Enhancement and Restoration of Microscopic Images Corrupted with Poisson's Noise Using a Nonlinear Partial Differential Equation-based Filter

An inherent characteristic of the many imaging modalities such as fluorescence microscopy and other microscopic modalities is the presence of intrinsic Poisson noise that may lead to degradation of the captured image during its formation. A nonlinear complex diffusion-based filter adapted to Poisson noise is proposed in this paper to restore and enhance the degraded microscopic images captured by imaging devices having photon limited light detectors. The proposed filter is based on a maximum a posterior approach to the image reconstruction problem. The formulation of the filtering problem as maximisation of a posterior is useful because it allows one to incorporate the Poisson likelihood term as a data attachment which can be added to an image prior model. Here, the Gibb's image prior model-based on energy functional defined in terms of gradient norm of the image is used. The performance of the proposed scheme has been compared with other standard techniques available in literature such as Wiener filter, regularised filter, Lucy-Richardson filter and another proposed nonlinear anisotropic diffusion-based filter in terms of mean square error, peak signal-to-noise ratio, correlation parameter and mean structure similarity index map.The results shows that the proposed complex diffusion-based filter adapted to Poisson noise performs better in comparison to other filters and is better choice for reduction of intrinsic Poisson noise from the digital microscopic images and it is also well capable of preserving edges and radiometric information such as luminance and contrast of the restored image.Defence Science Journal, 2011, 61(5), pp.452-461, DOI:http://dx.doi.org/10.14429/dsj.61.118

Development of Multiscale Spectro-microscopic Imaging System and Its Applications

A novel multi-modality spectro-microscopic system that combines far-field interferometry based optical microscopy imaging techniques (differential interference contrast microscopy and cross-polarized light microscopy), total internal reflection microscopy (total internal reflection fluorescence and scattering microscopy) and confocal spectroscopy (Raman spectroscopy and photoluminescence spectroscopy) is developed. Home-built post treatment stages (thermal annealing stage and solvent annealing stage) are integrated into the system to realize in situ measurements. Departing from conventional characterization methods in materials science mostly focused on structures on one length scale, the in situ multi-modality characterization system aims to uncover the structural information from the molecular level to the mesoscale. Applications of the system on the characterization of photoactive layers of bulk heterojunction solar cell, two-dimensional materials, gold nanoparticles, fabricated gold nanoparticle arrays and cells samples are shown in this dissertation

The development of optical microscopy techniques for the advancement of single-particle studies

Single particle orientation and rotational tracking (SPORT) has recently become a powerful optical microscopy tool that can expose many molecular motions. Unfortunately, there is not yet a single microscopy technique that can decipher all particle motions in all environmental conditions, thus there are limitations to current technologies. Within, the two powerful microscopy tools of total internal reflection and interferometry are advanced to determine the position, orientation, and optical properties of metallic nanoparticles in a variety of environments. Total internal reflection is an optical phenomenon that has been applied to microscopy to produce either fluorescent or scattered light. The non-invasive far-field imaging technique is coupled with a near-field illumination scheme that allows for better axial resolution than confocal microscopy and epi-fluorescence microscopy. By controlling the incident illumination angle using total internal reflection fluorescence (TIRF) microscopy, a new type of imaging probe called non-blinking quantum dots (NBQDs) were super-localized in the axial direction to sub-10-nm precision. These particles were also used to study the rotational motion of microtubules being propelled by the motor protein kinesin across the substrate surface. The same instrument was modified to function under total internal reflection scattering (TIRS) microscopy to study metallic anisotropic nanoparticles and their dynamic interactions with synthetic lipid bilayers. Utilizing two illumination lasers with opposite polarization directions at wavelengths corresponding to the short and long axis surface plasmon resonance (SPR) of the nanoparticles, both the in-plane and out-of-plane movements of many particles could be tracked simultaneously. When combined with Gaussian point spread function (PSF) fitting for particle super-localization, the binding status and rotational movement could be resolved without degeneracy. TIRS microscopy was also used to find the 3D orientation of stationary metallic anisotropic nanoparticles utilizing only long-axis SPR enhancement. The polarization direction of the illuminating light was rotated causing the relative intensity of p-polarized and s-polarized light within the evanescent field to change. The interaction of the evanescent field with the particles is dependent on the orientation of the particle producing an intensity curve. This curve and the in-plane angle can be compared with simulations to accurately determine the 3D orientation. Differential interference contrast (DIC) microscopy is another non-invasive far-field technique based upon interferometry that does not rely on staining or other contrast enhancing techniques. In addition, high numerical aperture condensers and objectives can be used to give a very narrow depth of field allowing for the optical tomography of samples, which makes it an ideal candidate to study biological systems. DIC microscopy has also proven itself in determining the orientation of gold nanorods in both engineered environments and within cells. Many types of nanoparticles and nanostructures have been synthesized using lithographic techniques on silicon wafer substrates. Traditionally, reflective mode DIC microscopes have been developed and applied to the topographical study of reflective substrates and the imaging of chips on silicon wafers. Herein, a laser-illuminated reflected-mode DIC was developed for studying nanoparticles on reflective surfaces

