellular traction forces was identified as a potential non-specific biomarker of the disease. The authors propose the development of a simple assay based on traction forces to support clinical decision-making or preclinical research.
BIOMATERIALS ADVANCES
(2023)
Article
Biochemical Research Methods
Giulia Lia Beatrice Spampinato, Emiliano Ronzitti, Valeria Zampini, Ulisse Ferrari, Francesco Trapani, Hanen Khabou, Anurag Agraval, Deniz Dalkara, Serge Picaud, Eirini Papagiakoumou, Olivier Marre, Valentina Emiliani
Summary: We developed a multi-unit microscope for all-optical inter-layers circuits interrogation, which enables simultaneous functional imaging and optogenetics, and provides precise detection of information transfer in multi-layered circuits.
CELL REPORTS METHODS
(2022)
