arXiv subjects

Sara Garbarino

Publications and source records attributed to Sara Garbarino.

At least 19 recordsLinked to original sources

arXiv2025

tiDAS: a time invariant approximation of the Delay and Sum algorithm for biomedical ultrasound PSF reconstructions

Ultrasound imaging is a real-time diagnostic modality that reconstructs acoustic signals into visual representations of internal body structures. A key component in this process is beamforming, with the Delay and Sum (DAS) algorithm being a standard due to its balance between simplicity and effectiveness. However, the computational cost of DAS can be a limiting factor, especially in real-time scenarios where fast frame reconstruction is essential. In this work, we introduce a time-invariant approximation of the DAS algorithm (tiDAS), designed to accelerate the reconstruction process without compromising image quality. By adopting a one-dimensional, row-wise convolutional formulation, tiDAS significantly reduces computational complexity while preserving the core properties of the original model. This approach not only enables faster image reconstruction but also provides a structured foundation for the application of deconvolution methods aimed at enhancing resolution. Synthetic experiments demonstrate that tiDAS achieves a favorable trade-off between speed and accuracy, making it a promising tool for improving the efficiency of real-time ultrasound imaging.

math.NA↗

arXiv2025

Solving Implicit Inverse Problems with Homotopy-Based Regularization Path

Implicit inverse problems, in which noisy observations of a physical quantity are used to infer a nonlinear functional applied to an associated function, are inherently ill posed and often exhibit non uniqueness of solutions. Such problems arise in a range of domains, including the identification of systems governed by Ordinary and Partial Differential Equations (ODEs/PDEs), optimal control, and data assimilation. Their solution is complicated by the nonlinear nature of the underlying constraints and the instability introduced by noise. In this paper, we propose a homotopy based optimization method for solving such problems. Beginning with a regularized constrained formulation that includes a sparsity promoting regularization term, we employ a gradient based algorithm in which gradients with respect to the model parameters are efficiently computed using the adjoint state method. Nonlinear constraints are handled through a Newton Raphson procedure. By solving a sequence of problems with decreasing regularization, we trace a solution path that improves stability and enables the exploration of multiple candidate solutions. The method is applied to the latent dynamics discovery problem in simulation, highlighting performance as a function of ground truth sparsity and semi convergence behavior.

math.NA↗

arXiv2025

Probabilistic approach to longitudinal response prediction: application to radiomics from brain cancer imaging

Longitudinal imaging analysis tracks disease progression and treatment response over time, providing dynamic insights into treatment efficacy and disease evolution. Radiomic features extracted from medical imaging can support the study of disease progression and facilitate longitudinal prediction of clinical outcomes. This study presents a probabilistic model for longitudinal response prediction, integrating baseline features with intermediate follow-ups. The probabilistic nature of the model naturally allows to handle the instrinsic uncertainty of the longitudinal prediction of disease progression. We evaluate the proposed model against state-of-the-art disease progression models in both a synthetic scenario and using a brain cancer dataset. Results demonstrate that the approach is competitive against existing methods while uniquely accounting for uncertainty and controlling the growth of problem dimensionality, eliminating the need for data from intermediate follow-ups.

stat.AP↗

arXiv2025

DISARM++: Beyond scanner-free harmonization

Harmonization of T1-weighted MR images across different scanners is crucial for ensuring consistency in neuroimaging studies. This study introduces a novel approach to direct image harmonization, moving beyond feature standardization to ensure that extracted features remain inherently reliable for downstream analysis. Our method enables image transfer in two ways: (1) mapping images to a scanner-free space for uniform appearance across all scanners, and (2) transforming images into the domain of a specific scanner used in model training, embedding its unique characteristics. Our approach presents strong generalization capability, even for unseen scanners not included in the training phase. We validated our method using MR images from diverse cohorts, including healthy controls, traveling subjects, and individuals with Alzheimer's disease (AD). The model's effectiveness is tested in multiple applications, such as brain age prediction (R2 = 0.60 \pm 0.05), biomarker extraction, AD classification (Test Accuracy = 0.86 \pm 0.03), and diagnosis prediction (AUC = 0.95). In all cases, our harmonization technique outperforms state-of-the-art methods, showing improvements in both reliability and predictive accuracy. Moreover, our approach eliminates the need for extensive preprocessing steps, such as skull-stripping, which can introduce errors by misclassifying brain and non-brain structures. This makes our method particularly suitable for applications that require full-head analysis, including research on head trauma and cranial deformities. Additionally, our harmonization model does not require retraining for new datasets, allowing smooth integration into various neuroimaging workflows. By ensuring scanner-invariant image quality, our approach provides a robust and efficient solution for improving neuroimaging studies across diverse settings. The code is available at this link.

