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Background In this paper, we introduce an image analysis approach for spatiotemporal segmentation, quantification, and visualization of movement or contraction patterns in 2D+t and 3D+t microscopy recordings of biological tissues. The development of this pipeline was motivated by the observation of contraction waves in the extra-embryonic membranes of the red flour beetle Tribolium castaneum . These contraction waves are a novel finding, whose origin and function are not yet understood. The objective of the proposed approach is to analyze the dynamics of the extra-embryonic membranes in order to provide quantitative evidence for the existence of contraction waves during late stages of embryonic development. Results We apply the pipeline to live-imaging data of Tribolium embryonic development recorded with light-sheet fluorescence microscopy. The proposed pipeline integrates particle image velocimetry (PIV) for quantitative movement analysis, surface detection, tissue cartography, and algorithmic identification of characteristic movement dynamics. We demonstrate that our approach reliably and efficiently detects contraction waves in both 2D+t and 3D+t recordings and enables automated quantitative analyses, such as measuring the area involved in contractile behavior, wave duration and frequency, spatiotemporal location of the contractile regions, and their relation to the underlying velocity distribution. Conclusions The pipeline will be employed in future work to conduct a large-scale characterization and quantification of contraction wave behavior in Tribolium development and can be readily adapted for the identification and segmentation of characteristic tissue dynamics in other biological systems.

Background The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms allow for time-resolved quantitative analyses of morphogenetic changes in three dimensions, but require efficient and automatable analysis pipelines to tackle the resulting Terabytes of image data. Particle image velocimetry (PIV) is a robust and segmentation-free technique that is suitable for quantifying collective cellular migration on data sets with different labeling schemes. This paper presents the implementation of an efficient 3D PIV package using the Julia programming language—quickPIV. Our software is focused on optimizing CPU performance and ensuring the robustness of the PIV analyses on biological data. Results QuickPIV is three times faster than the Python implementation hosted in openPIV, both in 2D and 3D. Our software is also faster than the fastest 2D PIV package in openPIV, written in C++. The accuracy evaluation of our software on synthetic data agrees with the expected accuracies described in the literature. Additionally, by applying quickPIV to three data sets of the embryogenesis of Tribolium castaneum , we obtained vector fields that recapitulate the migration movements of gastrulation, both in nuclear and actin-labeled embryos. We show normalized squared error cross-correlation to be especially accurate in detecting translations in non-segmentable biological image data. Conclusions The presented software addresses the need for a fast and open-source 3D PIV package in biological research. Currently, quickPIV offers efficient 2D and 3D PIV analyses featuring zero-normalized and normalized squared error cross-correlations, sub-pixel/voxel approximation, and multi-pass. Post-processing options include filtering and averaging of the resulting vector fields, extraction of velocity, divergence and collectiveness maps, simulation of pseudo-trajectories, and unit conversion. In addition, our software includes functions to visualize the 3D vector fields in Paraview.

In this paper, we introduce an image analysis approach for spatio-temporal segmentation, quantification and visualization of movement or contraction patterns in 2D+t or 3D+t microscopy recordings of biological tissues. The imaging pipeline is applied to time lapse images of the embryonic development of the red flour beetle Tribolium castaneum recorded with light-sheet fluorescence microscopy (LSFM). We are particularly interested in the dynamics of extra-embryonic membranes, and provide quantitative evidence of the existence of contraction waves during late stages of development. These contraction waves are a novel observation of which neither origin, nor function are yet known. The proposed pipeline relies on particle image velocimetry (PIV) for quantitative movement analysis, surface detection, tissue cartography, and an algorithmic approach to detect characteristic movement dynamics. This approach locates contraction waves in 2D+t and 3D+t reliably and efficiently and allows the automated quantitative analysis, such as the area involved in the contractile behavior, contraction wave duration and frequency, path of contractile area, or the relation to the spatio-temporal velocity distribution. The pipeline will be used in the future to conduct a large-scale characterization and quantification of contraction wave behavior in Tribolium castaneum development and can be adapted easily to the identification and segmentation of characteristic tissue dynamics in other systems of interest.

BackgroundCoronary angiography is often performed in patients with recurrent angina after successful coronary artery bypass grafting (CABG) in search of the progression of atherosclerosis. However, in many of these patients, no relevant stenosis can be detected. We speculate that coronary spasm may be associated with angina in these patients.MethodsFrom 2307 patients with unobstructed coronaries who underwent intracoronary acetylcholine spasm provocation testing (ACh-test) between 2012 and 2016, 54 consecutive patients who fulfilled the following inclusion criteria were included in this cohort study: previous left internal thoracic artery (LITA) bypass on the left anterior descending (LAD) coronary artery, ongoing/recurrent angina pectoris, no significant (< 50%) coronary artery or bypass stenosis. In all participants, the ACh-test was performed via the LITA bypass.ResultsIn 14 patients (26%) the ACh-test elicited epicardial spasm of the LAD distal to the anastomosis (≥ 90% diameter reduction with reproduction of the patient’s symptoms and ischemic ECG shifts). Microvascular spasm (reproduction of symptoms and ischemic ECG-changes but no epicardial spasm) was seen in 30 patients (55%). The ACh-test was normal in the remaining 10 patients (19%). ACh-testing did not elicit any relevant vasoconstriction in the LITA bypasses in contrast to the LAD on quantitative coronary analyses (4.89 ± 7.36% vs. 52.43 ± 36.07%, p < 0.01).ConclusionEpicardial and microvascular coronary artery spasm are frequent findings in patients with ongoing or recurrent angina after CABG but no relevant stenosis. Vasoreactivity to acetylcholine is markedly different between LITA bypasses and native LAD arteries with vasoconstriction almost exclusively occurring in the LAD.Graphic abstract

Background Preventable mortality is a good indicator of possible problems to be investigated in the primary prevention chain, making it also a useful tool with which to evaluate health policies particularly public health policies. This study describes inequalities in preventable avoidable mortality in relation to socioeconomic status in small urban areas of thirty three Spanish cities, and analyses their evolution over the course of the periods 1996–2001 and 2002–2007. Methods We analysed census tracts and all deaths occurring in the population residing in these cities from 1996 to 2007 were taken into account. The causes included in the study were lung cancer, cirrhosis, AIDS/HIV, motor vehicle traffic accidents injuries, suicide and homicide. The census tracts were classified into three groups, according their socioeconomic level. To analyse inequalities in mortality risks between the highest and lowest socioeconomic levels and over different periods, for each city and separating by sex, Poisson regression were used. Results Preventable avoidable mortality made a significant contribution to general mortality (around 7.5%, higher among men), having decreased over time in men (12.7 in 1996–2001 and 10.9 in 2002–2007), though not so clearly among women (3.3% in 1996–2001 and 2.9% in 2002–2007). It has been observed in men that the risks of death are higher in areas of greater deprivation, and that these excesses have not modified over time. The result in women is different and differences in mortality risks by socioeconomic level could not be established in many cities. Conclusions Preventable mortality decreased between the 1996–2001 and 2002–2007 periods, more markedly in men than in women. There were socioeconomic inequalities in mortality in most cities analysed, associating a higher risk of death with higher levels of deprivation. Inequalities have remained over the two periods analysed. This study makes it possible to identify those areas where excess preventable mortality was associated with more deprived zones. It is in these deprived zones where actions to reduce and monitor health inequalities should be put into place. Primary healthcare may play an important role in this process.

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