TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

<p>Abstract</p> <p>Background</p> <p>Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.</p> <p>Results</p> <p>TomoJ provides a user-friendly interface for alignment, reconstruction, and combination of multiple tomographic volumes and includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique and simultaneous iterative reconstruction technique) as well as the commonly used approach of weighted back-projection.</p> <p>Conclusion</p> <p>The software presented in this work is specifically designed for electron tomography. It has been written in Java as a plug-in for ImageJ and is distributed as freeware.</p

A high-level 3D visualization API for Java and ImageJ

BACKGROUND: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. RESULTS: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. CONCLUSIONS: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de

Surface‐Reactive Patchy Nanoparticles and Nanodiscs Prepared by Tandem Nanoprecipitation and Internal Phase Separation

Nanoparticles with structural or chemical anisotropy are promising materials in domains as diverse as cellular delivery, photonic materials, or interfacial engineering. The surface chemistry may play a major role in some of these contexts. Introducing reactivity into such polymeric nanomaterials is thus of great potential, yet is still a concept in its infancy. In the current contribution, a simple nanoprecipitation technique leads to nanoparticles with diameters as low as 150 nm and well‐defined reactive surface patches of less than 30 nm in width, as well as surface‐reactive flat, disc‐like nanoparticles with corresponding dimensions, via an additional crosslinking/delamination sequence. To this aim, chemically doped block copolymers (BCPs) are employed. Control over morphology is attained by tuning preparation conditions, such as polymer concentration, solvent mixture composition, and blending with non‐functional BCP. Surface reactivity is demonstrated using a modular ligation method for the site‐selective immobilization of thiol molecules. The current approach constitutes a straightforward methodology requiring minimal engineering to produce nanoparticles with confined surface reactivity and/or shape anisotropy.Nanoparticles with surface‐expressed reactive patches and corresponding nanodiscs are prepared by a simple nanoprecipitation technique with functional block copolymers. The surface pattern formation is controlled by preparation conditions (concentration, solvent, and functionality). Spatially confined functionalization is demonstrated by grafting model thiol compounds. These nanomaterials are structurally approaching biological particles and are interesting building blocks for colloidal assemblies.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146386/1/adfm201800846_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146386/2/adfm201800846.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146386/3/adfm201800846-sup-0001-S1.pd