Fast image reconstruction for fluorescence microscopy

Real-time image reconstruction is essential for improving the temporal resolution of fluorescence microscopy. A number of unavoidable processes such as, optical aberration, noise and scattering degrade image quality, thereby making image reconstruction an ill-posed problem. Maximum likelihood is an attractive technique for data reconstruction especially when the problem is ill-posed. Iterative nature of the maximum likelihood technique eludes real-time imaging. Here we propose and demonstrate a compute unified device architecture (CUDA) based fast computing engine for real-time 3D fluorescence imaging. A maximum performance boost of 210x is reported. Easy availability of powerful computing engines is a boon and may accelerate to realize real-time 3D fluorescence imaging. Copyright 2012 Author(s). This article is distributed under a Creative Commons Attribution 3.0 Unported License. http://dx.doi.org/10.1063/1.4754604]

Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.

Multidimensional data reconstruction for two color fluorescence microscopy

We propose an iterative data reconstruction technique specifically designed for multi-dimensional multi-color fluorescence imaging. Markov random field is employed (for modeling the multi-color image field) in conjunction with the classical maximum likelihood method. It is noted that, ill-posed nature of the inverse problem associated with multi-color fluorescence imaging forces iterative data reconstruction. Reconstruction of three-dimensional (3D) two-color images (obtained from nanobeads and cultured cell samples) show significant reduction in the background noise (improved signal-to-noise ratio) with an impressive overall improvement in the spatial resolution (approximate to 250 nm) of the imaging system. Proposed data reconstruction technique may find immediate application in 3D in vivo and in vitro multi-color fluorescence imaging of biological specimens. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4769058]

A Huber-loss-driven clustering technique and its application to robust cell detection in confocal microscopy images

We address the problem of detecting cells in biological images. The problem is important in many automated image analysis applications. We identify the problem as one of clustering and formulate it within the framework of robust estimation using loss functions. We show how suitable loss functions may be chosen based on a priori knowledge of the noise distribution. Specifically, in the context of biological images, since the measurement noise is not Gaussian, quadratic loss functions yield suboptimal results. We show that by incorporating the Huber loss function, cells can be detected robustly and accurately. To initialize the algorithm, we also propose a seed selection approach. Simulation results show that Huber loss exhibits better performance compared with some standard loss functions. We also provide experimental results on confocal images of yeast cells. The proposed technique exhibits good detection performance even when the signal-to-noise ratio is low.

Point Spread Function Engineering for Super-Resolution Single-Photon and Multiphoton Fluorescence Microscopy

Super-resolution imaging techniques are of paramount interest for applications in bioimaging and fluorescence microscopy. Recent advances in bioimaging demand application-tailored point spread functions. Here, we present some approaches for generating application-tailored point spread functions along with fast imaging capabilities. Aperture engineering techniques provide interesting solutions for obtaining desired system point spread functions. Specially designed spatial filters—realized by optical mask—are outlined both in a single-lens and 4Pi configuration. Applications include depth imaging, multifocal imaging, and super-resolution imaging. Such an approach is suitable for fruitful integration with most existing state-of-art imaging microscopy modalities.

Electron microscopy of microstructural transformation in electrodeposited Ni-rich, Ag-Ni film

Ag-Ni films were electrodeposited over a Cu substrate. Structural characterization revealed a fibrous microstructure with an amorphous structure for the as-deposited film. Isothermal annealing at 400 degrees C of the film inside transmission electron microscope led to amorphous-to-crystalline transition along with the evolution of nano-sized particles in the microstructure. The crystalline phase was Ni-Ag solid solution. The relative volume fraction of the nano-sized particles increased gradually with time. There was however no detectable decomposition of solid solution phase till about 4 h of annealing. Beyond 4 h phase separation initiated and pure Ag and Ni phases formed in the film. This study provides a methodology by which microstructural engineering of as-electrodeposited amorphous Ag-Ni films can be conducted to isolate a particular microstructure in order to tap specific potentially usable functionalities. (C) 2013 Elsevier B.V. All rights reserved.

Transmission electron microscopy study of Ni-rich, Ag-Ni nanowires

Present work provides an electrodeposition based methodology for synthesizing Ni-rich, Ag-Ni nanowires using an alumina template. Ag-Ni system shows negligible solid solubility in the bulk. Detailed structural and compositional characterization of as-synthesized nanowires using transmission electron microscopy technique revealed a two phase microstructure. Regions along and near the nanowire axis contained crystalline Ag-Ni solid solution phase with Ag-rich composition. Whereas, regions away from the axis and near the nanowire boundary predominantly contained nanocrystalline Ni-rich, Ni-Ag solid solution phase. (C) 2013 Elsevier B. V. All rights reserved.

Determination of electric field at and near the focus of a cylindrical lens for applications in fluorescence microscopy

We present an explicit computable integral solution of the electric field generated at the focal region of a cylindrical lens. This representation is based on vectorial diffraction theory and further enables the computation of the system point spread function of a cylindrical lens. It is assumed that there is no back-scattering and the contribution from the evanescent field is negligible. Stationary phase approximation along with the Fresnel transmission coefficients are employed for evaluating the polarization dependent electric field components. Studies were carried out to determine the polarization effects and to calculate the system resolution. The effect of s -, p - and randomly polarized light is studied on the fixed sample (electric dipole is fixed in space). Proposed approach allows better understanding of electric field effects at the focus of a cylindrical aplanatic system. This opens up future developments in the field of fluorescence microscopy and optical imaging. (C) 2013 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

Taylor series expansion based multidimensional image reconstruction for confocal and 4pi microscopy

We propose and experimentally demonstrate a three-dimensional (3D) image reconstruction methodology based on Taylor series approximation (TSA) in a Bayesian image reconstruction formulation. TSA incorporates the requirement of analyticity in the image domain, and acts as a finite impulse response filter. This technique is validated on images obtained from widefield, confocal laser scanning fluorescence microscopy and two-photon excited 4pi (2PE-4pi) fluorescence microscopy. Studies on simulated 3D objects, mitochondria-tagged yeast cells (labeled with Mitotracker Orange) and mitochondrial networks (tagged with Green fluorescent protein) show a signal-to-background improvement of 40% and resolution enhancement from 360 to 240 nm. This technique can easily be extended to other imaging modalities (single plane illumination microscopy (SPIM), individual molecule localization SPIM, stimulated emission depletion microscopy and its variants).