cs.CV↗

arXiv2025

Segmentation variability and radiomics stability for predicting Triple-Negative Breast Cancer subtype using Magnetic Resonance Imaging

Most papers caution against using predictive models for disease stratification based on unselected radiomic features, as these features are affected by contouring variability. Instead, they advocate for the use of the Intraclass Correlation Coefficient (ICC) as a measure of stability for feature selection. However, the direct effect of segmentation variability on the predictive models is rarely studied. This study investigates the impact of segmentation variability on feature stability and predictive performance in radiomics-based prediction of Triple-Negative Breast Cancer (TNBC) subtype using Magnetic Resonance Imaging. A total of 244 images from the Duke dataset were used, with segmentation variability introduced through modifications of manual segmentations. For each mask, explainable radiomic features were selected using the Shapley Additive exPlanations method and used to train logistic regression models. Feature stability across segmentations was assessed via ICC, Pearson's correlation, and reliability scores quantifying the relationship between feature stability and segmentation variability. Results indicate that segmentation accuracy does not significantly impact predictive performance. While incorporating peritumoral information may reduce feature reproducibility, it does not diminish feature predictive capability. Moreover, feature selection in predictive models is not inherently tied to feature stability with respect to segmentation, suggesting that an overreliance on ICC or reliability scores for feature selection might exclude valuable predictive features.

stat.AP↗

arXiv2024

Localized FDG loss in lung cancer lesions

Purpose: Analysis of [18F]-Fluorodeoxyglucose (FDG) kinetics in cancer has been most often limited to the evaluation of the average uptake over relatively large volumes. Nevertheless, tumor lesion almost contains inflammatory infiltrates whose cells are characterized by a significant radioactivity washout due to the hydrolysis of FDG-6P catalyzed by glucose-6P phosphatase. The present study aimed to verify whether voxel-wise compartmental analysis of dynamic imaging can identify tumor regions characterized by tracer washout. Materials & Methods: The study included 11 patients with lung cancer submitted to PET/CT imaging for staging purposes. Tumor was defined by drawing a volume of interest loosely surrounding the lesion and considering all inside voxels with standardized uptake value (SUV) >40% of the maximum. After 20 minutes dynamic imaging centered on the heart, eight whole body scans were repeated. Six parametric maps were progressively generated by computing six regression lines that considered all eight frames, the last seven ones, and so on, up to the last three. Results: Progressively delaying the starting point of regression line computation identified a progressive increase in the prevalence of voxels with a negative slope. Conclusions: The voxel-wise parametric maps provided by compartmental analysis permits to identify a measurable volume characterized by radioactivity washout. The spatial localization of this pattern is compatible with the recognized preferential site of inflammatory infiltrates populating the tumor stroma and might improve the power of FDG imaging in monitoring the effectiveness of treatments aimed to empower the host immune response against the cancer.

q-bio.TO↗

arXiv2023

STIX imaging I -- Concept

Aims. To provide a schematic mathematical description of the imaging concept of the Spectrometer/Telescope for Imaging X-rays (STIX) on board Solar Orbiter. The derived model is the fundamental starting point for both the interpretation of STIX data and the description of the data calibration process. Methods. We describe the STIX indirect imaging technique which is based on spatial modulation of the X-ray photon flux by means of tungsten grids. We show that each of 30 STIX imaging sub-collimators measures a complex Fourier component of the flaring X-ray source corresponding to a specific angular frequency. We also provide details about the count distribution model, which describes the relationship between the photon flux and the measured pixel counts. Results. We define the image reconstruction problem for STIX from both visibilities and photon counts. We provide an overview of the algorithms implemented for the solution of the imaging problem, and a comparison of the results obtained with these different methods in the case of the SOL2022-03-31T18 flaring event.

