Spherical harmonic based noise rejection and neuronal sampling with multi-axis OPMs
Ontology highlight
ABSTRACT:
SUBMITTER:
PROVIDER: S-EPMC10509822 | biostudies-literature | 2022 Sep
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Soil moisture (SM) is a vital climate variable in the interaction process between the Earth's atmosphere and land. However, global soil moisture products from various satellite missions and land surface models are affected by inherently discontinuous observations and coarse spatial resolution, which limits their application at fine spatial scales. To address this problem, this paper integrates three diverse types of datasets from in situ, satellites, and models through Spherical cap harmonic analysis (SCHA) and Helmert variance component estimation (HVCE) to produce 1 km of spatio-temporally continuous SM products with high accuracy. First, this paper eliminates the bias between different datasets and in situ sites and resamples the datasets before data fusion. Then, multi-source SM data fusion is performed based on the SCHA and HVCE methods. Finally, this paper evaluates the fused products from three aspects, including the performance of representative sites under different climate types, the overall performance of validation sites, and the comparison with other products. The results show that the fused products have better performance than other SM products. In the representative sites, the minimal correlation coefficient (R) of the fused products is above 0.85, and the largest root mean square error (RMSE) is below 0.040 m3 m-3. For all validation sites, the R and RMSE of the fused products are 0.889 and 0.036 m3 m-3, respectively, while the R for other products is below 0.75 and the RMSE is above 0.06 m3 m-3. In comparison to other SM products, the fused products exhibit superior performance, generally align more closely with in situ measurements, and possess the ability to accurately and finely capture the spatial and temporal variability of surface SM.
| S-EPMC10575404 | biostudies-literature
Project description:Metasurfaces are subwavelength spatial variations in geometry and material where the structures are of negligible thickness compared to the wavelength of light and are optimized for far-field applications, such as controlling the wavefronts of electromagnetic waves. Here, we investigate the potential of the metasurface near-field profile, generated by an incident few-cycle pulse laser, to facilitate the generation of high-frequency light from free electrons. In particular, the metasurface near-field contains higher-order spatial harmonics that can be leveraged to generate multiple higher-harmonic X-ray frequency peaks. We show that the X-ray spectral profile can be arbitrarily shaped by controlling the metasurface geometry, the electron energy, and the incidence angle of the laser input. Using ab initio simulations, we predict bright and monoenergetic X-rays, achieving energies of 30 keV (with harmonics spaced by 3 keV) from 5-MeV electrons using 3.4-eV plasmon polaritons on a metasurface with a period of 85 nm. As an example, we present the design of a four-color X-ray source, a potential candidate for tabletop multicolor hard X-ray spectroscopy. Our developments could help pave the way for compact multi-harmonic sources of high-energy photons, which have potential applications in industry, medicine, and the fundamental sciences.
| S-EPMC6143620 | biostudies-literature
Project description:Label-free LC-MS analysis allows determining the differential expression level of proteins in multiple samples, without the use of stable isotopes. This technique is based on the direct comparison of multiple runs, obtained by continuous detection in MS mode. Only differentially expressed peptides are selected for further fragmentation, thus avoiding the bias toward abundant peptides typical of data-dependent tandem MS. The computational framework includes detection, alignment, normalization and matching of peaks across multiple sets, and several software packages are available to address these processing steps. Yet, more care should be taken to improve the quality of the LC-MS maps entering the pipeline, as this parameter severely affects the results of all downstream analyses. In this paper we show how the inclusion of a preprocessing step of background subtraction in a common laboratory pipeline can lead to an enhanced inclusion list of peptides selected for fragmentation and consequently to better protein identification.
| S-EPMC2817556 | biostudies-literature
Project description:This work reports a harmonic-rejection scheme based on the combination of Si(111) monochromator and Si(220) harmonic-rejection crystal optics. This approach is of importance to a wide range of X-ray applications in all three major branches of modern X-ray science (scattering, spectroscopy, imaging) based at major facilities, and especially relevant to the capabilities offered by the new diffraction-limited storage rings. It was demonstrated both theoretically and experimentally that, when used with a synchrotron undulator source over a broad range of X-ray energies of interest, the harmonic-rejection crystals transmit the incident harmonic X-rays on the order of 10-6. Considering the flux ratio of fundamental and harmonic X-rays in the incident beam, this scheme achieves a total flux ratio of harmonic radiation to fundamental radiation on the order of 10-10. The spatial coherence of the undulator beam is preserved in the transmitted fundamental radiation while the harmonic radiation is suppressed, making this scheme suitable not only for current third-generation synchrotron sources but also for the new diffraction-limited storage rings where coherence preservation is an even higher priority. Compared with conventional harmonic-rejection mirrors, where coherence is poorly preserved and harmonic rejection is less effective, this scheme has the added advantage of lower cost and footprint. This approach has been successfully utilized at the ultra-small-angle X-ray scattering instrument at the Advanced Photon Source for scattering, imaging and coherent X-ray photon correlation spectroscopy experiments. With minor modification, the harmonic rejection can be improved by a further five orders of magnitude, enabling even more performance capabilities.
