arXiv subjects

Emine Ulku Saritas

Publications and source records attributed to Emine Ulku Saritas.

13 recordsLinked to original sources

arXiv2025

A Model-Based Dictionary Approach for Magnetic Nanoparticle Signal Prediction

Magnetic particle imaging (MPI) is a tracer-based medical imaging modality that enables quantification and spatial mapping of magnetic nanoparticle (MNP) distribution. The magnetization response of MNPs depends on experimental conditions such as drive field (DF) settings and medium viscosity, as well as on magnetic parameters of MNPs such as magnetic core diameter, hydrodynamic diameter, and magnetic anisotropy constant. A comprehensive understanding of the magnetization response of MNPs can facilitate the optimization of DF and MNP type for a given MPI application, without the need for extensive experimentation. In this work, we propose a calibration-free iterative algorithm using model-based dictionaries for MNP signal prediction at untested settings. Dictionaries were constructed with the MNP signals simulated using the coupled Brown-Néel rotation model. Based on the available measurements, the proposed algorithm jointly estimates the dictionary weights and the transfer functions due to non-model-based dynamics. These dynamics include the system response of the measurement setup as well as magnetization dynamics not accounted for by the employed coupled Brown-Néel rotation model. The algorithm was first validated on synthetic signals at SNR levels of 1 and 10, and then tested on an in-house MPS setup across six viscosity levels (0.89-15.33 mPa.s) and DF frequencies of 0.25-2 kHz using two commercial MNPs. Validation on synthetic signals showed accurate weight and transfer function estimation even at SNR 1. MPS experiments demonstrated successful prediction of MNP signals at untested viscosities, with NRMSE below 1.51% and 3.5% for the two tested MNPs across all DF settings. Predicted signals captured viscosity dependent trends, and NWD values remained low (<0.10 and <0.07 for the two tested MNPs), confirming robust weight estimation.

eess.SP↗

arXiv2024

Vector Modulator Based Active Compensation of Direct Feedthrough in Magnetic Particle Imaging

In magnetic particle imaging (MPI), simultaneous excitation and signal acquisition leads to direct feedthrough interference. While this interference can be mitigated up to some extent with passive compensation, its time-varying nature necessitates active compensation methods to achieve the sensitivity levels needed for applications such as stem cell tracking. We have recently proposed an active compensation technique for MRI, which uses a vector modulator and a lookup-table-based algorithm for reducing the direct feedthrough in the analog domain. Here, we adapt this technique to MPI, demonstrating a successful recovery of the fundamental frequency and a significant increase in detection sensitivity.

physics.ins-det↗

arXiv2023

DEQ-MPI: A Deep Equilibrium Reconstruction with Learned Consistency for Magnetic Particle Imaging

Magnetic particle imaging (MPI) offers unparalleled contrast and resolution for tracing magnetic nanoparticles. A common imaging procedure calibrates a system matrix (SM) that is used to reconstruct data from subsequent scans. The ill-posed reconstruction problem can be solved by simultaneously enforcing data consistency based on the SM and regularizing the solution based on an image prior. Traditional hand-crafted priors cannot capture the complex attributes of MPI images, whereas recent MPI methods based on learned priors can suffer from extensive inference times or limited generalization performance. Here, we introduce a novel physics-driven method for MPI reconstruction based on a deep equilibrium model with learned data consistency (DEQ-MPI). DEQ-MPI reconstructs images by augmenting neural networks into an iterative optimization, as inspired by unrolling methods in deep learning. Yet, conventional unrolling methods are computationally restricted to few iterations resulting in non-convergent solutions, and they use hand-crafted consistency measures that can yield suboptimal capture of the data distribution. DEQ-MPI instead trains an implicit mapping to maximize the quality of a convergent solution, and it incorporates a learned consistency measure to better account for the data distribution. Demonstrations on simulated and experimental data indicate that DEQ-MPI achieves superior image quality and competitive inference time to state-of-the-art MPI reconstruction methods.

eess.IV↗

arXiv2023

FD-Net: An Unsupervised Deep Forward-Distortion Model for Susceptibility Artifact Correction in EPI

Recent learning-based correction approaches in EPI estimate a displacement field, unwarp the reversed-PE image pair with the estimated field, and average the unwarped pair to yield a corrected image. Unsupervised learning in these unwarping-based methods is commonly attained via a similarity constraint between the unwarped images in reversed-PE directions, neglecting consistency to the acquired EPI images. This work introduces an unsupervised deep-learning method for fast and effective correction of susceptibility artifacts in reversed phase-encode (PE) image pairs acquired with EPI. FD-Net predicts both the susceptibility-induced displacement field and the underlying anatomically-correct image. Unlike previous methods, FD-Net enforces the forward-distortions of the correct image in both PE directions to be consistent with the acquired reversed-PE image pair. FD-Net further leverages a multiresolution architecture to maintain high local and global performance. FD-Net performs competitively with a gold-standard reference method (TOPUP) in image quality, while enabling a leap in computational efficiency. Furthermore, FD-Net outperforms recent unwarping-based methods for unsupervised correction in terms of both image and field quality. The unsupervised FD-Net method introduces a deep forward-distortion approach to enable fast, high-fidelity correction of susceptibility artifacts in EPI by maintaining consistency to measured data. Therefore, it holds great promise for improving the anatomical accuracy of EPI imaging.

