Springer protocols feed by Imaging/Radiology 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Direct Stochastic Optical Reconstruction Microscopy (dSTORM)
Single-molecule localization-based super-resolution microscopy can be performed with regular, bright, and photostable organic fluorophores. We review a concept termed direct stochastic optical reconstruction microscopy (dSTORM), which operates conventional fluorophores as photoswitches and provides an optical resolution of ~20 nm. We introduce the principle of dSTORM, illustrate experimental schemes, and discuss approaches for data analysis. (Source: Springer protocols feed by Imaging/Radiology)
Source: Springer protocols feed by Imaging/Radiology - November 13, 2014 Category: Radiology Source Type: news
Three-Dimensional Photoactivated Localization Microscopy with Genetically Expressed Probes
We describe methods for converting a 2D PALM into a system capable of acquiring such 3D images, with a particular emphasis on instrumentation that is compatible with choosing relatively dim, genetically expressed photoactivatable fluorescent proteins (PA-FPs) as PALM probes. After reviewing the basics of 2D PALM, we detail astigmatic and multiphoton imaging approaches well suited to working with PA-FPs. We also discuss the use of open-source localization software appropriate for 3D PALM. (Source: Springer protocols feed by Imaging/Radiology)
Source: Springer protocols feed by Imaging/Radiology - November 13, 2014 Category: Radiology Source Type: news
Application of STED Microscopy to Cell Biology Questions
The increasing interest in “seeing” the molecular environment in biological systems has led to the recent quest for breaking the diffraction barrier in far-field fluorescence microscopy. The first nanoscopy method successfully applied to conventional biological probes was stimulated emission depletion microscopy (STED). It is based on a physical principle that instantly delivers diffraction-unlimited images, with no need for further computational processing: the excitation laser beam is overlaid with a doughnut-shaped depleting beam that switches off previously excited fluorophores, thereby resulting in what is...
Source: Springer protocols feed by Imaging/Radiology - November 13, 2014 Category: Radiology Source Type: news
4Pi Microscopy of the Nuclear Pore Complex
4Pi microscopy is a far-field fluorescence microscopy technique, in which the wave fronts of two opposing illuminating beams are adjusted to constructively interfere in a common focus. This yields a diffraction pattern in the direction of the optical axis, which essentially consists of a main focal spot accompanied by two smaller side lobes. At optimal conditions, the main peak of this so-called point spread function has a full width at half maximum: fixed phrase of 100 nm in the direction of the optical axis, and thus is 6–7-fold smaller than that of a confocal microscope. In this chapter, we describe the basic feat...
Source: Springer protocols feed by Imaging/Radiology - November 13, 2014 Category: Radiology Source Type: news
Practical Structured Illumination Microscopy
Structured illumination microscopy (SIM) is a method that can double the spatial resolution of wide-field fluorescence microscopy in three dimensions by using spatially structured illumination light. In this chapter, we introduce the basic principles of SIM and describe in detail several different implementations based on either a diffraction grating or liquid crystal spatial light modulators. We also describe nonlinear SIM, a method that in theory can achieve unlimited resolution. In addition, we discuss a number of key points important for high-resolution imaging. (Source: Springer protocols feed by Imaging/Radiology)
Source: Springer protocols feed by Imaging/Radiology - November 13, 2014 Category: Radiology Source Type: news
Imaging of Plant Materials Using Indirect Desorption Electrospray Ionization Mass Spectrometry
Indirect desorption electrospray ionization mass spectrometry (DESI-MS) imaging is a method for imaging distributions of metabolites in plant materials, in particular leaves and petals. The challenge in direct imaging of such plant materials with DESI-MS is particularly the protective layer of cuticular wax present in leaves and petals. The cuticle protects the plant from drying out, but also makes it difficult for the DESI sprayer to reach the analytes of interest inside the plant material. A solution to this problem is to imprint the plant material onto a surface, thus releasing the analytes of interest from parts of the...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
Desorption Electrospray Ionization Imaging of Small Organics on Mineral Surfaces
Desorption electrospray ionization (DESI)-mass spectrometry facilitates the ambient chemical analysis of a variety of surfaces. Here we describe the protocol for using DESI imaging to measure the distributions of small prebiotically relevant molecules on granite surfaces. Granites that contain a variety of juxtaposed mineral species were reacted with formamide in order to study the role of local mineral environment on the production of purines and pyrimidines. The mass spectrometry imaging (MSI) methods described here can also be applied to the surface analysis of rock samples involved in other applications such as petrole...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
DESI Imaging of Small Molecules in Biological Tissues
