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Noah Jaitner

Publications and source records attributed to Noah Jaitner.

7 recordsLinked to original sources

MRpro: open framework for model-based, learned, and quantitative MR imaging

We preseent an open-source image reconstruction package built upon PyTorch, enabling modern deep-learning reconstructions. It uses open data formats for input and output (ISMRMRD, DICOM, NIfTI), allowing easy integration into existing pipelines and support for data from different devices. The framework comprises three main areas. First, it provides unified data structures for the consistent manipulation of MR datasets and their associated metadata (e.g., k-space trajectories). Second, it offers a library of composable operators, proximable functionals, and optimization algorithms, including a unified Fourier operator for all common trajectories and operators specifically developed for low-field applications, such as a B0-correction operator. These components are used to create ready-to-use implementations of key reconstruction algorithms. Third, for deep learning, MRpro includes essential building blocks such as data-consistency layers, differentiable optimization layers, state-of-the-art backbone networks, and access to public datasets to facilitate reproducibility. We demonstrate MRpro across automatic reconstruction, iterative SENSE, deep-learning-based reconstruction, and quantitative parameter estimation. Applications use public and simulated datasets and measured lowfield data acquired at 0.3 T, 0.6 T, and 47 mT.

eess.IV

ARGUS: Accelerated, Robust, General, and Unsupervised Cell Tracking Solutions

Background and Objective: Quantitative analysis of cell dynamics is central to modern biological research, providing critical insights into immune cell interactions, disease progression, and drug mechanisms. Automated cell tracking in time-lapse microscopy remains challenging due to noise, morphological variations, overlapping cells, and dynamic events such as divisions and fusions. Methods: We present ARGUS, a framework for Accelerated, Robust, General, and Unsupervised Cell Tracking Solutions. ARGUS combines adaptive cell detection, dense Farneback optical-flow prediction, frame-to-frame linear assignment, and a sequence-level tracklet-refinement step that reconnects trajectory fragments across short temporal gaps. Results: On publicly available Cell Tracking Challenge datasets, ARGUS achieved detection accuracy of 0.905-0.971 and tracking accuracy of 0.897-0.964, with runtimes within 1 minute (5-6 seconds for 3 frames). Conclusions: ARGUS is a modular, interpretable framework that can be adapted to different imaging modalities and biological applications without training data or GPU infrastructure. The implementation is publicly available at https://github.com/Gitinc/argus

cs.CV

In Vivo Quantification of Glioma-Induced Solid Stress Using MR Elastography and Deformable Image Registration

Solid stress is increasingly being recognized as a key driver of tumor progression and aggressiveness, yet it has not been directly measured in patients so far. Here, we combine multifrequency magnetic resonance elastography with 3D magnetic resonance imaging (MRI)-based diffeomorphic deformable image registration network analysis to noninvasively quantify glioma-induced solid stress. In both a mouse model and patients, we identified spatially heterogeneous deformation patterns extending well beyond tumor margins. While deformation magnitude was not found to correlate with tumor size or clinical outcome, excess solid stress - defined as the product of peritumoral volumetric strain and stiffness differential between unaffected brain and peritumoral tissue - was inversely associated with patient survival, highlighting its potential as a quantitative, imaging-derived biomarker. To our knowledge, this study provides the first direct quantification of mechanical stress in patients with glioma.

physics.med-ph

ILPU: Iterative Laplace-Based Phase Unwrapping via Bi-Level Optimization

Phase unwrapping is an essential preprocessing step for phase-based MRI applications, including susceptibility mapping, field mapping, thermometry, and MR elastography. We present Iterative Laplace-Based Phase Unwrapping (ILPU), a bi-level optimization algorithm. In this method, a lower-level solver recovers a continuous phase increment from an incremental Poisson equation using the discrete cosine transform (DCT), while an upper-level solver refines an integer offset map through quality-guided spatial regularization and a restricted local search. This coupling enables robust unwrapping in low-SNR regions through adaptive smoothness penalties and quality-weighted regularization. We evaluated ILPU on 2D and 3D brain MRI phase images against manually unwrapped reference data, using standard Laplace unwrapping, Flynn, and SEGUE as comparison methods. In 2D, ILPU achieves accuracy comparable to SEGUE. In 3D, ILPU attains a relative error of 2.12% compared with 67.59% for SEGUE and 81.02% for Laplace, demonstrating a clear advantage in volumetric unwrapping. The algorithm has O(N log N) complexity per iteration through DCT-based Laplacian estimation and is numerically faster than both Flynn and SEGUE while preserving superior accuracy. These results indicate that the bi-level optimization framework provides a robust and computationally efficient solution for phase unwrapping in MRI.