eess.IV↗

arXiv2022

TranSMS: Transformers for Super-Resolution Calibration in Magnetic Particle Imaging

Magnetic particle imaging (MPI) offers exceptional contrast for magnetic nanoparticles (MNP) at high spatio-temporal resolution. A common procedure in MPI starts with a calibration scan to measure the system matrix (SM), which is then used to set up an inverse problem to reconstruct images of the MNP distribution during subsequent scans. This calibration enables the reconstruction to sensitively account for various system imperfections. Yet time-consuming SM measurements have to be repeated under notable changes in system properties. Here, we introduce a novel deep learning approach for accelerated MPI calibration based on Transformers for SM super-resolution (TranSMS). Low-resolution SM measurements are performed using large MNP samples for improved signal-to-noise ratio efficiency, and the high-resolution SM is super-resolved via model-based deep learning. TranSMS leverages a vision transformer module to capture contextual relationships in low-resolution input images, a dense convolutional module for localizing high-resolution image features, and a data-consistency module to ensure measurement fidelity. Demonstrations on simulated and experimental data indicate that TranSMS significantly improves SM recovery and MPI reconstruction for up to 64-fold acceleration in two-dimensional imaging.

eess.IV↗

arXiv2022

Effect of colloidal weight at different planar interfaces

In many physical and biological systems, particles and microorganisms move in the proximity of an interface. Understanding the dynamics of a particle suspended close to an interface is not only important conceptually but is crucial for practical applications ranging from the treatment of waste waters to industrial applications of self-assemblies. In this work, we experimentally investigate the effects of colloidal weight on its dynamics while moving in the close proximity of a variety of liquid-solid and liquid-air interfaces. Using an upward magnetic force, we change the effective weight of a superparamagnetic colloid. At water-glass interfaces, we observe the expected decrease of the diffusion coefficients with increasing effective weight. At liquid-air interfaces, while for a pure water-air interface there is a negligible dependency between the diffusivity and the effective weight, we find that in semi-dilute polymer solution at the solution-air interface the diffusivity of the particle shows similar behavior as those at liquid-solid interfaces. We implement a Brownian dynamics simulation to support our results and show how the interplay between hydrodynamic interactions and electrostatic interface repulsion explains the experimental results.

cond-mat.soft↗

arXiv2021

Rapid TAURUS for Relaxation-Based Color Magnetic Particle Imaging

Magnetic particle imaging (MPI) is a rapidly developing medical imaging modality that exploits the non-linear response of magnetic nanoparticles (MNPs). Color MPI widens the functionality of MPI, empowering it with the capability to distinguish different MNPs and/or MNP environments. The system function approach for color MPI relies on extensive calibrations that capture the differences in the harmonic responses of the MNPs. An alternative calibration-free x-space-based method called TAURUS estimates a map of the relaxation time constant, by recovering the underlying mirror symmetry in the MPI signal. However, TAURUS requires a back and forth scanning of a given region, restricting its usage to slow trajectories with constant or piecewise constant focus fields (FFs). In this work, we propose a novel technique to increase the performance of TAURUS and enable $τ$ map estimation for rapid and multi-dimensional trajectories. The proposed technique is based on correcting the mirror symmetry distortion induced by time-varying FFs. We demonstrate via simulations and experiments in our in-house MPI scanner that the proposed method successfully estimates high-fidelity time constant maps for rapid trajectories that provide orders of magnitude reduction in scanning time while preserving the calibration-free property of TAURUS.

eess.SP↗

arXiv2021

Vicinity Effects of Field Free Point on the Relaxation Behavior of MNPs

In Magnetic Particle Imaging (MPI), the distribution of magnetic nanoparticles (MNPs) is imaged by moving a field free point (FFP) in space. All MNPs in close vicinity of the FFP contribute to the signal induced on the receive coil. The relaxation behavior of these MNPs are subject to a DC field due to the selection field (SF). In this work, we investigate the effects of the DC field on the relaxation behavior of the MNPs, with the goal of understanding the differences between the measured relaxations in Magnetic Particle Spectrometer (MPS) setups vs. MPI scanners.

eess.SP↗

arXiv2020

Simultaneous use of Individual and Joint Regularization Terms in Compressive Sensing: Joint Reconstruction of Multi-Channel Multi-Contrast MRI Acquisitions

