ML parameter estimation for Markov random fields with applications to Bayesian tomography

Machine learning-driven prediction of medical expenses in triple-vessel PCI patients using feature selection

Revascularization therapies, such as percutaneous coronary intervention (PCI) and coronary artery bypass grafting (CABG), alleviate symptoms and treat myocardial ischemia. Patients with multivessel disease, particularly those undergoing 3-vessel PCI, are more susceptible to procedural complications, which can increase healthcare costs. Developing efficient strategies for resource allocation has become a paramount concern due to tightening healthcare budgets and the escalating costs of treating heart conditions. Therefore, it is essential to develop an evaluation model to estimate the costs of PCI surgeries and identify the key factors influencing these costs to enhance healthcare quality. This study utilized the National Health Insurance Research Database (NHIRD), encompassing data from multiple hospitals across Taiwan and covering up to 99% of the population. The study examined data from triple-vessel PCI patients treated between January 2015 and December 2017. Additionally, six machine-learning algorithms and five cross-validation techniques were employed to identify key features and construct the evaluation model. The machine learning algorithms used included linear regression (LR), random forest (RF), support vector regression (SVR), generalized linear model boost (GLMBoost), Bayesian generalized linear model (BayesGLM), and extreme gradient boosting (eXGB). Among these, the eXGB model exhibited outstanding performance, with the following metrics: MSE (0.02419), RMSE (0.15552), and MAPE (0.00755). We found that the patient's medication use in the previous year is also crucial in determining subsequent surgical costs. Additionally, 25 significant features influencing surgical expenses were identified. The top variables included 1-year medical expenditure before PCI surgery (hospitalization and outpatient costs), average blood transfusion volume, ventilator use duration, Charlson Comorbidity Index scores, emergency department visits, and patient age. This research is crucial for estimating potential expenses linked to complications from the procedure, directing the allocation of resources in the future, and acting as an important resource for crafting medical management policies.

Solving the MPI reconstruction problem with automatically tuned regularization parameters

In the field of medical imaging, magnetic particle imaging (MPI) poses a promising non-ionizing tomographic technique with high spatial and temporal resolution. In MPI, iterative solvers are used to reconstruct the particle distribution out of the measured voltage signal based on a system matrix. The amount of regularization needed to reconstruct an image of good quality differs from measurement to measurement, depending on the MPI system and the measurement settings. Finding the right choice for the three major parameters controlling the regularization is commonly done by hand and requires time and experience. In this work, we study the reduction to a single regularization parameter and propose a method that enables automatic reconstruction. The method is qualitatively and quantitatively validated on several MPI data sets showing promising results.

Smoothed-NUV Priors for Imaging

Variations of L1 -regularization including, in particular, total variation regularization, have hugely improved computational imaging. However, sharper edges and fewer staircase artifacts can be achieved with convex-concave regularizers. We present a new class of such regularizers using normal priors with unknown variance (NUV), which include smoothed versions of the logarithm function and smoothed versions of Lp norms with p ≤ 1 . All NUV priors allow variational representations that lead to efficient algorithms for image reconstruction by iterative reweighted descent. A preferred such algorithm is iterative reweighted coordinate descent, which has no parameters (in particular, no step size to control) and is empirically robust and efficient. The proposed priors and algorithms are demonstrated with applications to tomography. We also note that the proposed priors come with built-in edge detection, which is demonstrated by an application to image segmentation.

Far-field thermal imaging below diffraction limit

Non-uniform self-heating and temperature hotspots are major concerns compromising the performance and reliability of submicron electronic and optoelectronic devices. At deep submicron scales where effects such as contact-related artifacts and diffraction limits accurate measurements of temperature hotspots, non-contact thermal characterization can be extremely valuable. In this work, we use a Bayesian optimization framework with generalized Gaussian Markov random field (GGMRF) prior model to obtain accurate full-field temperature distribution of self-heated metal interconnects from their thermoreflectance thermal images (TRI) with spatial resolution 2.5 times below Rayleigh limit for 530nm illumination. Finite element simulations along with TRI experimental data were used to characterize the point spread function of the optical imaging system. In addition, unlike iterative reconstruction algorithms that use ad hoc regularization parameters in their prior models to obtain the best quality image, we used numerical experiments and finite element modeling to estimate the regularization parameter for solving a real experimental inverse problem.

