Iterative Restoration of the Fringe Phase (REFRASE) for QSM.
Ontology highlight
ABSTRACT:
SUBMITTER: Lindemeyer J
PROVIDER: S-EPMC8155380 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:PurposeHomodyne filtering is a standard preprocessing step in the estimation of SWI. Unfortunately, SWI is not quantitative, and QSM cannot be accurately estimated from filtered phase images. Compared with gradient-echo sequences suitable for computing QSM, SWI is more readily available and is often the only susceptibility-sensitive sequence acquired in the clinical setting. In this project, we aimed to quantify susceptibility from the homodyne-filtered phase (HFP), acquired for computing susceptibility-weighted images, using convolutional neural networks to solve the compounded problem of (1) computing the solution to the inverse dipole problem, and (2) compensating for the effects of the homodyne filtering.MethodsTwo convolutional neural networks, the U-Net and a modified QSMGAN architecture (HFP-QSMGAN), were trained to predict QSM maps at different TEs from HFP images. The QSM maps were quantified from a gradient-echo sequence acquired in the same individuals using total generalized variation (TGV)-QSM. The QSM maps estimated directly from the HFP were also included for comparison. Voxel-wise predictions and, importantly, regional predictions of susceptibility with adjustment to a reference region, were compared.ResultsOur results indicate that the U-Net model provides more accurate voxel-wise predictions of susceptibility compared with HFP-QSMGAN and HFP-QSM. However, regional estimates of susceptibility predicted by HFP-QSMGAN are more strongly correlated with the values from TGV-QSM compared with those of U-Net and HFP-QSM.ConclusionAccurate prediction of susceptibility can be achieved from filtered SWI phase using convolutional neural networks.
| S-EPMC9323427 | biostudies-literature
Project description:Quantum entanglement can help to increase the precision of optical phase measurements beyond the shot noise limit (SNL) to the ultimate Heisenberg limit. However, the N-photon parity measurements required to achieve this optimal sensitivity are extremely difficult to realize with current photon detection technologies, requiring high-fidelity resolution of N + 1 different photon distributions between the output ports. Recent experimental demonstrations of precision beyond the SNL have therefore used only one or two photon-number detection patterns instead of parity measurements. Here we investigate the achievable phase sensitivity of the simple and efficient single interference fringe detection technique. We show that the maximally-entangled "NOON" state does not achieve optimal phase sensitivity when N > 4, rather, we show that the Holland-Burnett state is optimal. We experimentally demonstrate this enhanced sensitivity using a single photon-counted fringe of the six-photon Holland-Burnett state. Specifically, our single-fringe six-photon measurement achieves a phase variance three times below the SNL.
| S-EPMC3783035 | biostudies-other
Project description:Grating-based phase-contrast computed tomography (PCCT) is a promising imaging tool on the horizon for pre-clinical and clinical applications. Until now PCCT has been plagued by strong artifacts when dense materials like bones are present. In this paper, we present a new statistical iterative reconstruction algorithm which overcomes this limitation. It makes use of the fact that an X-ray interferometer provides a conventional absorption as well as a dark-field signal in addition to the phase-contrast signal. The method is based on a statistical iterative reconstruction algorithm utilizing maximum-a-posteriori principles and integrating the statistical properties of the raw data as well as information of dense objects gained from the absorption signal. Reconstruction of a pre-clinical mouse scan illustrates that artifacts caused by bones are significantly reduced and image quality is improved when employing our approach. Especially small structures, which are usually lost because of streaks, are recovered in our results. In comparison with the current state-of-the-art algorithms our approach provides significantly improved image quality with respect to quantitative and qualitative results. In summary, we expect that our new statistical iterative reconstruction method to increase the general usability of PCCT imaging for medical diagnosis apart from applications focused solely on soft tissue visualization.
| S-EPMC4464273 | biostudies-other
Project description:Fringes are glycosyltransferases that transfer a GlcNAc to O-fucose residues on Epidermal Growth Factor-like (EGF) repeats. Three Fringes exist in mammals: LUNATIC FRINGE (LFNG), MANIC FRINGE (MFNG), and RADICAL FRINGE (RFNG). Fringe modification of O-fucose on EGF repeats in the NOTCH1 (N1) extracellular domain modulates the activation of N1 signaling. Not all O-fucose residues of N1 are modified by all Fringes; some are modified by one or two Fringes and others not modified at all. The distinct effects on N1 activity depend on which Fringe is expressed in a cell. However, little data is available on the effect that more than one Fringe has on the modification of O-fucose residues and the resulting downstream consequence on Notch activation. Using mass spectral glycoproteomic site mapping and cell-based N1 signaling assays, we compared the effect of co-expression of N1 with one or more Fringes on modification of O-fucose and activation of N1 in three cell lines. Individual expression of each Fringe with N1 in the three cell lines revealed differences in modulation of the Notch pathway dependent on the presence of endogenous Fringes. Despite these cell-based differences, co-expression of several Fringes with N1 demonstrated a dominant effect of LFNG over MFNG or RFNG. MFNG and RFNG appeared to be co-dominant but strongly dependent on the ligands used to activate N1 and on the endogenous expression of Fringes. These results show a hierarchy of Fringe activity and indicate that the effect of MFNG and/or RFNG could be small in the presence of LFNG.