Multi-contrast images are commonly acquired together to maximize complementary diagnostic information, albeit at the expense of longer scan times. A time-efficient strategy to acquire high-quality multi-contrast images is to accelerate individual sequences and then reconstruct undersampled data with joint regularization terms that leverage common information across contrasts. However, these terms can cause features that are unique to a subset of contrasts to leak into the other contrasts. Such leakage-of-features may appear as artificial tissues, thereby misleading diagnosis. The goal of this study is to develop a compressive sensing method for multi-channel multi-contrast magnetic resonance imaging (MRI) that optimally utilizes shared information while preventing feature leakage. Joint regularization terms group sparsity and colour total variation are used to exploit common features across images while individual sparsity and total variation are also used to prevent leakage of distinct features across contrasts. The multi-channel multi-contrast reconstruction problem is solved via a fast algorithm based on Alternating Direction Method of Multipliers. The proposed method is compared against using only individual and only joint regularization terms in reconstruction. Comparisons were performed on single-channel simulated and multi-channel in-vivo datasets in terms of reconstruction quality and neuroradiologist reader scores. The proposed method demonstrates rapid convergence and improved image quality for both simulated and in-vivo datasets. Furthermore, while reconstructions that solely use joint regularization terms are prone to leakage-of-features, the proposed method reliably avoids leakage via simultaneous use of joint and individual terms, thereby holding great promise for clinical use.

physics.med-ph↗

arXiv2020

Anisotropic dynamics of a self-assembled colloidal chain in an active bath

Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid-air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient $D$ features a non-monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of $D$ parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.

cond-mat.soft↗

arXiv2019

Partial FOV Center Imaging (PCI): A Robust X-Space Image Reconstruction for Magnetic Particle Imaging

Magnetic Particle Imaging (MPI) is an emerging medical imaging modality that images the spatial distribution of superparamagnetic iron oxide (SPIO) nanoparticles using their nonlinear response to applied magnetic fields. In standard x-space approach to MPI, the image is reconstructed by gridding the speed-compensated nanoparticle signal to the instantaneous position of the field free point (FFP). However, due to safety limits on the drive field, the field-of-view (FOV) needs to be covered by multiple relatively small partial field-of-views (pFOVs). The image of the entire FOV is then pieced together from individually processed pFOVs. These processing steps can be sensitive to non-ideal signal conditions such as harmonic interference, noise, and relaxation effects. In this work, we propose a robust x-space reconstruction technique, Partial FOV Center Imaging (PCI), with substantially simplified pFOV processing. PCI first forms a raw image of the entire FOV by mapping MPI signal directly to pFOV center locations. The corresponding MPI image is then obtained by deconvolving this raw image by a fully known, compact kernel, which solely depends on the pFOV size. We analyze the performance of the proposed reconstruction via extensive simulations, as well as imaging experiments on our in-house FFP MPI scanner. The results show that PCI offers a trade-off between noise robustness and interference robustness, outperforming standard x-space reconstruction in terms of both robustness against non-ideal signal conditions and image quality.

physics.med-ph↗

arXiv2017

Calibration-Free Relaxation-Based Multi-Color Magnetic Particle Imaging

Magnetic Particle Imaging (MPI) is a novel imaging modality with important applications such as angiography, stem cell tracking, and cancer imaging. Recently, there have been efforts to increase the functionality of MPI via multi-color imaging methods that can distinguish the responses of different nanoparticles, or nanoparticles in different environmental conditions. The proposed techniques typically rely on extensive calibrations that capture the differences in the harmonic responses of the nanoparticles. In this work, we propose a method to directly estimate the relaxation time constant of the nanoparticles from the MPI signal, which is then used to generate a multi-color relaxation map. The technique is based on the underlying mirror symmetry of the adiabatic MPI signal when the same region is scanned back and forth. We validate the proposed method via extensive simulations, and via experiments on our in-house Magnetic Particle Spectrometer (MPS) setup at 550 Hz and our in-house MPI scanner at 9.7 kHz. Our results show that nanoparticles can be successfully distinguished with the proposed technique, without any calibration or prior knowledge about the nanoparticles.

physics.med-ph↗

arXiv2017

Relaxation-based viscosity mapping for magnetic particle imaging

Magnetic Particle Imaging (MPI) has been shown to provide remarkable contrast for imaging applications such as angiography, stem cell tracking, and cancer imaging. Recently, there is growing interest in the functional imaging capabilities of MPI, where color MPI techniques have explored separating different nanoparticles, which could potentially be used to distinguish nanoparticles in different states or environments. Viscosity mapping is a promising functional imaging application for MPI, as increased viscosity levels in vivo have been associated with numerous diseases such as hypertension, atherosclerosis, and cancer. In this work, we propose a viscosity mapping technique for MPI through the estimation of the relaxation time constant of the nanoparticles. Importantly, the proposed time constant estimation scheme does not require any prior information regarding the nanoparticles. We validate this method with extensive experiments in an in-house magnetic particle spectroscopy (MPS) setup at four different frequencies (between 250 Hz and 10.8 kHz) and at three different field strengths (between 5 mT and 15 mT) for viscosities ranging between 0.89 mPa.s to 15.33 mPa.s. Our results demonstrate the viscosity mapping ability of MPI in the biologically relevant viscosity range.

physics.med-ph↗