arXiv subjects

Tobias Knopp

Publications and source records attributed to Tobias Knopp.

At least 37 records · Page 2Linked to original sources

arXiv2024

Characterization of the Clinically Approved MRI Tracer Resotran for Magnetic Particle Imaging in a Comparison Study

Objective. The availability of magnetic nanoparticles with medical approval for human intervention is fundamental to the clinical translation of magnetic particle imaging (MPI). In this work, we thoroughly evaluate and compare the magnetic properties of an magnetic resonance imaging (MRI) approved tracer to validate its performance for MPI in future human trials. Approach. We analyze whether the recently approved MRI tracer Resotran is suitable for MPI. In addition, we compare Resotran with the previously approved and extensively studied tracer Resovist, with Ferrotran, which is currently in a clinical phase III study, and with the tailored MPI tracer Perimag. Main results. Initial magnetic particle spectroscopy measurements indicate that Resotran exhibits performance characteristics akin to Resovist, but below Perimag. We provide data on four different tracers using dynamic light scattering, transmission electron microscopy, vibrating sample magnetometry measurements, magnetic particle spectroscopy to derive hysteresis, point spread functions, and a serial dilution, as well as system matrix based MPI measurements on a preclinical scanner (Bruker 25/20 FF), including reconstructed images. Significance. Numerous approved magnetic nanoparticles used as tracers in MRI lack the necessary magnetic properties essential for robust signal generation in MPI. The process of obtaining medical approval for dedicated MPI tracers optimized for signal performance is an arduous and costly endeavor, often only justifiable for companies with a well-defined clinical business case. Resotran is an approved tracer that has become available in Europe for MRI. In this work, we study the eligibility of Resotran for MPI in an effort to pave the way for human MPI trials.

physics.med-ph↗

arXiv2023

System Characterization of a Human-Sized 3D Real-Time Magnetic Particle Imaging Scanner for Cerebral Applications

Since the initial patent in 2001, the Magnetic Particle Imaging (MPI) community has been striving to develop an MPI scanner suitable for human applications. Numerous contributions from different research fields, regarding tracer development, reconstruction methods, hardware engineering, and sequence design have been employed in pursuit of this objective. In this work, we introduce and thoroughly characterize an improved head-sized MPI scanner with an emphasis on human safety. The scanner is operated by open-source software that enables scanning, monitoring, analysis, and reconstruction, designed to be handled by end users. Our primary focus is to present all technical components of the scanner, with the ultimate objective to investigate brain perfusion imaging in phantom experiments. We have successfully achieved full 3D single- and multi-contrast imaging capabilities at a frame rate of 4 Hz with sufficient sensitivity and resolution for brain applications. To assess system characterization, we devised sensitivity, resolution, perfusion, and multi-contrast experiments, as well as field measurements and sequence analysis. The acquired images were captured using a clinically approved tracer and suitable magnetic field strengths, while adhering to the established human peripheral nerve stimulation thresholds. This advanced scanner holds potential as a tomographic imager for diagnosing conditions such as ischemic stroke or intracranial hemorrhage in environments lacking electromagnetic shielding. Furthermore, due to its low power consumption it may have the potential to facilitate long-term monitoring within intensive care units for various applications.

physics.med-ph↗

arXiv2023

Saline bolus for negative contrast perfusion imaging in magnetic particle imaging

Objective. Magnetic Particle Imaging (MPI) is capable of high temporal resolution measurements of the spatial distribution of magnetic nanoparticles and therefore well suited for perfusion imaging, which is an important tool in medical diagnosis. Perfusion imaging in MPI usually requires a fresh bolus of tracer material to capture the key signal dynamics. Here, we propose a method to decouple the imaging sequence from the injection of additional tracer material, without further increasing the administered iron dose in the body with each image. Approach. A bolus of physiological saline solution without any particles (negative contrast) diminishes the steady-state concentration of a long-circulating tracer during passage. This depression in the measured concentration contributes to the required contrast dynamics. The presence of a long-circulating tracer is therefore a prerequisite to obtain the negative contrast. As a quantitative tracer based imaging method, the signal is linear in the tracer concentration for any location that contains nanoparticles and zero in the surrounding tissue which does not provide any intrinsic signal. After tracer injection, the concentration over time (positive contrast) can be utilized to calculate dynamic diagnostic parameters like perfusion parameters in vessels and organs. Every acquired perfusion image thus requires a new bolus of tracer with a sufficiently large iron dose to be visible above the background. Main results. Perfusion parameters are calculated based on the time response of the proposed negative bolus and compared to a positive bolus. Results from phantom experiments show that normalized signals from positive and negative boli are concurrent and deviations of calculated perfusion maps are low. Significance. Our method opens up the possibility to increase the total monitoring time, while minimizing the iron dose per acquired image.