Enhancement of dynamic myocardial perfusion PET images based on low-rank plus sparse decomposition

BACKGROUND AND OBJECTIVE

The absolute quantification of dynamic myocardial perfusion (MP) PET imaging is challenged by the limited spatial resolution of individual frame images due to division of the data into shorter frames. This study aims to develop a method for restoration and enhancement of dynamic PET images.

METHODS

We propose that the image restoration model should be based on multiple constraints rather than a single constraint, given the fact that the image characteristic is hardly described by a single constraint alone. At the same time, it may be possible, but not optimal, to regularize the image with multiple constraints simultaneously. Fortunately, MP PET images can be decomposed into a superposition of background vs. dynamic components via low-rank plus sparse (L + S) decomposition. Thus, we propose an L + S decomposition based MP PET image restoration model and express it as a convex optimization problem. An iterative soft thresholding algorithm was developed to solve the problem. Using realistic dynamic ⁸²Rb MP PET scan data, we optimized and compared its performance with other restoration methods.

RESULTS

The proposed method resulted in substantial visual as well as quantitative accuracy improvements in terms of noise versus bias performance, as demonstrated in extensive ⁸²Rb MP PET simulations. In particular, the myocardium defect in the MP PET images had improved visual as well as contrast versus noise tradeoff. The proposed algorithm was also applied on an 8-min clinical cardiac ⁸²Rb MP PET study performed on the GE Discovery PET/CT, and demonstrated improved quantitative accuracy (CNR and SNR) compared to other algorithms.

CONCLUSIONS

The proposed method is effective for restoration and enhancement of dynamic PET images.

Enhanced Wiener filter for ultrasound image restoration

BACKGROUND AND OBJECTIVE

Speckle phenomenon strongly affects UltraSound (US) images. In the last years, several efforts have been done in order to provide an effective denoising methodology. Although good results have been achieved in terms of noise reduction effectiveness, most of the proposed approaches are not characterized by low computational burden and require the supervision of an external operator for tuning the input parameters.

METHODS

Within this manuscript, a novel approach is investigated, based on Wiener filter. Working in the frequency domain, it is characterized by high computational efficiency. With respect to classical Wiener filter, the proposed Enhanced Wiener filter is able to locally adapt itself by tuning its kernel in order to combine edges and details preservation with effective noise reduction. This characteristic is achieved by implementing a Local Gaussian Markov Random Field for modeling the image. Due to its intrinsic characteristics, the computational burden of the algorithm is sensibly low compared to other widely adopted filters and the parameter tuning effort is minimal, being well suited for quasi real time applications.

RESULTS

The approach has been tested on both simulated and real datasets, showing interesting performances compared to other state of art methods.

CONCLUSIONS

A novel denoising method for UltraSound images is proposed. The approach is able to combine low computational burden with interesting denoising performances and details preservation.

A 3D MRI denoising algorithm based on Bayesian theory

BACKGROUND

Within this manuscript a noise filtering technique for magnetic resonance image stack is presented. Magnetic resonance images are usually affected by artifacts and noise due to several reasons. Several denoising approaches have been proposed in literature, with different trade-off between computational complexity, regularization and noise reduction. Most of them is supervised, i.e. requires the set up of several parameters. A completely unsupervised approach could have a positive impact on the community.

RESULTS

The method exploits Markov random fields in order to implement a 3D maximum a posteriori estimator of the image. Due to the local nature of the considered model, the algorithm is able do adapt the smoothing intensity to the local characteristics of the images by analyzing the 3D neighborhood of each voxel. The effect is a combination of details preservation and noise reduction. The algorithm has been compared to other widely adopted denoising methodologies in MRI. Both simulated and real datasets have been considered for validation. Real datasets have been acquired at 1.5 and 3 T. The methodology is able to provide interesting results both in terms of noise reduction and edge preservation without any supervision.

CONCLUSIONS

A novel method for regularizing 3D MR image stacks is presented. The approach exploits Markov random fields for locally adapt filter intensity. Compared to other widely adopted noise filters, the method has provided interesting results without requiring the tuning of any parameter by the user.