| S-EPMC6242334 | biostudies-literature
Project description:PurposeTo propose a new method for the recovery of combined in-plane- and multi-band (MB)-accelerated diffusion MRI data.MethodsCombining MB acceleration with in-plane acceleration is crucial to improve the time efficiency of high (angular and spatial) resolution diffusion scans. However, as the MB factor and in-plane acceleration increase, the reconstruction becomes challenging due to the heavy aliasing. The new reconstruction utilizes an additional q-space prior to constrain the recovery, which is derived from the previously proposed qModeL framework. Specifically, the qModeL prior provides a pre-learned representation of the diffusion signal space to which the measured data belongs. We show that the pre-learned q-space prior along with a model-based iterative reconstruction that accommodate multi-band unaliasing, can efficiently reconstruct the in-plane- and MB-accelerated data. The power of joint reconstruction is maximally utilized by using an incoherent under-sampling pattern in the k-q domain. We tested the proposed method on single- and multi-shell data, with high/low angular resolution, high/low spatial resolution, healthy/abnormal tissues, and 3T/7T field strengths. Furthermore, the learning is extended to the spherical harmonic basis, to provide a rotational invariant learning framework.ResultsThe qModeL joint reconstruction is shown to simultaneously unalias and jointly recover DWIs with reasonable accuracy in all the cases studied. The reconstruction error from 18-fold accelerated multi-shell datasets was <3%. The microstructural maps derived from the accelerated acquisitions also exhibit reasonable accuracy for both healthy and abnormal tissues. The deep learning (DL)-enabled reconstructions are comparable to those derived using traditional methods.ConclusionqModeL enables the joint recovery of combined in-plane- and MB-accelerated dMRI utilizing DL.
| S-EPMC8855531 | biostudies-literature
Project description:Several recent multi-compartment diffusion MRI investigations and modeling strategies have utilized the orientationally-averaged, or spherical mean, diffusion-weighted signal to study tissue microstructure of the central nervous system. Most experimental designs sample a large number of diffusion weighted directions in order to calculate the spherical mean signal, however, sampling a subset of these directions may increase scanning efficiency and enable either a decrease in scan time or the ability to sample more diffusion weightings. Here, we aim to determine the minimum number of gradient directions needed for a robust measurement of the spherical mean signal. We used computer simulations to characterize the variation of the measured spherical mean signal as a function of the number of gradient directions, while also investigating the effects of diffusion weighting (b-value), signal-to-noise ratio (SNR), available hardware, and spherical mean fitting strategy. We then utilize empirically acquired data in the brain and spinal cord to validate simulations, showing experimental results are in good agreement with simulations. We summarize these results by providing an intuitive lookup table to facilitate the determination of the minimal number of sampling directions needed for robust spherical mean measurements, and give recommendations based on SNR and experimental conditions.
| S-EPMC9904413 | biostudies-literature
Project description:Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interactions deform vesicle membranes is a fundamental question in biophysics. In this article we develop a fast algorithm to compute the surface configurations of lipid vesicles by introducing surface harmonic functions to approximate the membrane surface. This parameterization allows an analytical computation of the membrane curvature energy and its gradient for the efficient minimization of the curvature energy using a nonlinear conjugate gradient method. Our approach drastically reduces the degrees of freedom for approximating the membrane surfaces compared to the previously developed finite element and finite difference methods. Vesicle deformations with a reduced volume larger than 0.65 can be well approximated by using as small as 49 surface harmonic functions. The method thus has a great potential to reduce the computational expense of tracking multiple vesicles which deform for their interaction with external fields.
