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Background: Developmental biology relies to a large extent on the observation and comparison of phenotypic traits through time using high resolution microscopes. In this context, transparent model organisms such as the zebrafish Danio rerio in which developing tissues and organs can be easily observed and imaged using fluorescent proteins have become very popular. One limiting factor however is the acquisition of a sufficient amount of data, in standardized and reproducible conditions, to allow robust quantitative analysis. One way to improve this is by developing mounting methods to increase the number of embryos that can be imaged simultaneously in near-to-identical orientation.
Results: Here we present an improved mounting method allowing semi-automated and high-content imaging of zebrafish embryos. It is based on a 3D-printed stamp which is used to create a 2D coordinate system of multiple μ-wells in an agarose cast. Each μ-well models a negative of the average zebrafish embryo morphology between 22 and 96 h-post-fertilization. Due to this standardized and reproducible arrangement, it is possible to define a custom well plate in the respective imaging software that allows for a semi-automated imaging process. Furthermore, the improvement in Z-orientation significantly reduces post-processing and improves comparability of volumetric data while reducing light exposure and thus photo-bleaching and photo-toxicity, and improving signal-to-noise ratio (SNR).
Conclusions: We present here a new method that allows to standardize and improve mounting and imaging of embryos. The 3D-printed stamp creates a 2D coordinate system of μ-wells in an agarose cast thus standardizing specimen mounting and allowing high-content imaging of up to 44 live or mounted zebrafish embryos simultaneously in a semi-automated, well-plate like manner on inverted confocal microscopes. In summary, image data quality and acquisition efficiency (amount of data per time) are significantly improved. The latter might also be crucial when using the services of a microscopy facility.
Background: High reproducibility of LV mass and volume measurement from cine cardiovascular magnetic resonance (CMR) has been shown within single centers. However, the extent to which contours may vary from center to center, due to different training protocols, is unknown. We aimed to quantify sources of variation between many centers, and provide a multi-center consensus ground truth dataset for benchmarking automated processing tools and facilitating training for new readers in CMR analysis.
Methods: Seven independent expert readers, representing seven experienced CMR core laboratories, analyzed fifteen cine CMR data sets in accordance with their standard operating protocols and SCMR guidelines. Consensus contours were generated for each image according to a statistical optimization scheme that maximized contour placement agreement between readers.
Results: Reader-consensus agreement was better than inter-reader agreement (end-diastolic volume 14.7 ml vs 15.2–28.4 ml; end-systolic volume 13.2 ml vs 14.0–21.5 ml; LV mass 17.5 g vs 20.2–34.5 g; ejection fraction 4.2 % vs 4.6–7.5 %). Compared with consensus contours, readers were very consistent (small variability across cases within each reader), but bias varied between readers due to differences in contouring protocols at each center. Although larger contour differences were found at the apex and base, the main effect on volume was due to small but consistent differences in the position of the contours in all regions of the LV.
Conclusions: A multi-center consensus dataset was established for the purposes of benchmarking and training. Achieving consensus on contour drawing protocol between centers before analysis, or bias correction after analysis, is required when collating multi-center results.
Orientation: The purpose of this editorial was to provide an introduction and a general overview of the special issue on Open Science Practices: A Vision for the Future of SAJIP, as hosted in the 45th edition of the South African Journal of Industrial Psychology (SAJIP). Specifically, the aim was to provide a viable, practical and implementable strategy for enhancing the scientific credibility, transparency and international stature of SAJIP.
Problematisation: The credibility and transparency of industrial and organisational psychological (IOP) research within South Africa was recently challenged by Efendic and Van Zyl (2019). The authors briefly showed inconsistencies in statistical results reported by authors of the South African Journal of Industrial Psychology (SAJIP), that various studies were insufficiently powered, that best-practice guidelines for the reporting of results were mostly only partially followed and that no transparency exists with regard to the research process. They demonstrated that authors of the SAJIP may knowingly or unknowingly be engaging in questionable research practices, which directly affects the credibility of both the discipline and the journal. Furthermore, they suggested practical guidelines for both authors and the SAJIP on how this could be managed.
Implications: Based on these suggestions, the authors invited prominent members of the IOP scientific community to provide scholarly commentary on their paper in order to aid in the development of ‘a clear strategy on how [the confidence crisis in IOP] could be managed, what the role of SAJIP is in this process and how SAJIP and its contributors could proactively engage to address these issues’. Seven members of the editorial board and two international scholars provided commentaries in an attempt to further the debate about the nature, causes, consequences and management of the credibility crisis within the South African context.
Purpose: The purpose of this final rebuttal article was to summarise and critically reflect on the commentaries of the nine articles to advance the debate on the confidence crisis within the South African IOP discipline.
Recommendations: All SAJIP’s stakeholders (authors, editors, reviewers, the publication house, universities and the journal) can play an active role in enhancing the credibility of the discipline. It is suggested that SAJIP should develop a clear and structured strategy to promote credible, transparent and ethical research practices within South Africa.