Spatial filtering nearly eliminates the side-lobes in single- and multi-photon 4pi-type-C super-resolution fluorescence microscopy

Super-resolution microscopy has tremendously progressed our understanding of cellular biophysics and biochemistry. Specifically, 4pi fluorescence microscopy technique stands out because of its axial super-resolution capability. All types of 4pi-microscopy techniques work well in conjugation with deconvolution techniques to get rid of artifacts due to side-lobes. In this regard, we propose a technique based on spatial filter in a 4pi-type-C confocal setup to get rid of these artifacts. Using a special spatial filter, we have reduced the depth-of-focus. Interference of two similar depth-of-focus beams in a 4 pi geometry result in substantial reduction of side-lobes. Studies show a reduction of side-lobes by 46% and 76% for single and two photon variant compared to 4pi - type - C confocal system. This is incredible considering the resolving capability of the existing 4pi - type - C confocal microscopy. Moreover, the main lobe is found to be 150 nm for the proposed spatial filtering technique as compared to 690 nm of the state-of-art confocal system. Reconstruction of experimentally obtained 2PE - 4pi data of green fluorescent protein (GFP)-tagged mitocondrial network shows near elimination of artifacts arising out of side-lobes. Proposed technique may find interesting application in fluorescence microscopy, nano-lithography, and cell biology. (C) 2013 AIP Publishing LLC.

Image reconstruction enables high resolution imaging at large penetration depths in fluorescence microscopy

Imaging thick specimen at a large penetration depth is a challenge in biophysics and material science. Refractive index mismatch results in spherical aberration that is responsible for streaking artifacts, while Poissonian nature of photon emission and scattering introduces noise in the acquired three-dimensional image. To overcome these unwanted artifacts, we introduced a two-fold approach: first, point-spread function modeling with correction for spherical aberration and second, employing maximum-likelihood reconstruction technique to eliminate noise. Experimental results on fluorescent nano-beads and fluorescently coated yeast cells (encaged in Agarose gel) shows substantial minimization of artifacts. The noise is substantially suppressed, whereas the side-lobes (generated by streaking effect) drops by 48.6% as compared to raw data at a depth of 150 mu m. Proposed imaging technique can be integrated to sophisticated fluorescence imaging techniques for rendering high resolution beyond 150 mu m mark. (C) 2013 AIP Publishing LLC.

Image deconvolution research: its scope and importance in live cell microscopy

Fluorescence microscopy has become an indispensable tool in cell biology research due its exceptional specificity and ability to visualize subcellular structures with high contrast. It has highest impact when applied in 4D mode, i.e. when applied to record 3D image information as a function of time, since it allows the study of dynamic cellular processes in their native environment. The main issue in 4D fluorescence microscopy is that the phototoxic effect of fluorescence excitation gets accumulated during 4D image acquisition to the extent that normal cell functions are altered. Hence to avoid the alteration of normal cell functioning, it is required to minimize the excitation dose used for individual 2D images constituting a 4D image. Consequently, the noise level becomes very high degrading the resolution. According to the current status of technology, there is a minimum required excitation dose to ensure a resolution that is adequate for biological investigations. This minimum is sufficient to damage light-sensitive cells such as yeast if 4D imaging is performed for an extended period of time, for example, imaging for a complete cell cycle. Nevertheless, our recently developed deconvolution method resolves this conflict forming an enabling technology for visualization of dynamical processes of light-sensitive cells for durations longer than ever without perturbing normal cell functioning. The main goal of this article is to emphasize that there are still possibilities for enabling newer kinds of experiment in cell biology research involving even longer 4D imaging, by only improving deconvolution methods without any new optical technologies.

Next-generation optical microscopy

A new breed of microscopy techniques is coming to the forefront of optical imaging. They enhance the attainable 3D resolution of imaging in live and ``fixed'' cells' (with minimal structural perturbation) by greater than tenfold, bringing subcellular structures in sharp focus Along with long-term imaging, deep tissue and high throughput capablities, new insights in various fields of biology are being generated. The main set of these next-generation optical microscopy techniques along with select applications is described in this article.

Optical microscopy methods for understanding learning and memory

Structural dynamics of dendritic spines is one of the key correlative measures of synaptic plasticity for encoding short-term and long-term memory. Optical studies of structural changes in brain tissue using confocal microscopy face difficulties of scattering. This results in low signal-to-noise ratio and thus limiting the imaging depth to few tens of microns. Multiphoton microscopy (MpM) overcomes this limitation by using low-energy photons to cause localized excitation and achieve high resolution in all three dimensions. Multiple low-energy photons with longer wavelengths minimize scattering and allow access to deeper brain regions at several hundred microns. In this article, we provide a basic understanding of the physical phenomena that give MpM an edge over conventional microscopy. Further, we highlight a few of the key studies in the field of learning and memory which would not have been possible without the advent of MpM.