Bootstrap-Optimised Regularised Image Reconstruction for Emission Tomography

Supporting data and MATLAB code for the paper: A. J. Reader and S. Ellis, "Bootstrap-Optimised Regularised Image Reconstruction for Emission Tomography," in IEEE Transactions on Medical Imaging (2020) DOI: 10.1109/TMI.2019.2956878 Instructions for use (tested on MATLAB R2017a): - unzip the file bootstrap_optimised_PET_image_reconstruction.zip Dependencies - add the utils directory to your path before running the scripts. Figures - there is a directory for each figure, not including those figures which do not contain experimental results. Each directory contains a .m script file and a .mat data file. Running the .m file produces the figure roughly as it appears in the manuscript. Independent exploration of the data can be performed if desired. Sample code - Running the example.m file will perform example 2D reconstructions with MLEM, bootstrap optimised guided quadratic MAPEM, and bootstrap optimised unweighted quadratic MAPEM. The reconstruction code is contained in the @reconClass folder. This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) [EP/M020142/1]; and the Wellcome/EPSRC Centre for Medical Engineering [WT 203148/Z/16/Z]

Efficient deformable motion correction for 3-D abdominal MRI using manifold regression

We present a novel framework for efficient retrospective respiratory motion correction of 3-D abdominal MRI using manifold regression. K-space data are continuously acquired under free breathing using the stack-of-stars radial gold-en-angle trajectory. The stack-of-profiles (SoP) from all temporal positions are embedded into a common manifold, in which SoPs that were acquired at similar respiratory states are close together. Next, the SoPs in the manifold are clustered into groups using the k-means algorithm. One 3-D volume is reconstructed at the central SoP position of each cluster (a.k.a. key-volumes). Motion fields are estimated using deformable image registration between each of these key-volumes and a reference end-exhale volume. Subsequently, the motion field at any other SoP position in the manifold is derived using manifold regression. The regressed motion fields for each of the SoPs are used to deter-mine a final motion-corrected MRI volume. The method was evaluated on realistic synthetic datasets which were generated from real MRI data and also tested on an in vivo dataset. The framework enables more accurate motion correction compared to the conventional binning-based approach, with high computational efficiency

The significance of prey avoidance behaviour for the maintenance of a predator colour polymorphism

The existence of conspicuous colour polymorphisms in animals provides an ideal opportunity to examine the mechanisms which determine genetic and phenotypic variation in populations. It is well known that directional and negative frequency-dependent selection by predators can influence the persistence of colour polymorphisms in their prey, but much less attention has been paid to the idea that prey behaviour could generate selection on predator colour morphs. In this study, we examine the role that avoidance behaviour by honeybees might play in selection on a colour-polymorphic sit-and-wait predator, the crab spider Synema globosum. In two field experiments, we offered flowers harbouring spiders of different colour morphs to foraging honeybees. In the first, we tested for a pre-existing propensity in honeybees to avoid one spider morph over another, and whether this behaviour is influenced by the flower species on which spiders hunt. In the second, we tested the ability of bees to learn to avoid spider morphs associated with a previous simulated attack. Our results suggest that honeybees do not impose strong directional selection on spider morphs in our study population, and that avoidance behaviour is not influenced by flower species. However, we find evidence that honeybees learn to avoid spiders of a colour morph that has previously been associated with a simulated attack. These findings are the first empirical evidence for a mechanism by which prey behaviour might generate negative frequency-dependent selection on predator colour morphs, and hence potentially influence the long-term persistence of genetic and phenotypic diversity in predator populations

High-resolution self-gated dynamic abdominal MRI using manifold alignment

We present a novel retrospective self-gating method based on manifold alignment (MA), which enables reconstruction of free-breathing, high spatial and temporal resolution abdominal MRI sequences. Based on a radial golden-angle (RGA) acquisition trajectory, our method enables a multi-dimensional self-gating signal to be extracted from the k-space data for more accurate motion representation. The k-space radial profiles are evenly divided into a number of overlapping groups based on their radial angles. MA is then used to simultaneously learn and align the low dimensional manifolds of all groups, and embed them into a common manifold. In the manifold, k-space profiles that represent similar respiratory positions are close to each other. Image reconstruction is performed by combining radial profiles with evenly distributed angles that are close in the manifold. Our method was evaluated on both 2D and 3D synthetic and in vivo datasets. On the synthetic datasets, our method achieved high correlation with the ground truth in terms of image intensity and virtual navigator values. Using the in vivo data, compared to a state-of-the-art approach based on centre of k-space gating, our method was able to make use of much richer profile data for self-gating, resulting in statistically significantly better quantitative measurements in terms of organ sharpness and image gradient entropy

The endothelin antagonist BQ123 reduces pulmonary vascular resistance after surgical intervention for congenital heart disease

AbstractObjective: Postoperative pulmonary hypertension in children after surgical intervention for congenital heart disease has been attributed to failure of the pulmonary endothelium to provide adequate vasodilation. Although we have shown that the impaired vasodilatory component attributable to the l-arginine-nitric oxide pathway is almost completely reversible, a nonrestorable component persists, implying an additional vasoconstrictive mechanism in postoperative pulmonary endothelial dysfunction. In this study of children after surgical intervention for congenital heart disease, we measured endothelin-1 levels and used BQ123, a selective endothelin-A receptor antagonist, together with inhaled nitric oxide to discriminate dysfunctional pulmonary endothelial vasodilation from endothelin-mediated pulmonary vasoconstriction. Methods: All children were examined early after surgical intervention in the intensive care unit. Pulmonary vascular resistance (with respiratory mass spectrometry), as well as arterial and venous endothelin-1 levels (measured by means of a quantitative enzyme-linked immunosorbent assay), were determined in 7 children (age range, 3.3-13.7 months; median age, 6.3 months) with intracardiac shunting defects at baseline and during ventilation with a fraction of inspired oxygen of 0.65, with additional BQ123 (0.1 mg/kg infused over 20 minutes), and with inhaled nitric oxide (20 ppm). Results: Pulmonary vascular resistance decreased from 7.7 ± 3.4 at baseline to 6.1 ± 2.8 Woods units · m−2 (P =.022) at a fraction of inspired oxygen of 0.65 and to 4.7 ± 2.7 Woods units · m−2 (P =.013) during BQ123 infusion. Inhaled nitric oxide had no further effect on pulmonary vascular resistance. Left atrial endothelin-1 levels (1.35-5.12 pg/mL; mean, 2.4 pg/mL) correlated significantly with the decrease in pulmonary vascular resistance in response to BQ123 infusion (r2 = 0.89, P =.003). Conclusion: Postoperative elevation of pulmonary vascular resistance in children after surgical intervention for congenital heart disease is responsive to endothelin-A blockade with BQ123. Increased levels of endothelin-1 predict the response to this therapy, which might become an important addition to the clinical armamentarium in postoperative pulmonary hypertensive disease.J Thorac Cardiovasc Surg 2002;124:435-4