| S-EPMC8512825 | biostudies-literature
Project description:Soft elastic layers with top and bottom surfaces adhered to rigid bodies are abundant in biological organisms and engineering applications. As the rigid bodies are pulled apart, the stressed layer can exhibit various modes of mechanical instabilities. In cases where the layer's thickness is much smaller than its length and width, the dominant modes that have been studied are the cavitation, interfacial and fingering instabilities. Here we report a new mode of instability which emerges if the thickness of the constrained elastic layer is comparable to or smaller than its width. In this case, the middle portion along the layer's thickness elongates nearly uniformly while the constrained fringe portions of the layer deform nonuniformly. When the applied stretch reaches a critical value, the exposed free surfaces of the fringe portions begin to undulate periodically without debonding from the rigid bodies, giving the fringe instability. We use experiments, theory and numerical simulations to quantitatively explain the fringe instability and derive scaling laws for its critical stress, critical strain and wavelength. We show that in a force controlled setting the elastic fingering instability is associated with a snap-through buckling that does not exist for the fringe instability. The discovery of the fringe instability will not only advance the understanding of mechanical instabilities in soft materials but also have implications for biological and engineered adhesives and joints.
| S-EPMC5266787 | biostudies-literature
Project description:We report a novel optical single-emitter-localization methodology that uses the phase induced by path length differences in a Mach-Zehnder interferometer to improve localization precision. Using information theory, we demonstrate that the localization capability of a modified Fourier domain signal generated by photon interference enables a more precise localization compared to a standard Gaussian intensity distribution of the corresponding point-spread function. The calculations were verified by numerical simulations and an exemplary experiment, where the centers of metal nanoparticles were localized to a precision of 3 nm.
| S-EPMC4827330 | biostudies-literature
Project description:BackgroundThis study explores the magnetostatic properties of the Alzheimer's disease brain using a recently proposed, magnetic resonance imaging, postprocessed contrast mechanism. Quantitative susceptibility mapping (QSM) has the potential to monitor in vivo iron levels by reconstructing magnetic susceptibility sources from field perturbations. However, with phase data acquired at a single head orientation, the technique relies on several theoretical approximations and requires fast-evolving regularisation strategies.MethodsIn this context, the present study describes a complete methodological framework for magnetic susceptibility measurements with a review of its theoretical foundations.Findings and significanceThe regional and whole-brain cross-sectional comparisons between Alzheimer's disease subjects and matched controls indicate that there may be significant magnetic susceptibility differences for deep brain nuclei--particularly the putamen--as well as for posterior grey and white matter regions. The methodology and findings described suggest that the QSM method is ready for larger-scale clinical studies.
| S-EPMC3836742 | biostudies-literature
Project description:Quantitative susceptibility mapping (QSM) is an MRI-based, computational method for anatomically localizing and measuring concentrations of specific biomarkers in tissue such as iron. Growing research suggests QSM is a viable method for evaluating the impact of iron overload in neurological disorders and on cognitive performance in aging. Several software toolboxes are currently available to reconstruct QSM maps from 3D GRE MR Images. However, few if any software packages currently exist that offer fully automated pipelines for QSM-based data analyses: from DICOM images to region-of-interest (ROI) based QSM values. Even less QSM-based software exist that offer quality control measures for evaluating the QSM output. Here, we address these gaps in the field by introducing and demonstrating the reliability and external validity of Ironsmith; an open-source, fully automated pipeline for creating and processing QSM maps, extracting QSM values from subcortical and cortical brain regions (89 ROIs) and evaluating the quality of QSM data using SNR measures and assessment of outlier regions on phase images. Ironsmith also features automatic filtering of QSM outlier values and precise CSF-only QSM reference masks that minimize partial volume effects. Testing of Ironsmith revealed excellent intra- and inter-rater reliability. Finally, external validity of Ironsmith was demonstrated via an anatomically selective relationship between motor performance and Ironsmith-derived QSM values in motor cortex. In sum, Ironsmith provides a freely-available, reliable, turn-key pipeline for QSM-based data analyses to support research on the impact of brain iron in aging and neurodegenerative disease.
| S-EPMC8935985 | biostudies-literature
Project description:Previous studies have identified roles of the modulation of Notch activation by Fringe homologues in boundary formation and in regulating the differentiation of vertebrate thymocytes and Drosophila glial cells. We have investigated the role of Lunatic fringe (Lfng) expression during neurogenesis in the vertebrate neural tube. We find that in the zebrafish hindbrain, Lfng is expressed by progenitors in neurogenic regions and downregulated in cells that have initiated neuronal differentiation. Lfng is required cell autonomously in neural epithelial cells to limit the amount of neurogenesis and to maintain progenitors. By contrast, Lfng is not required for the role of Notch in interneuronal fate choice, which we show is mediated by Notch1a. The expression of Lfng does not require Notch activity, but rather is regulated downstream of proneural genes that are widely expressed by neural progenitors. These findings suggest that Lfng acts in a feedback loop downstream of proneural genes, which, by promoting Notch activation, maintains the sensitivity of progenitors to lateral inhibition and thus limits further proneural upregulation.
| S-EPMC2709061 | biostudies-literature
Project description:Due to its low complexity and acceptable accuracy, phase retrieval technique has been proposed as an alternative to solve the classic optical surface measurement task. However, to capture the overall wave field, phase retrieval based optical surface measurement (PROSM) system has to moderate the CCD position during the multiple-sampling procedure. The mechanical modules of CCD movement may bring about unexpectable deviation to the final results. To overcome this drawback, we propose a new PROSM method based on spatial light modulator (SLM). The mechanical CCD movement can be replaced by an electrical moderation of SLM patterns; thus the deviation can be significantly suppressed in the new PROSM method. In addition, to further improve the performance, we propose a new iterative threshold phase retrieval algorithm with sparsity-constraint to effectively reconstruct the phase of wave field. Experimental results show that the new method provides a more simple and robust solution for the optical surface measurement than the traditional techniques and achieves higher accuracy.
| S-EPMC4000659 | biostudies-other