physics.med-ph↗

arXiv2023

Dynamic image reconstruction with motion priors in application to 3D magnetic particle imaging

Various imaging modalities allow for time-dependent image reconstructions from measurements where its acquisition also has a time-dependent nature. Magnetic particle imaging (MPI) falls into this class of imaging modalities and it thus also provides a dynamic inverse problem. Without proper consideration of the dynamic behavior, motion artifacts in the reconstruction become an issue. More sophisticated methods need to be developed and applied to the reconstruction of the time-dependent sequences of images. In this context, we investigate the incorporation of motion priors in terms of certain flow-parameter-dependent PDEs in the reconstruction process of time-dependent 3D images in magnetic particle imaging. The present work comprises the method development for a general 3D+time setting for time-dependent linear forward operators, analytical investigation of necessary properties in the MPI forward operator, modeling aspects in dynamic MPI, and extensive numerical experiments on 3D+time imaging including simulated data as well as measurements from a rotation phantom and in-vivo data from a mouse.

math.NA↗

arXiv2023

Morphological Classification of Radio Galaxies with wGAN-supported Augmentation

Machine learning techniques that perform morphological classification of astronomical sources often suffer from a scarcity of labelled training data. Here, we focus on the case of supervised deep learning models for the morphological classification of radio galaxies, which is particularly topical for the forthcoming large radio surveys. We demonstrate the use of generative models, specifically Wasserstein GANs (wGANs), to generate data for different classes of radio galaxies. Further, we study the impact of augmenting the training data with images from our wGAN on three different classification architectures. We find that this technique makes it possible to improve models for the morphological classification of radio galaxies. A simple Fully Connected Neural Network (FCN) benefits most from including generated images into the training set, with a considerable improvement of its classification accuracy. In addition, we find it is more difficult to improve complex classifiers. The classification performance of a Convolutional Neural Network (CNN) can be improved slightly. However, this is not the case for a Vision Transformer (ViT).

astro-ph.IM↗

arXiv2023

Unique Compact Representation of Magnetic Fields using Truncated Solid Harmonic Expansions

Precise knowledge of magnetic fields is crucial in many medical imaging applications like magnetic resonance imaging or magnetic particle imaging (MPI) as they are the foundation of these imaging systems. For the investigation of the influence of field imperfections on imaging, a compact and unique representation of the magnetic fields using real solid spherical harmonics, which can be obtained by measuring a few points of the magnetic field only, is of great assistance. In this manuscript, we review real solid harmonic expansions as a general solution of Laplace's equation including an efficient calculation of their coefficients using spherical t-designs. We also provide a method to shift the reference point of an expansion by calculating the coefficients of the shifted expansion from the initial ones. These methods are used to obtain the magnetic fields of an MPI system. Here, the field-free-point of the spatial encoding field serves as unique expansion point. Lastly, we quantify the severity of the distortions of the static and dynamic fields in MPI by analyzing the expansion coefficients.

physics.med-ph↗

arXiv2023

NFFT.jl: Generic and Fast Julia Implementation of the Nonequidistant Fast Fourier Transform

The non-equidistant fast Fourier transform (NFFT) is an extension of the famous fast Fourier transform (FFT), which can be applied to non-equidistantly sampled data in time/space or frequency domain. It is an approximative algorithm that allows to control the approximation error in such a way that machine precision is reached while keeping the algorithmic complexity in the same order as a regular FFT. The NFFT plays a major role in many signal processing applications and has been intensively studied from a theoretical and computational perspective. The fastest CPU implementations of the NFFT are implemented in the low-level programming languages C and C++ and require a compromise between code generalizability, code readability, and code efficiency. The programming language Julia promises new opportunities in optimizing these three conflicting goals. In this work we show that Julia indeed allows to develop an NFFT implementation, which is completely generic, dimension-agnostic and requires about 2-3 times less code than other famous libraries while still being one of the fastest NFFT implementations developed to date.

cs.MS↗

arXiv2022

Design of a Head Coil for High Resolution Mouse Brain Perfusion Imaging using Magnetic Particle Imaging