astro-ph.IM↗

arXiv2022

Forward-fitting STIX visibilities

Aima. To determine to what extent the problem of forward fitting visibilities measured by the Spectrometer/Telescope Imaging X-rays (STIX) on-board Solar Orbiter is more challenging with respect to the same problem in the case of previous hard X-ray solar imaging missions; to identify an effective optimization scheme for parametric imaging for STIX. Methods. This paper introduces a Particle Swarm Optimization (PSO) algorithm for forward fitting STIX visibilities and compares its effectiveness with respect to the standard simplex-based optimization algorithm used so far for the analysis of visibilities measured by the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI). This comparison is made by considering experimental visibilities measured by both RHESSI and STIX, and synthetic visibilities generated by accounting for the STIX signal formation model. Results. We found out that the parametric imaging approach based on PSO is as reliable as the one based on the simplex method in the case of RHESSI visibilities. However, PSO is significantly more robust when applied to STIX simulated and experimental visibilities. Conclusions. Standard deterministic optimization is not effective enough for forward-fitting the few visibilities sampled by STIX in the angular frequency plane. Therefore a more sofisticated optimization scheme must be introduced for parametric imaging in the case of the Solar Orbiter X-ray telescope. The forward-fitting routine based on PSO we introduced in this paper proved to be significantly robust and reliable, and could be considered as an effective candidate tool for parametric imaging in the STIX context.

astro-ph.SR↗

arXiv2022

First hard X-ray imaging results by Solar Orbiter STIX

Context. The Spectrometer/Telescope for Imaging X-rays (STIX) is one of 6 remote sensing instruments on-board Solar Orbiter. It provides hard X-ray imaging spectroscopy of solar flares by sampling the Fourier transform of the incoming flux. Aims. To show that the visibility amplitude and phase calibration of 24 out of 30 STIX sub-collimators is well advanced and that a set of imaging methods is able to provide the first hard X-ray images of the flaring Sun from Solar Orbiter. Methods. We applied four visibility-based image reconstruction methods and a count-based one to calibrated STIX observations. The resulting reconstructions are compared to those provided by an optimization algorithm used for fitting the amplitudes of STIX visibilities. Results. When applied to six flares with GOES class between C4 and M4 which occurred in May 2021, the five imaging methods produce results morphologically consistent with the ones provided by the Atmospheric Imaging Assembly on-board the Solar Dynamic Observatory (SDO/AIA) in UV wavelengths. The $χ^2$ values and the parameters of the reconstructed sources are comparable between methods, thus confirming their robustness. Conclusions. This paper shows that the current calibration of the main part of STIX sub-collimators has reached a satisfactory level for scientific data exploitation, and that the imaging algorithms already available in the STIX data analysis software provide reliable and robust reconstructions of the morphology of solar flares.

astro-ph.SR↗

arXiv2021

Regularization from examples via neural networks for parametric inverse problems: topology matters

In this work we deal with parametric inverse problems, which consist in recovering a finite number of parameters describing the structure of an unknown object, from indirect measurements. State-of-the-art methods for approximating a regularizing inverse operator by using a dataset of input-output pairs of the forward model rely on deep learning techniques. In these approaches, a neural network is trained to predict the value of the sought parameters directly from the data. In this paper, we show that these methods provide suboptimal results when the topology of the parameter space is strictly coarser than the Euclidean one. To overcome this issue, we propose a two-step strategy for approximating a regularizing inverse operator by means of a neural network, which works under general topological conditions. First, we embed the parameters into a subspace of a low-dimensional Euclidean space; second, we use a neural network to approximate a homeomorphism between the subspace and the image of the parameter space through the forward operator. The parameters are then retrieved by applying the inverse of the embedding to the network predictions. The results are shown for the problem of X-ray imaging of solar flares with data from the Spectrometer/Telescope for Imaging X-rays. In this case, the parameter space is a family of Moebius strips that collapse into a point. Our simulation studies show that the use of a neural network for predicting the parameters directly from the data yields systematic errors due to the non-Euclidean topology of the parameter space. The proposed strategy overcomes the topological issues and furnishes stable and accurate reconstructions.