Incorporating Spatial Information and Endmember Variability Into Unmixing Analyses to Improve Abundance Estimates

Incorporating endmember variability and spatial information into spectral unmixing analyses is important for producing accurate abundance estimates. However, most methods do not incorporate endmember variability with spatial regularization. This paper proposes a novel 2-step unmixing approach, which incorporates endmember variability and spatial information. In step 1, a probability distribution representing abundances is estimated by spectral unmixing within a multi-task Gaussian process framework (SUGP). In step 2, spatial information is incorporated into the probability distribution derived by SUGP through an a priori distribution derived from a Markov random field (MRF). The proposed method (SUGP-MRF) is different to the existing unmixing methods because it incorporates endmember variability and spatial information at separate steps in the analysis and automatically estimates parameters controlling the balance between the data fit and spatial smoothness. The performance of SUGP-MRF is compared with the existing unmixing methods using synthetic imagery with precisely known abundances and real hyperspectral imagery of rock samples. Results show that SUGP-MRF outperforms the existing methods and improves the accuracy of abundance estimates by incorporating spatial information.

A Generative Model of Terrain for Autonomous Navigation in Vegetation

Current approaches to off-road autonomous navigation are often limited by their ability to build a terrain model from sensor data. Available sensors make very indirect measurements of quantities of interest such as the supporting ground height and the location of obstacles, especially in domains where vegetation may hide the ground surface or partially obscure obstacles. A generative, probabilistic terrain model is introduced that exploits natural structure found in off-road environments to constrain the problem and use ambiguous sensor data more effectively. The model includes two Markov random fields that encode the assumptions that ground heights smoothly vary and terrain classes tend to cluster. The model also includes a latent variable that encodes the assumption that vegetation of a single type has a similar height. The model parameters can be trained by simply driving through representative terrain. Results from a number of challenging test scenarios in an agricultural domain reveal that exploiting the 3D structure inherent in outdoor domains significantly improves ground estimates and obstacle detection accuracy, and allows the system to infer the supporting ground surface even when it is hidden under dense vegetation.

A Bayesian approach for relaxation times estimation in MRI

Relaxation time estimation in MRI field can be helpful in clinical diagnosis. In particular, T1 and T2 changes can be related to tissues modification, being an effective tool for detecting the presence of several pathologies and measure their development, thus their estimation is a useful research field. Currently, most techniques work pixel-wise, and transfer the noise reduction task to post processing filters. A novel method for estimating spin-spin and spin-lattice relaxation times is proposed. The approach exploits Markov Random Field theory for modeling the unknown data and implements an a posteriori estimator in the Bayesian framework. The effect is the joint parameters estimation and noise reduction. Proposed methodology, with respect to already existing techniques, is able to provide effective results while preserving details also in case of few acquisitions or severe signal to noise ratio. The algorithm has been tested on both simulated and real datasets.

Single image defogging by multiscale depth fusion

Restoration of fog images is important for the deweathering issue in computer vision. The problem is ill-posed and can be regularized within a Bayesian context using a probabilistic fusion model. This paper presents a multiscale depth fusion (MDF) method for defog from a single image. A linear model representing the stochastic residual of nonlinear filtering is first proposed. Multiscale filtering results are probabilistically blended into a fused depth map based on the model. The fusion is formulated as an energy minimization problem that incorporates spatial Markov dependence. An inhomogeneous Laplacian-Markov random field for the multiscale fusion regularized with smoothing and edge-preserving constraints is developed. A nonconvex potential, adaptive truncated Laplacian, is devised to account for spatially variant characteristics such as edge and depth discontinuity. Defog is solved by an alternate optimization algorithm searching for solutions of depth map by minimizing the nonconvex potential in the random field. The MDF method is experimentally verified by real-world fog images including cluttered-depth scene that is challenging for defogging at finer details. The fog-free images are restored with improving contrast and vivid colors but without over-saturation. Quantitative assessment of image quality is applied to compare various defog methods. Experimental results demonstrate that the accurate estimation of depth map by the proposed edge-preserved multiscale fusion should recover high-quality images with sharp details.