Magnetic Particle Imaging (MPI) is a novel and versatile imaging modality developing towards human application. When up-scaling to human size, the sensitivity of the systems naturally drops as the coil sensitivity depends on the bore diameter. Thus, new methods to push the sensitivity limit further have to be investigated to cope for this loss. In this paper a dedicated surface coil for mice is developed, improving the sensitivity in cerebral imaging applications. Similar to MRI the developed surface coil improves the sensitivity due to the closer vicinity to the region of interest. With the developed surface coil presented in this work, it is possible to image tracer samples containing only 896 pg Fe and detect even small vessels and anatomical structures within a wild type mouse model. As current sensitivity measures require a tracer system a new method for determining a sensitivity measure without this requirement is presented and verified to enable comparison between MPI receiver systems.

physics.med-ph↗

arXiv2022

Simultaneous Imaging of Widely Differing Particle Concentrations in MPI: Problem Statement and Algorithmic Proposal for Improvement

Magnetic Particle Imaging (MPI) is a tomographic imaging technique for determining the spatial distribution of superparamagnetic nanoparticles. Current MPI systems are capable of imaging iron masses over a wide dynamic range of more than four orders of magnitude. In theory, this range could be further increased using adaptive amplifiers, which prevent signal clipping. While this applies to a single sample, the dynamic range is severely limited if several samples with different concentrations or strongly inhomogeneous particle distributions are considered. One scenario that occurs quite frequently in pre-clinical applications is that a highly concentrated tracer bolus in the vascular system "shadows" nearby organs with lower effective tracer concentrations. The root cause of the problem is the ill-posedness of the MPI imaging operator, which requires regularization for stable reconstruction. In this work, we introduce a simple two-step algorithm that increases the dynamic range by a factor of four. Furthermore, the algorithm enables spatially adaptive regularization, i.e. highly concentrated signals can be reconstructed with maximum spatial resolution, while low concentrated signals are strongly regularized to prevent noise amplification.

physics.med-ph↗

arXiv2022

Generalized MPI Multi-Patch Reconstruction using Clusters of similar System Matrices

The tomographic imaging method magnetic particle imaging (MPI) requires a multi-patch approach for capturing large field of views. This approach consists of a continuous or stepwise spatial shift of a small sub-volume of only few cubic centimeters size, which is scanned using one or multiple excitation fields in the kHz range. Under the assumption of ideal magnetic fields, the MPI system matrix is shift invariant and in turn a single matrix suffices for image reconstruction significantly reducing the calibration time and reconstruction effort. For large field imperfections, however, the method can lead to severe image artifacts. In the present work we generalize the efficient multi-patch reconstruction to work under non-ideal field conditions, where shift invariance holds only approximately for small shifts of the sub-volume. Patches are clustered based on a magnetic-field-based metric such that in each cluster the shift invariance holds in good approximation. The total number of clusters is the main parameter of our method and allows to trade off calibration time and image artifacts. The magnetic-field-based metric allows to perform the clustering without prior knowledge of the system matrices. The developed reconstruction algorithm is evaluated on a multi-patch measurement sequence with 15 patches, where efficient multi-patch reconstruction with a single calibration measurement leads to strong image artifacts. Analysis reveals that calibration measurements can be decreased from 15 to 11 with no visible image artifacts. A further reduction to 9 is possible with only slight degradation in image quality.

physics.med-ph↗

arXiv2022

Suppression of Motion Artifacts Caused by Temporally Recurring Tracer Distributions in Multi-Patch Magnetic Particle Imaging

Magnetic particle imaging is a tracer based imaging technique to determine the spatial distribution of superparamagnetic iron oxide nanoparticles with a high spatial and temporal resolution. Due to physiological constraints, the imaging volume is restricted in size and larger volumes are covered by shifting object and imaging volume relative to each other. This results in reduced temporal resolution, which can lead to motion artifacts when imaging dynamic tracer distributions. A common source of such dynamic distributions are cardiac and respiratory motion in in-vivo experiments, which are in good approximation periodic. We present a raw data processing technique that combines data snippets into virtual frames corresponding to a specific state of the dynamic motion. The technique is evaluated on the basis of measurement data obtained from a rotational phantom at two different rotational frequencies. These frequencies are determined from the raw data without reconstruction and without an additional navigator signal. The reconstructed images give reasonable representations of the rotational phantom frozen in several different states of motion while motion artifacts are suppressed.