| S-EPMC5552105 | biostudies-other
Project description:PurposeTo describe and implement a strategy for dynamic slice-by-slice and multiband B0 shimming using spherical harmonic shims in the human brain at 7T.TheoryFor thin axial slices, spherical harmonic shims can be divided into pairs of shims (z-degenerate and non-z-degenerate) that are spatially degenerate, such that only ½ of the shims (non-z-degenerate) are required for single slice optimizations. However, when combined, the pairs of shims can be used to simultaneously generate the same in-plane symmetries but with different amplitudes as a function of their z location. This enables multiband shimming equivalent to that achievable by single slice-by-slice optimization.MethodsAll data were acquired at 7T using a spherical harmonic shim insert enabling shimming up through 4th order with two additional 5th order shims (1st-4th+). Dynamic shim updating was achieved using a 10A shim power supply with 2 ms ramps and constrained optimizations to minimize eddy currents.ResultsIn groups of eight subjects, we demonstrated that: 1) dynamic updating using 1st-4th+ order shims reduced the SD of the B0 field over the whole brain from 32.4 ± 2.6 and 24.9 ± 2 Hz with 1st-2nd and 1st-4th+ static global shimming to 15.1 ± 1.7 Hz; 2) near equivalent performance was achieved when dynamically updating only the non-z-degenerate shims (14.3 ± 1.5 Hz), or when a using multiband shim factor of 2, MBs = 2, and all shims (14.4 ± 2.0 Hz).ConclusionHigh order spherical harmonics provide substantial improvements over static global shimming and enable dynamic multiband shimming with near equivalent performance to that of dynamic slice-by-slice shimming. This reduces distortion in echo planar imaging.
| S-EPMC8098050 | biostudies-literature
Project description:PurposeSpatial position accuracy in magnetic resonance imaging (MRI) is an important concern for a variety of applications, including radiation therapy planning, surgical planning, and longitudinal studies of morphologic changes to study neurodegenerative diseases. Spatial accuracy is strongly influenced by gradient linearity. This work presents a method for characterizing the gradient non-linearity fields on a per-system basis, and using this information to provide improved and higher-order (9th vs. 5th) spherical harmonic coefficients for better spatial accuracy in MRI.MethodsA large fiducial phantom containing 5229 water-filled spheres in a grid pattern is scanned with the MR system, and the positions all the fiducials are measured and compared to the corresponding ground truth fiducial positions as reported from a computed tomography (CT) scan of the object. Systematic errors from off-resonance (i.e., B0) effects are minimized with the use of increased receiver bandwidth (±125kHz) and two acquisitions with reversed readout gradient polarity. The spherical harmonic coefficients are estimated using an iterative process, and can be subsequently used to correct for gradient non-linearity. Test-retest stability was assessed with five repeated measurements on a single scanner, and cross-scanner variation on four different, identically-configured 3T wide-bore systems.ResultsA decrease in the root-mean-square error (RMSE) over a 50cm diameter spherical volume from 1.80mm to 0.77mm is reported here in the case of replacing the vendor's standard 5th order spherical harmonic coefficients with custom fitted 9th order coefficients, and from 1.5mm to 1mm by extending custom fitted 5th order correction to the 9th order. Minimum RMSE varied between scanners, but was stable with repeated measurements in the same scanner.ConclusionsThe results suggest that the proposed methods may be used on a per-system basis to more accurately calibrate MR gradient non-linearity coefficients when compared to vendor standard corrections.
| S-EPMC5360473 | biostudies-literature
Project description:Cancer vaccines must activate multiple immune cell types to be effective against aggressive tumours. Here we report the impact of the structural presentation of two antigenic peptides on immune responses at the transcriptomic, cellular and organismal levels. We used spherical nucleic acid (SNA) nanoparticles to investigate how the spatial distribution and placement of two antigen classes affect antigen processing, cytokine production and the induction of memory. Compared with single-antigen SNAs, a single dual-antigen SNA elicited a 30% increase in antigen-specific T cell activation and a two-fold increase in T cell proliferation. Antigen placement within dual-antigen SNAs altered the gene expression of T cells and tumour growth. Specifically, dual-antigen SNAs encapsulating antigens targeting helper T cells and with externally conjugated antigens targeting cytotoxic T cells elevated antitumour genetic pathways, stalling lymphoma tumours in mice. Additionally, when combined with the checkpoint inhibitor anti-programmed-cell-death protein-1 in a mouse model of melanoma, a specific antigen arrangement within dual-antigen SNAs suppressed tumour growth and increased the levels of circulating memory T cells. The structural design of multi-antigen vaccines substantially impacts their efficacy.
| S-EPMC10424220 | biostudies-literature