Conference Paper

3,3’-thiodipropanol as a refractive index matching mounting medium for fluorescence microscopy

February 2020

DOI:10.1117/12.2551802

Conference: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVII

Authors:

Milvia Alata

KU Leuven

Juan Carlos Martínez Cervantes

Georgetown University

Valeria Piazza

Centro de Investigaciones en Optica

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ResearchGate has not been able to resolve any references for this publication.

KU Leuven. Ideas. People. Careers.

December 2024

At KU Leuven, we believe in the power of ideas. But we also believe that ideas are just the start. Peel back the layers of any great idea, and you’ll find that people are at its core. Every achievement, every innovation, every discovery and every breakthrough at KU Leuven starts and ends with...

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Quantitative depth-variant imaging for fluorescence microscopy using the COSMOS software package

February 2010 · Proceedings of SPIE - The International Society for Optical Engineering

The previously developed depth-variant expectation maximization (DVEM) restoration algorithm for fluorescent microscopy [1] has been implemented as part of the computational optical sectioning microscopy open source (COSMOS) software package [2]. COSMOS facilitates the development and dissemination of the DVEM algorithm which addresses depth-variant imaging due to spherical aberrations. Physical ... [Show full abstract] parameters such as the imaging lens, the size of the object and its refractive index contribute to the amount of spherical aberrations present in the image. The algorithm is based on a depth-variant imaging model and it requires a small number of point-spread functions (PSFs) defined at different depths within the sample. An acceptable choice for the number of PSFs needed for the computation provides a tradeoff between accuracy of the result and computational complexity. In this paper we show results obtained from simulation studies in which the performance of the DVEM algorithm is investigated for different parameters that contribute to depth variability. Some of the DVEM algorithm results are compared to results obtained with a space-invariant (or deconvolution) method from the same simulated data. The main conclusion from these studies is that a small number of PSFs can be used for the estimation without a significant loss in algorithm performance rendering the algorithm suitable for practical use. Furthermore, DVEM offers improvements over deconvolution methods with a small increase in computational complexity.

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With the application of surface acoustic wave (SAW) of 39.5 MHz to a model polymer liquid film,polyisobutylene, deposited on the solid substrates, the liquid film is densified, proved by the decrease of film thickness and the increase of refractive index, measured by ellipsometry. Rotational motion of fluorescent probes doped inside the liquid film, measured by polarization-resolved single ... [Show full abstract] molecule fluorescence microscopy, is retarded and the dynamical heterogeneity is reduced. It is demonstrated that the application of SAW of high frequency makes the thin polymeric liquid film densified and more dynamically homogeneous.

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Light-Sheet Microscopy for Whole-Brain Imaging

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The brain is a complex system of interconnected and interacting structures. To fully understand its architecture, we need an imaging method that is capable of imaging the entire brain at sufficient resolution to capture single cells and projections and discriminate between cells with different functions. This has been made possible by the combination of light-sheet fluorescence microscopy with ... [Show full abstract] optical tissue clearing. In this chapter, we briefly describe the currently known methods of tissue clearing, discussing the advantages and disadvantages of different approaches. Next, we explain the principles of light-sheet fluorescence microscopy focusing on its application, the whole-brain imaging. We discuss the technical challenges specific to this approach, in particular those resulting from high refractive index of cleared tissue as well as from the large size of collected data. Finally, we list some of the recent papers which make use of light-sheet imaging of cleared tissue.

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In Situ Detection of Birefringent Mesoscopic H and J Aggregates of Thiacarbocyanine Dye in Solution

March 2005 · Langmuir

Polarized-light microscopy, fluorescence microscopy, atomic force microscopy as well as absorption and fluorescence spectroscopy were used to characterize mesoscopic structures of both supramolecular H and J aggregates of 3,3'-disulfopropyl-5,5'-dichloro-9-methyl thiacarbocyanine dye in aqueous solution. Polarized-light microscopy visualizes in situ the mesoscopic morphology of the H and J ... [Show full abstract] aggregates and distinguishes between them by their own colors. The H aggregate having a fibrous structure showed negative birefringence, namely, the refractive index along the fiber short axis was higher than that of the long axis, so that pi-electron chromophores of the dye molecule are likely to orient along the short axis of the elongated fibers. The degree of birefringence of the H aggregate fiber was approximately -0.3. Investigations on the concentration dependence of the absorption spectra showed that the amount of J aggregates increased at the expense of a decrease in the amount of H aggregates. With respect to the J aggregates, a small dot morphology was observed at a relatively low dye concentration of 3.0 mM. With an increase of the dye concentration up to 10 mM, the morphology changed into mesoscopic fibers. In contrast, fluorescence microscopy for the fibrous J aggregates reveals that the constituent molecules are approximately aligned along the long axis of the fibers.

Calibration Routine for Quantitative Three-Dimensional Flow Field Measurements in Drying Polymer Sol...

March 2019 · Colloids and Interfaces

Surface-tension induced flows may have a significant impact on the surface topography of thin films or small printed structures derived from polymer solution processing. Despite a century of research on Marangoni convection, the community lacks quantitative experimental flow field data, especially from within drying solutions. We utilize multifocal micro particle tracking velocimetry (µPTV) to ... [Show full abstract] obtain these data and show a calibration routine based on point spread function (PSF) simulations as well as experimental data. The results account for a varying sample refractive index, beneficial cover-glass correction collar settings as well as a multifocal lens system. Finally, the calibration procedure is utilized exemplarily to reconstruct a three-dimensional, transient flow field within a poly(vinyl acetate)-methanol solution dried with inhomogeneous boundary conditions.

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Effects of index-mismatch-induced spherical aberration on two-photon imaging in skin and tissue-like...

July 2003 · Proceedings of SPIE - The International Society for Optical Engineering

Index mismatch induced spherical aberration is studied by comparing imaging ability of different immersion objectives in both uniformly fluorescent solutions and fluorescently labeled skin samples using scanning two-photon fluorescence microscopy. We investigated the performances of the objectives (air, water, glycerin, and oil immersion) by measuring the fluorescence profiles at different ... [Show full abstract] depths. In homogeneous fluorescent samples, we found that immersion medium with compatible refractive index as the samples yields better results, and small differences in refractive indices did not cause noticeable effects. Similar results were found in skin samples. Except for the air objective, we found that the choice of immersion medium did not have significant effects for in-depth imaging in the fluorescent solutions or skin samples.

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Technical Report

The X-CLARITY™ Mounting Solution: an Improved RI Matching Solution for Tissues Cleared by the X-CLAR...

January 2015

Yong Weon Yi

The X-CLARITY Tissue Clearing System is the world’s first instrument of cutting edge technology that enables to transform biological tissue into a transparent state to light. The X-CLARITY Tissue Clearing System electrophoretically remove lipids, the main component of light scattering in biological tissues, from the tissue-hydrogel hybrid. The cleared tissue is labeled with appropriate probes ... [Show full abstract] such as fluorescent-labeled antibodies. Finally, the labeled tissue is infused and mounted in a refractive index (RI) matching medium to enhance optical clarity for 3D imaging. Here we described the newly developed RI matching medium, the X-CLARITY Mounting Solution, as an excellent optical clearing agent to provide an environment for 3D imaging with fluorescence microscopy and for prolonged preservation of fluorescence signals in the labeled tissue.

3,3’-thiodipropanol as a refractive index matching mounting medium for fluorescence microscopy

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