The application of the grazing-incidence small-angle X-ray scattering (GISAXS) technique for the investigation of three-dimensional lattices of nanostructures is demonstrated. A successful analysis of three-dimensionally ordered nanostructures requires applying a suitable model for the description of the nanostructure ordering. Otherwise, it is possible to get a good agreement between the experimental and the simulated data, but the parameters obtained by fitting may be completely incorrect. In this paper, we theoretically examine systems having different types of nanostructure ordering, and we show how the choice of the correct model for the description of ordering influences the analysis results. Several theoretical models are compared in order to show how to use GISAXS in the investigation of self-assembled arrays of nanoparticles, and also in arrays of nanostructures obtained by ion-beam treatment of thin films or surfaces. All models are supported by experimental data, and the possibilities and limitations of GISAXS for the determination of material structure are discussed.

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Automated Programming Assessment Systems (APAS) are used for overcoming problems associated with manually managed programming assignments, such as objective and efficient assessing in large classes and providing timely and helpful feedback. In this paper we survey the literature and software in this field and identify the set of necessary features that make APAS comprehensive -such that it can support all key stages in the assessment process. Put differently, comprehensive APAS is generic enough to meet the demands of ''any'' computer science course. Despite the vast number of publications, the choice of software turns out to be very limited. We contribute by developing Edgar, a comprehensive open-source APAS which, to the best of our knowledge, exceeds any other similar free and/or open-source tool. Edgar is the result of three years of development and usage in, for the time being, eight courses dealing with various programming languages and paradigms (C, Java, SQL, etc.). Edgar supports various text-based programming languages, multi-correct multiple-choice questions, provides rich exam logging and monitoring infrastructure to prevent potential fraudulent behaviour, and subsequent data analysis and visualization of students' scores, exams, question quality, etc. It can be deployed on all major operating systems and is written in a modular fashion so that it can be adjusted and scaled to a custom fit. We comment on the architecture and present data from real-world use-cases to support these claims. Edgar is in active use today (1000+ students per semester) and it is being constantly developed with new features.

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BackgroundThe software available to date for analyzing image sequences from time-lapse microscopy works only for certain bacteria and under limited conditions. These programs, mostly MATLAB-based, fail for microbes with irregular shape, indistinct cell division sites, or that grow in closely packed microcolonies. Unfortunately, many organisms of interest have these characteristics, and analyzing their image sequences has been limited to time consuming manual processing.ResultsHere we describe BactImAS – a modular, multi-platform, open-source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time-lapse movies. BactImAS uses a semi-automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The program segments and tracks cells using a newly-developed algorithm designed for movies with difficult-to-segment cells that exhibit small frame-to-frame differences. Measurements are extracted from images in a configurable, automated fashion and an SQLite database is used to store, retrieve, and exchange all acquired data. Finally, the BactImAS can generate configurable lineage tree visualizations and export data as CSV files. We tested BactImAS on time-lapse movies of Mycobacterium smegmatis and achieved at least 10-fold reduction of processing time compared to manual analysis. We illustrate the power of the visualization tool by showing heterogeneity of both icl expression and cell growth atop of a lineage tree.ConclusionsThe presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-251) contains supplementary material, which is available to authorized users.