Desorption electrospray ionization (DESI) allows the direct analysis of ordinary objects or preprocessed samples under ambient conditions. Among other applications, DESI is used to identify and to record spatial distributions of small molecules in situ, sliced or imprinted biological tissue. Manipulation of the chemistry accompanying ambient analysis ionization can be used to optimize chemical analysis, including molecular imprinting. Images are obtained by continuously moving the sample relative to the DESI sprayer and the inlet of the mass spectrometer. The acquisition time depends on the size of the surface to be analyz...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
Multiplex MALDI-MS Imaging of Plant Metabolites Using a Hybrid MS System
Plant tissues present intriguing systems for study by mass spectrometry imaging, as they exhibit a complex metabolism and a high degree of spatial localization. This chapter presents a methodology for preparation of plant tissue sections for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) analysis and the use of a hybrid mass spectrometer for “multiplex” imaging. The multiplex method described here provides a wide range of analytical information, including high-resolution, accurate mass imaging and tandem MS scans for structural information, all within a single experiment. Whil...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
MALDI Mass Spectrometry Imaging of Lipids and Primary Metabolites on Rat Brain Sections
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) enables the localization and the structural identification of a large set of molecules on a surface with 10–20 μm resolution. MALDI is often coupled to time-of-flight (TOF) tandem analyzers which remain a versatile instrument for the detection and the structural analysis of molecular ions. This technique can be used to locate either large biomolecules, such as peptides/proteins, or small endogenous or exogenous ones. Among them, lipids and primary metabolites are of high interest because they can reflect the cell state. This chapter ...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
MALDI-MS-Assisted Molecular Imaging of Metabolites in Legume Plants
Mass spectrometric imaging (MSI) is a powerful analytical tool that provides spatial information of several compounds in a single experiment. This technique has been used extensively to study proteins, peptides, and lipids, and is becoming more common for studying small molecules such as endogenous metabolites. With matrix-assisted laser desorption/ionization (MALDI)-MSI, spatial distributions of multiple metabolites can be simultaneously detected within a biological tissue section. Herein, we present a method developed specifically for imaging metabolites in legume plant roots and root nodules which can be adapted for stu...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
TOF-SIMS Imaging of Lipids on Rat Brain Sections
Since several decades, secondary ion mass spectrometry (SIMS) coupled to time of flight (TOF) is used for atomic or small inorganic/organic fragments imaging on different materials. With the advent of polyatomic ion sources leading to a significant increase of sensitivity in combination with a reasonable spatial resolution (1–10 μm), TOF-SIMS is becoming a more and more popular analytical platform for MS imaging. Even if this technique is limited to small molecules (typically below 1,000 Da), it offers enough sensitivity to detect and locate various classes of lipids directly on the surface of tissue sections. Thi...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
Sample Preparation for 3D SIMS Chemical Imaging of Cells
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is an emerging technique for the characterization of biological systems. With the development of novel ion sources such as cluster ion beams, ionization efficiency has been increased, allowing for greater amounts of information to be obtained from the sample of interest. This enables the plotting of the distribution of chemical compounds against position with submicrometer resolution, yielding a chemical map of the material. In addition, by combining imaging with molecular depth profiling, a complete 3-dimensional rendering of the object is possible. The study of si...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
Current Status and Future Prospects of Mass Spectrometry Imaging of Small Molecules
In the field of small-molecule studies, vast efforts have been put forth in order to comprehensively characterize and quantify metabolites formed from complex mechanistic pathways within biochemical and biological organisms. Many technologies and methodologies have been developed to aid understanding of the inherent complexities within biological metabolomes. Specifically, mass spectroscopy imaging (MSI) has emerged as a foundational technique in gaining insight into the molecular entities within cells, tissues, and whole-body samples. In this chapter we provide a brief overview of major technical components involved in MS...
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
Data Processing and Analysis for Mass Spectrometry Imaging
Mass spectrometry imaging produces large numbers of spectra that need to be efficiently stored, processed, and analyzed. In this chapter, we describe the protocol and methods for data processing, visualization, and statistical analysis, with related techniques and tools available presented. Examples are given with data collected for a 3D MS imaging of a mouse brain and 2D MS imaging of human bladder tissues. (Source: Springer protocols feed by Imaging/Radiology)
Source: Springer protocols feed by Imaging/Radiology - November 3, 2014 Category: Radiology Source Type: news