Interstellar Turbulence II: Implications and Effects

Interstellar turbulence has implications for the dispersal and mixing of the elements, cloud chemistry, cosmic ray scattering, and radio wave propagation through the ionized medium. This review discusses the observations and theory of these effects. Metallicity fluctuations are summarized, and the theory of turbulent transport of passive tracers is reviewed. Modeling methods, turbulent concentration of dust grains, and the turbulent washout of radial abundance gradients are discussed. Interstellar chemistry is affected by turbulent transport of various species between environments with different physical properties and by turbulent heating in shocks, vortical dissipation regions, and local regions of enhanced ambipolar diffusion. Cosmic rays are scattered and accelerated in turbulent magnetic waves and shocks, and they generate turbulence on the scale of their gyroradii. Radio wave scintillation is an important diagnostic for small scale turbulence in the ionized medium, giving information about the power spectrum and amplitude of fluctuations. The theory of diffraction and refraction is reviewed, as are the main observations and scintillation regions.Comment: 46 pages, 2 figures, submitted to Annual Reviews of Astronomy and Astrophysic

Development and applications of single particle orientation and rotational tracking in dynamic systems

Optical microscopy has successfully been used to visualize the dynamics of living systems for decades. Numerous microscopic techniques, including single particle tracking (SPT), have been developed to measure dynamic processes in living cells with minimum disruption to the cellular functions. SPT is capable of accessing individual behaviors of imaging probe (single molecule or nanoparticle) with high spatial and temporal resolution. It has been utilized for investigating dynamic events of single molecule and nanoparticle in many different biological systems. Single particle orientation and rotational tracking (SPORT) studies not only the spatial movements as in conventional SPT but also the orientation and rotational behavior of imaging probes in order to reveal the molecular mechanisms involved in fundamental motions. A variety of experimental techniques have been reported for determining the orientation and rotational motions of optical imaging probes. Differential interference contrast (DIC) microscopy, along with the use of anisotropic plasmonic nanoparticles as optical probes, offers unique ability in SPORT study. Synthesis of novel imaging probes, innovations in optical implementation, advance in data analysis could all contribute to the development and expanding the applications of SPORT techniques in dynamic studies. Multishell Au/Ag/SiO2 core-shell hybrid nanorods with tunable optical properties were synthesized and used as new SPORT probes in DIC microscopy. These nanorods provided enhanced detection sensitivity, improved stability and additional surface modification possibility. The addition of a wedge prism and the implementation of auto-focusing algorithm formed Parallax-DIC microscopy in the 5D-SPT method. It enables the simultaneous 3D spatial tracking and orientation determination in visualization of intracellular transport of cargos in live cells. Autocorrelation function analysis and binning function in imageJ was utilized for DIC data processing. Experimental parameters, such as trajectory length of the SPT tracking and frame rate (exposure time) were investigated for the rotation of surface modified gold nanorods on synthetic lipid bilayers with assistance of computer simulations. However, much effort is still required in exploring new imaging probes, optical microscopic implementations, and data analysis methods to further extend the potential of DIC-based SPORT techniques in dynamic studies