physics.med-ph↗

arXiv2022

System Matrix based Reconstruction for Pulsed Sequences in Magnetic Particle Imaging

Improving resolution and sensitivity will widen possible medical applications of magnetic particle imaging. Pulsed excitation promises such benefits, at the cost of more complex hardware solutions and restrictions on drive field amplitude and frequency. State-of-the-art systems utilize a sinusoidal excitation to drive superparamagnetic nanoparticles into the non-linear part of their magnetization curve, which creates a spectrum with a clear separation of direct feed-through and higher harmonics caused by the particles response. One challenge for rectangular excitation is the discrimination of particle and excitation signals, both broad-band. Another is the drive-field sequence itself, as particles that are not placed at the same spatial position, may react simultaneously and are not separable by their signal phase or shape. To overcome this potential loss of information in spatial encoding for high amplitudes, a superposition of shifting fields and drive-field rotations is proposed in this work. Upon close view, a system matrix approach is capable to maintain resolution, independent of the sequence, if the response to pulsed sequences still encodes information within the phase. Data from an Arbitrary Waveform Magnetic Particle Spectrometer with offsets in two spatial dimensions is measured and calibrated to guarantee device independence. Multiple sequence types and waveforms are compared, based on frequency space image reconstruction from emulated signals, that are derived from measured particle responses. A resolution of 1.0 mT (0.8 mm for a gradient of (-1.25,\,-1.25,\,2.5) T/m) in x- and y-direction was achieved and a superior sensitivity for pulsed sequences was detected on the basis of reference phantoms.

physics.med-ph↗

arXiv2021

Efficient Joint Estimation of Tracer Distribution and Background Signals in Magnetic Particle Imaging using a Dictionary Approach

Background signals are a primary source of artifacts in magnetic particle imaging and limit the sensitivity of the method since background signals are often not precisely known and vary over time. The state-of-the art method for handling background signals uses one or several background calibration measurements with an empty scanner bore and subtracts a linear combination of these background measurements from the actual particle measurement. This approach yields satisfying results in case that the background measurements are taken in close proximity to the particle measurement and when the background signal drifts linearly. In this work, we propose a joint estimation of particle distribution and background signal based on a dictionary that is capable of representing typical background signals and allows for precise estimation of the background even when the latter is drifting non-linearly over time. Using a singular-value decomposition, the dictionary is derived from a large number of background calibration scans that do not need to be recorded in close proximity to the particle measurement. The dictionary is sufficiently expressive and represented by its principle components. The proposed joint estimation of particle distribution and background signal is expressed as a linear Tikhonov-regularized least squares problem, which can be efficiently solved. In phantom experiments it is shown that the method strongly suppresses background artifacts and even allows to estimate and remove the direct feed-through of the excitation field.

eess.IV↗

arXiv2021

Modeling the Magnetization Dynamics for Large Ensembles of Immobilized Magnetic Nanoparticles in Multi-dimensional Magnetic Particle Imaging

Magnetic nanoparticles (MNPs) play an important role in biomedical applications including imaging modalities such as MRI and magnetic particle imaging (MPI). The latter one exploits the non-linear magnetization response of a large ensemble of magnetic nanoparticles to magnetic fields which allows determining the spatial distribution of the MNP concentration from measured voltage signals. Currently, modeling the voltage signals of large ensembles of MNPs in an MPI environment is not yet accurately possible, especially for liquid tracers in multi-dimensional magnetic excitation fields. Thus, the voltage-to-image mapping is still obtained in a time consuming calibration procedure. While the ferrofluidic case can be seen as the typical setting, more recently immobilized and potentially oriented MNPs have received considerable attention. By aligning the particles during immobilization, one can encode the angle of the easy axis into the magnetization response providing a sophisticated benchmark system for model-based approaches. In this work, we address the modeling problem for immobilized, oriented MNPs in the context of MPI. We investigate a model-based approach where the magnetization response is simulated by a Néel rotation model for the particle's magnetic moments and the ensemble magnetization is obtained by solving a Fokker-Planck equation approach. Since the parameters of the model are a-priori unknown, we investigate different methods for performing a parameter identification and discuss two models: One where a single function vector is used from the space spanned by the model parameters and another where a superposition of function vectors is considered. We show that our model can much more accurately reproduce the orientation dependent signal response when compared to the equilibrium model, which marks the current state-of-the-art for model-based system matrix simulations in MPI.