math.NA↗

arXiv2021

Imaging from STIX visibility amplitudes

Aims: To provide the first demonstration of STIX Fourier-transform X-ray imaging using semi-calibrated (amplitude-only) visibility data acquired during the Solar Orbiter's cruise phase. Methods: We use a parametric imaging approach by which STIX visibility amplitudes are fitted by means of two non-linear optimization methods: a fast meta-heuristic technique inspired by social behavior, and a Bayesian Monte Carlo sampling method, which, although slower, provides better quantification of uncertainties. Results: When applied to a set of solar flare visibility amplitudes recorded by STIX on November 18, 2020 the two parametric methods provide very coherent results. The analysis also demonstrates the ability of STIX to reconstruct high time resolution information and, from a spectral viewpoint, shows the reliability of a double-source scenario consistent with a thermal versus nonthermal interpretation. Conclusions: In this preliminary analysis of STIX imaging based only on visibility amplitudes, we formulate the imaging problem as a non-linear parametric issue we addressed by means of two high-performance optimization techniques that both showed the ability to sample the parametric space in an effective fashion, thus avoiding local minima.

astro-ph.SR↗

arXiv2019

Modeling and inference of spatio-temporal protein dynamics across brain networks

Models of misfolded proteins (MP) aim at discovering the bio-mechanical propagation properties of neurological diseases (ND) by identifying plausible associated dynamical systems. Solving these systems along the full disease trajectory is usually challenging, due to the lack of a well defined time axis for the pathology. This issue is addressed by disease progression models (DPM) where long-term progression trajectories are estimated via time reparametrization of individual observations. However, due to their loose assumptions on the dynamics, DPM do not provide insights on the bio-mechanical properties of MP propagation. Here we propose a unified model of spatio-temporal protein dynamics based on the joint estimation of long-term MP dynamics and time reparameterization of individuals observations. The model is expressed within a Gaussian Process (GP) regression setting, where constraints on the MP dynamics are imposed through non--linear dynamical systems. We use stochastic variational inference on both GP and dynamical system parameters for scalable inference and uncertainty quantification of the trajectories. Experiments on simulated data show that our model accurately recovers prescribed rates along graph dynamics and precisely reconstructs the underlying progression. When applied to brain imaging data our model allows the bio-mechanical interpretation of amyloid deposition in Alzheimer's disease, leading to plausible simulations of MP propagation, and achieving accurate predictions of individual MP deposition in unseen data.

q-bio.QM↗

arXiv2019

DIVE: A spatiotemporal progression model of brain pathology in neurodegenerative disorders

Here we present DIVE: Data-driven Inference of Vertexwise Evolution. DIVE is an image-based disease progression model with single-vertex resolution, designed to reconstruct long-term patterns of brain pathology from short-term longitudinal data sets. DIVE clusters vertex-wise biomarker measurements on the cortical surface that have similar temporal dynamics across a patient population, and concurrently estimates an average trajectory of vertex measurements in each cluster. DIVE uniquely outputs a parcellation of the cortex into areas with common progression patterns, leading to a new signature for individual diseases. DIVE further estimates the disease stage and progression speed for every visit of every subject, potentially enhancing stratification for clinical trials or management. On simulated data, DIVE can recover ground truth clusters and their underlying trajectory, provided the average trajectories are sufficiently different between clusters. We demonstrate DIVE on data from two cohorts: the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Dementia Research Centre (DRC), UK, containing patients with Posterior Cortical Atrophy (PCA) as well as typical Alzheimer's disease (tAD). DIVE finds similar spatial patterns of atrophy for tAD subjects in the two independent datasets (ADNI and DRC), and further reveals distinct patterns of pathology in different diseases (tAD vs PCA) and for distinct types of biomarker data: cortical thickness from Magnetic Resonance Imaging (MRI) vs amyloid load from Positron Emission Tomography (PET). Finally, DIVE can be used to estimate a fine-grained spatial distribution of pathology in the brain using any kind of voxelwise or vertexwise measures including Jacobian compression maps, fractional anisotropy (FA) maps from diffusion imaging or other PET measures. DIVE source code is available online: https://github.com/mrazvan22/dive

cs.CV↗

arXiv2018

A physiology--based parametric imaging method for FDG--PET data

Parametric imaging is a compartmental approach that processes nuclear imaging data to estimate the spatial distribution of the kinetic parameters governing tracer flow. The present paper proposes a novel and efficient computational method for parametric imaging which is potentially applicable to several compartmental models of diverse complexity and which is effective in the determination of the parametric maps of all kinetic coefficients. We consider applications to [{18}F]-fluorodeoxyglucose Positron Emission Tomography (FDG-PET) data and analyze the two-compartment catenary model describing the standard FDG metabolization by an homogeneous tissue and the three-compartment non-catenary model representing the renal physiology. We show uniqueness theorems for both models. The proposed imaging method starts from the reconstructed FDG-PET images of tracer concentration and preliminarily applies image processing algorithms for noise reduction and image segmentation. The optimization procedure solves pixelwise the non-linear inverse problem of determining the kinetic parameters from dynamic concentration data through a regularized Gauss-Newton iterative algorithm. The reliability of the method is validated against synthetic data, for the two-compartment system, and experimental real data of murine models, for the renal three-compartment system.

