I argue that Open Science as currently conceptualised and implemented does not take sufficient account of epistemic diversity within research. I use three case studies to exemplify how Open Science threatens to privilege some forms of inquiry over others, thus exasperating divides within and across systems of practice, and overlooking important sources and forms of epistemic diversity. Building on insights from pluralist philosophy, I then identify four aspects of diverse research practices that should serve as reference points for debates around Open Science: (1) specificity to local conditions, (2) entrenchment within repertoires, (3) permeability to newcomers and (4) demarcation strategies.

NeXL is a collection of Julia language packages (libraries) for X-ray microanalysis data processing. NeXLCore provides basic atomic and X-ray physics data and models including support for microanalysis-related data types for materials and k-ratios. NeXLMatrixCorrection provides algorithms for matrix correction and iteration. NeXLSpectrum provides utilities and tools for energy-dispersive X-ray spectrum and hyperspectrum analysis including display, manipulation, and fitting. NeXL is integrated with the Julia language infrastructure. NeXL builds on the Gadfly plotting library and the DataFrames tabular data library. When combined with the DrWatson package, NeXL can provide a highly reproducible environment in which to process microanalysis data. Data availability and reproducible data analysis are two keys to scientific reproducibility. Not only should readers of journal articles have access to the data, they should also be able to reproduce the analysis steps that take the data to final results. This paper will both discuss the NeXL framework and provide examples of how it can used for reproducible data analysis.

Providing high-quality electron images and hyperspectral X-ray maps is a focus of many modern electron microscopy laboratories. Nevertheless, further image processing and annotations are often needed to prepare them for publications and reports. For multi-user facilities, accessibility to processing software can be a limitation either through license costs or availability of processing stations. Open-source software running on multiple platforms allows for post-acquisition data processing in-lab or on user-owned devices. We developed Probelab ReImager to supersede our vendor-supplied acquisition software's exportation by being efficient and highly customizable. This article describes its main features and capabilities.

Species inventories are essential to the implementation of conservation policies to mitigate biodiversity loss and maintain ecosystem services and their value to the society. This is particularly topical with respect to climate change and direct anthropogenic effects on Antarctic biodiversity, with the identification of the most at-risk taxa and geographical areas becoming a priority. Identification tools are often neglected and considered helpful only for taxonomists. However, the development of new online information technologies and computer-aided identification tools provides an opportunity to promote them to a wider audience, especially considering the emerging generation of scientists who apply an integrative approach to taxonomy. This paper aims to clarify essential concepts and provide convenient and accessible tools, tips and suggested systems to use and develop knowledge bases (KBs). The software Xper3 was selected as an example of a user-friendly KB management system to give a general overview of existing tools and functionalities through two applications: the ‘Antarctic Echinoids’ and ‘Odontasteridae Southern Ocean (Asteroids)’ KBs. We highlight the advantages provided by KBs over more classical tools, and future potential uses are highlighted, including the production of field guides to aid in the compilation of species inventories for biodiversity conservation purposes.

The Murchison Widefield Array (MWA) is an electronically steered low-frequency (<300 MHz) radio interferometer, with a ‘slew’ time less than 8 s. Low-frequency (∼100 MHz) radio telescopes are ideally suited for rapid response follow-up of transients due to their large field of view, the inverted spectrum of coherent emission, and the fact that the dispersion delay between a 1 GHz and 100 MHz pulse is on the order of 1–10 min for dispersion measures of 100–2000 pc/cm3. The MWA has previously been used to provide fast follow-up for transient events including gamma-ray bursts (GRBs), fast radio bursts (FRBs), and gravitational waves, using systems that respond to gamma-ray coordinates network packet-based notifications. We describe a system for automatically triggering MWA observations of such events, based on Virtual Observatory Event standard triggers, which is more flexible, capable, and accurate than previous systems. The system can respond to external multi-messenger triggers, which makes it well-suited to searching for prompt coherent radio emission from GRBs, the study of FRBs and gravitational waves, single pulse studies of pulsars, and rapid follow-up of high-energy superflares from flare stars. The new triggering system has the capability to trigger observations in both the regular correlator mode (limited to ≥0.5 s integrations) and using the Voltage Capture System (VCS, 0.1 ms integration) of the MWA and represents a new mode of operation for the MWA. The upgraded standard correlator triggering capability has been in use since MWA observing semester 2018B (July–Dec 2018), and the VCS and buffered mode triggers will become available for observing in a future semester.

A new era in radio astronomy will begin with the upcoming large-scale surveys planned at the Australian Square Kilometre Array Pathfinder (ASKAP). ASKAP started its Early Science programme in October 2017 and several target fields were observed during the array commissioning phase. The Scorpio field was the first observed in the Galactic Plane in Band 1 (792–1 032 MHz) using 15 commissioned antennas. The achieved sensitivity and large field of view already allow to discover new sources and survey thousands of existing ones with improved precision with respect to previous surveys. Data analysis is currently ongoing to deliver the first source catalogue. Given the increased scale of the data, source extraction and characterisation, even in this Early Science phase, have to be carried out in a mostly automated way. This process presents significant challenges due to the presence of extended objects and diffuse emission close to the Galactic Plane.

In this context, we have extended and optimised a novel source finding tool, named Caesar, to allow extraction of both compact and extended sources from radio maps. A number of developments have been done driven by the analysis of the Scorpio map and in view of the future ASKAP Galactic Plane survey. The main goals are the improvement of algorithm performances and scalability as well as of software maintainability and usability within the radio community. In this paper, we present the current status of Caesar and report a first systematic characterisation of its performance for both compact and extended sources using simulated maps. Future prospects are discussed in the light of the obtained results.

This article introduces an intuitive understanding of electron Ronchigrams and how they are affected by aberrations. This is accomplished through a portable web application, http://Ronchigram.com. The history of the Ronchigram, the physics which define it, and its visual features are reviewed in the context of aberration-corrected scanning transmission electron microscopy.

Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.

The internet has considerable potential to improve health-related food choice at low-cost. Online solutions in this field can be deployed quickly and at very low cost, especially if they are not dependent on bespoke devices or offline processes such as the provision and analysis of biological samples. One key challenge is the automated delivery of personalised dietary advice in a replicable, scalable and inexpensive way, using valid nutrition assessment methods and effective recommendations. We have developed a web-based personalised nutrition system (eNutri) which assesses dietary intake using a validated graphical FFQ and provides personalised food-based dietary advice automatically. Its effectiveness was evaluated during an online randomised controlled trial dietary intervention (EatWellUK study) in which personalised dietary advice was compared with general population recommendations (control) delivered online. The present paper presents a review of literature relevant to this work, and describes the strategies used during the development of the eNutri app. Its design and source code have been made publicly available under a permissive open source license, so that other researchers and organisations can benefit from this work. In a context where personalised diet advice has great potential for health promotion and disease prevention at-scale and yet is not currently being offered in the most popular mobile apps, the strategies and approaches described in the present paper can help to inform and advance the design and development of technologies for personalised nutrition.