cond-mat.mes-hall↗

arXiv2021

MRIReco.jl: An MRI Reconstruction Framework written in Julia

Purpose: The aim of this work is to develop a high-performance, flexible and easy-to-use MRI reconstruction framework using the scientific programming language Julia. Methods: Julia is a modern, general purpose programming language with strong features in the area of signal / image processing and numerical computing. It has a high-level syntax but still generates efficient machine code that is usually as fast as comparable C/C++ applications. In addition to the language features itself, Julia has a sophisticated package management system that makes proper modularization of functionality across different packages feasible. Our developed MRI reconstruction framework MRIReco.jl can therefore reuse existing functionality from other Julia packages and concentrate on the MRI-related parts. This includes common imaging operators and support for MRI raw data formats. Results: MRIReco.jl is a simple to use framework with a high degree of accessibility. While providing a simple-to-use interface, many of its components can easily be extended and customized. The performance of MRIReco.jl is compared to the Berkeley Advanced Reconstruction Toolbox (BART) and we show that the Julia framework achieves comparable reconstruction speed as the popular C/C++ library. Conclusion: Modern programming languages can bridge the gap between high performance and accessible implementations. MRIReco.jl leverages this fact and contributes a promising environment for future algorithmic development in MRI reconstruction.

physics.med-ph↗

arXiv2020

A simulation framework for particle magnetization dynamics of large ensembles of single domain particles: Numerical treatment of Brown/Néel dynamics and parameter identification problems in magnetic particle imaging

Magnetic nanoparticles and their magnetization dynamics play an important role in many applications. We focus on magnetization dynamics in large ensembles of single domain nanoparticles being characterized by either Brownian or Néel rotation mechanisms. Simulations of the respective behavior are obtained by solving advection-diffusion equations on the sphere, for which a unified computational framework is developed and investigated. This builds the basis for solving two parameter identification problems, which are formulated in the context of the chosen application, magnetic particle imaging. The functionality of the computational framework is illustrated by numerical results in the parameter identification problems either compared quantitatively or qualitatively to measured data.

eess.IV↗

arXiv2020

Smart Chest X-ray Worklist Prioritization using Artificial Intelligence: A Clinical Workflow Simulation

The aim is to evaluate whether smart worklist prioritization by artificial intelligence (AI) can optimize the radiology workflow and reduce report turnaround times (RTAT) for critical findings in chest radiographs (CXRs). Furthermore, we investigate a method to counteract the effect of false negative predictions by AI -- resulting in an extremely and dangerously long RTAT, as CXRs are sorted to the end of the worklist. We developed a simulation framework that models the current workflow at a university hospital by incorporating hospital specific CXR generation rates, reporting rates and pathology distribution. Using this, we simulated the standard worklist processing "first-in, first-out" (FIFO) and compared it with a worklist prioritization based on urgency. Examination prioritization was performed by the AI, classifying eight different pathological findings ranked in descending order of urgency: pneumothorax, pleural effusion, infiltrate, congestion, atelectasis, cardiomegaly, mass and foreign object. Furthermore, we introduced an upper limit for the maximum waiting time, after which the highest urgency is assigned to the examination. The average RTAT for all critical findings was significantly reduced in all Prioritization-simulations compared to the FIFO-simulation (e.g. pneumothorax: 35.6 min vs. 80.1 min; p $<0.0001$), while the maximum RTAT for most findings increased at the same time (e.g. pneumothorax: 1293 min vs 890 min; p $<0.0001$). Our "upper limit" substantially reduced the maximum RTAT all classes (e.g. pneumothorax: 979 min vs. 1293 min / 1178 min; p $<0.0001$). Our simulations demonstrate that smart worklist prioritization by AI can reduce the average RTAT for critical findings in CXRs while maintaining a small maximum RTAT as FIFO.

cs.LG↗

arXiv2020

MDF: Magnetic Particle Imaging Data Format

Magnetic particle imaging (MPI) is a tomographic method to determine the spatio-temporal distribution of magnetic nanoparticles. In this document, a file format for the standardized storage of MPI and magnetic particle spectroscopy (MPS) data is introduced. The aim of the Magnetic Particle Imaging Data Format (MDF) is to provide a coherent way of exchanging MPI and MPS data acquired with different devices worldwide. The focus of the MDF is on sequence parameters, measurement data, calibration data, and reconstruction data. The format is based on the hierarchical document format in version 5 (HDF5). This document discusses the MDF version 2.1.0, which is not backward compatible with version 1.x.y.

physics.med-ph↗