math.NA↗

arXiv2017

Iterative algorithms for a non-linear inverse problem in atmospheric lidar

We consider the inverse problem of retrieving aerosol extinction coefficients from Raman lidar measurements. In this problem the unknown and the data are related through the exponential of a linear operator, the unknown is non-negative and the data follow the Poisson distribution. Standard methods work on the log-transformed data and solve the resulting linear inverse problem, but neglect to take into account the noise statistics. In this study we show that proper modelling of the noise distribution can improve substantially the quality of the reconstructed extinction profiles. To achieve this goal, we consider the non-linear inverse problem with non-negativity constraint, and propose two iterative algorithms derived using the Karush-Kuhn-Tucker conditions. We validate the algorithms with synthetic and experimental data. As expected, the proposed algorithms outperform standard methods in terms of sensitivity to noise and reliability of the estimated profile.

math.NA↗

arXiv2017

Parametric Imaging of FDG-PET Data Using Physiology and Iterative Regularization: Application to the Hepatic and Renal Systems

The present paper proposes a novel computational method for parametric imaging of nuclear medicine data. The mathematical procedure is general enough to work for compartmental models of diverse complexity and is effective in the determination of the parametric maps of all kinetic parameters governing tracer flow. We consider applications to [18F]-fluorodeoxyglucose Positron Emission Tomography (FDG-PET) data and analyze the two-compartment catenary model describing the standard FDG metabolization by an homogeneous tissue, e.g. the liver, and the three-compartment non-catenary model representing the renal physiology. The proposed imaging method starts from the reconstructed FDG-PET images of tracer concentration and preliminarily applies image processing algorithms for noise reduction and image segmentation processes for selecting the region enclosing the organ of physiologic interest. The optimization scheme solves pixelwise the non-linear inverse problem of determining the kinetic parameters from dynamic concentration data through a Gauss-Newton iterative algorithm with a penalty term accounting for the ill-posedness of the problem. We tested our imaging approach on FDG-PET data of murine models obtained by means of a dedicated microPET system, and we analyzed different PET slices containing axial sections of the liver and axial sections of the kidneys. The reconstructed parametric images proved to be reliable and qualitatively effective in the description of the local FDG metabolism with respect to the different physiologies.

q-bio.TO↗

arXiv2016

Compartmental analysis of dynamic nuclear medicine data: models and identifiability

Compartmental models based on tracer mass balance are extensively used in clinical and pre-clinical nuclear medicine in order to obtain quantitative information on tracer metabolism in the biological tissue. This paper is the first of a series of two that deal with the problem of tracer coefficient estimation via compartmental modelling in an inverse problem framework. Specifically, here we discuss the identifiability problem for a general n-dimension compartmental system and provide uniqueness results in the case of two-compartment and three-compartment compartmental models. The second paper will utilize this framework in order to show how non-linear regularization schemes can be applied to obtain numerical estimates of the tracer coefficients in the case of nuclear medicine data corresponding to brain, liver and kidney physiology.

q-bio.QM↗

arXiv2016

Expectation Maximization and the retrieval of the atmospheric extinction coefficients by inversion of Raman lidar data

We consider the problem of retrieving the aerosol extinction coefficient from Raman lidar measurements. This is an ill--posed inverse problem that needs regularization, and we propose to use the Expectation--Maximization (EM) algorithm to provide stable solutions. Indeed, EM is an iterative algorithm that imposes a positivity constraint on the solution, and provides regularization if iterations are stopped early enough. We describe the algorithm and propose a stopping criterion inspired by a statistical principle. We then discuss its properties concerning the spatial resolution. Finally, we validate the proposed approach by using both synthetic data and experimental measurements; we compare the reconstructions obtained by EM with those obtained by the Tikhonov method, by the Levenberg-Marquardt method, as well as those obtained by combining data smoothing and numerical derivation.

math.NA↗