Super-resolution and super-localization microscopy: a novel tool for imaging chemical and biological processes

Optical microscopy imaging of single molecules and single particles is an essential method for studying fundamental biological and chemical processes at the molecular and nanometer scale. The best spatial resolution (~ λ/2) achievable in traditional optical microscopy is governed by the diffraction of light. However, single molecule-based super-localization and super-resolution microscopy imaging techniques have emerged in the past decade. Individual molecules can be localized with nanometer scale accuracy and precision for studying of biological and chemical processes. The obtained spatial resolution for plant cell imaging is not yet as good as that achieved in mammalian cell imaging. Numerous technical challenges, including the generally high fluorescence background due to significant autofluorescence of endogenous components, and the presence of the cell wall (\u3e 250 nm thickness) limit the potential of super-resolution imaging in studying the cellular processes in plants. Here variable-angle epi-fluorescence microscopy (VAEM) was combined with localization based super-resolution imaging, direct stochastic optical reconstruction microscopy (dSTORM), to demonstrate imaging of cortical microtubule (CMT) network in the Arabidopsis thaliana root cells with 20 – 40 nm spatial resolution for the first time. With such high spatial resolution, the subcellular organizations of CMTs within single cells, and different cells in many regions along the root, were analyzed quantitatively. Nearly all of these technical advances in super-localization and super-resolution microscopy imaging were originally developed for biological studies. More recently, however, efforts in super-resolution chemical imaging started to gain momentum. New discoveries that were previously unattainable with conventional diffraction-limited techniques have been made, such as a) super-resolution mapping of catalytic reactions on single nanocatalysts and b) mechanistic insight into protein ion-exchange adsorptive separations. Furthermore, single molecules and single particles were localized with nanometer precision for resolving the dynamic behavior of single molecules in porous materials. This work uncovered the heterogeneous properties of the pore structures. In this dissertation, the coupling of molecular transport and catalytic reaction at the single molecule and single particle level in multilayer mesoporous nanocatalysts was elucidated. Most previous studies dealt with these two important phenomena separately. A fluorogenic oxidation reaction of non-fluorescent amplex red to highly fluorescent resorufin was tested. The diffusion behavior of single resorufin molecules in aligned nanopores was studied using total internal reflection fluorescence microscopy (TIRFM). To fully understand the working mechanisms of biological processes such as stepping of motor proteins requires resolving both the translational movement and the rotational motions of biological molecules or molecular complexes. Nanoparticle optical probes have been widely used to study biological processes such as membrane diffusion, endocytosis, and so on. The greatly enhanced absorption and scattering cross sections at the surface plasmon resonance (SPR) wavelength make nanoparticles an ideal probe for high precision tracking. Furthermore, gold nanorods (AuNRs) were used for resolving orientation changes in all three dimensions. The translational and rotational motions of AuNRs in glycerol solutions were tracked with fast imaging rate up to 500 frames per second (fps) in reflected light sheet microscopy (RLSM). The effect of imaging rates on resolving details of single AuNR motions was studied

Plasmonic Biosensors for Single-Molecule Biomedical Analysis

Review[EN] The rapid spread of epidemic diseases (i.e., coronavirus disease 2019 (COVID-19)) has contributed to focus global attention on the diagnosis of medical conditions by ultrasensitive detection methods. To overcome this challenge, increasing efforts have been driven towards the development of single-molecule analytical platforms. In this context, recent progress in plasmonic biosensing has enabled the design of novel detection strategies capable of targeting individual molecules while evaluating their binding affinity and biological interactions. This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level. Functional applications are discussed according to plasmonic sensing modes based on either nanoapertures or nanoparticle approaches. A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses). The utility of plasmonic-based single-molecule analysis for personalized medicine, considering technological limitations and future prospects, is also overviewedS