math.OC

In Vivo Wideband MR Elastography for Assessing Age-Related Viscoelastic Changes of the Human Brain

Magnetic Resonance Elastography (MRE) noninvasively maps brain biomechanics and is highly sensitive to alterations associated with aging and neurodegenerative disease. Most implementations use a single frequency or a narrow frequency band, limiting the analysis of frequency-dependent viscoelastic parameters. We developed a dual-actuator wideband MRE (5-50 Hz) protocol and acquired wavefields at 13 frequencies in 24 healthy adults (young: 23-39 years; older: 50-63 years). Shear wave speed (SWS) maps were generated as a proxy for stiffness, and SWS dispersion was modeled using Newtonian, Kelvin-Voigt, and power-law rheological models. Whole-brain stiffness declined with age, with the strongest effect observed at low frequencies (5-16 Hz: -0.24%/year; p=0.019) compared with mid (20-35 Hz: -0.12%/year; p=0.030) and high frequencies (40-50 Hz: -0.10%/year; p=0.165). Compared to older brains, younger adults showed 14.3% higher baseline stiffness in the power-law model (p=0.001) and 8.5-9.0% higher viscosity according to the Newtonian and Kelvin-Voigt model (p<0.05). White and cortical gray matter exhibited similar age-related decreases, while deep gray matter showed an increase in the power-law exponent (+0.001/year; p=0.036), suggesting a transition toward more fluid-like properties associated with aging. Wideband MRE revealed frequency-dependent and region-specific biomechanical alterations with aging, with the strongest effects observed at low frequencies. Extending brain MRE into the low frequency regime potentially enhances sensitivity to solid-fluid interactions. Therefore, low frequency MRE may serve as an early biomechanical marker of microstructural brain changes due to aging and neurodegeneration.

physics.med-ph

Time-Harmonic Optical Flow with Applications in Elastography

In this paper, we propose mathematical models for reconstructing the optical flow in time-harmonic elastography. In this image acquisition technique, the object undergoes a special time-harmonic oscillation with known frequency so that only the spatially varying amplitude of the velocity field has to be determined. This allows for a simpler multi-frame optical flow analysis using Fourier analytic tools in time. We propose three variational optical flow models and show how their minimization can be tackled via Fourier transform in time. Numerical examples with synthetic as well as real-world data demonstrate the benefits of our approach. Keywords: optical flow, elastography, Fourier transform, iteratively reweighted least squares, Horn--Schunck method

math.NA

Optical time-harmonic elastography for multiscale stiffness mapping across the phylogenetic tree

Rapid mapping of the mechanical properties of soft biological tissues from light microscopy to macroscopic imaging could transform fundamental biophysical research by providing clinical biomarkers to complement in vivo elastography. We here introduce superfast optical time-harmonic elastography (OTHE) to remotely encode surface and subsurface shear wave fields for generating maps of tissue stiffness with unprecedented detail resolution. OTHE rigorously exploits the space-time propagation characteristics of time-harmonic waves to address current limitations of biomechanical imaging and elastography. Key solutions are presented for stimulation, encoding, and stiffness reconstruction of time-harmonic, multifrequency shear waves, all tuned to provide consistent stiffness values across resolutions from microns to millimeters. OTHE's versatility is demonstrated in Bacillus subtilis biofilms, zebrafish embryos, adult zebrafish, and human skeletal muscle, reflecting the diversity of the phylogenetic tree from a mechanics perspective. By zooming in on stiffness details from coarse to finer scales, OTHE advances developmental biology and offers a way to perform biomechanics-based tissue histology that consistently matches in vivo time-harmonic elastography in patients.

physics.bio-ph