Quality and precision of parametric images created from PET sinogram data by direct reconstruction: proof of concept

We have previously implemented the direct reconstruction of dense kinetic model parameter images ("parametric images") from sinogram data, and compared it to conventional image domain kinetic parameter estimation methods . Although it has been shown that the direct reconstruction algorithm estimates the kinetic model parameters with lower root mean squared error than the conventional image domain techniques, some theoretical obstacles remain. These obstacles include the difficulty of evaluating the accuracy and precision of the estimated parameters. In image domain techniques, the reconstructed time activity curve (TAC) and the model predicted TAC are compared, and the goodness-of-fit is evaluated as a measure of the accuracy and precision of the estimated parameters. This approach cannot be applied to the direct reconstruction technique as there are no reconstructed TACs. In this paper, we propose ways of evaluating the precision and goodness-of-fit of the kinetic model parameters estimated by the direct reconstruction algorithm. Specifically, precision of the estimates requires the calculation of variance images for each parameter, and goodness-of-fit is addressed by reconstructing the difference between the measured and the fitted sinograms. We demonstrate that backprojecting the difference from sinogram space to image space creates error images that can be examined for goodness-of-fit and model selection purposes. The presence of nonrandom structures in the error images may indicate an inadequacy of the kinetic model that has been incorporated into the direct reconstruction algorithm. We introduce three types of goodness-of-fit images. We propose and demonstrate a number-of-runs image as a means of quantifying the adequacy or deficiency of the model. We further propose and demonstrate images of the F statistic and the change in the Akaike Information Criterion as devices for identifying the statistical advantage of one model over another at each voxel. As direct reconstruction to parametric images proliferates, it will be essential for imagers to adopt methods such as those proposed herein to assess the accuracy and precision of their parametric images.

3.5D dynamic PET image reconstruction incorporating kinetics-based clusters

Standard 3D dynamic positron emission tomographic (PET) imaging consists of independent image reconstructions of individual frames followed by application of appropriate kinetic model to the time activity curves at the voxel or region-of-interest (ROI). The emerging field of 4D PET reconstruction, by contrast, seeks to move beyond this scheme and incorporate information from multiple frames within the image reconstruction task. Here we propose a novel reconstruction framework aiming to enhance quantitative accuracy of parametric images via introduction of priors based on voxel kinetics, as generated via clustering of preliminary reconstructed dynamic images to define clustered neighborhoods of voxels with similar kinetics. This is then followed by straightforward maximum a posteriori (MAP) 3D PET reconstruction as applied to individual frames; and as such the method is labeled '3.5D' image reconstruction. The use of cluster-based priors has the advantage of further enhancing quantitative performance in dynamic PET imaging, because: (a) there are typically more voxels in clusters than in conventional local neighborhoods, and (b) neighboring voxels with distinct kinetics are less likely to be clustered together. Using realistic simulated (11)C-raclopride dynamic PET data, the quantitative performance of the proposed method was investigated. Parametric distribution-volume (DV) and DV ratio (DVR) images were estimated from dynamic image reconstructions using (a) maximum-likelihood expectation maximization (MLEM), and MAP reconstructions using (b) the quadratic prior (QP-MAP), (c) the Green prior (GP-MAP) and (d, e) two proposed cluster-based priors (CP-U-MAP and CP-W-MAP), followed by graphical modeling, and were qualitatively and quantitatively compared for 11 ROIs. Overall, the proposed dynamic PET reconstruction methodology resulted in substantial visual as well as quantitative accuracy improvements (in terms of noise versus bias performance) for parametric DV and DVR images. The method was also tested on a 90 min (11)C-raclopride patient study performed on the high-resolution research tomography. The proposed method was shown to outperform the conventional method in visual as well as quantitative accuracy improvements (in terms of noise versus regional DVR value performance).

Prostate cancer segmentation with simultaneous estimation of Markov random field parameters and class

Prostate cancer is one of the leading causes of death from cancer among men in the United States. Currently, high-resolution magnetic resonance imaging (MRI) has been shown to have higher accuracy than trans-rectal ultrasound (TRUS) when used to ascertain the presence of prostate cancer. As MRI can provide both morphological and functional images for a tissue of interest, some researchers are exploring the uses of multispectral MRI to guide prostate biopsies and radiation therapy. However, success with prostate cancer localization based on current imaging methods has been limited due to overlap in feature space of benign and malignant tissues using any one MRI method and the interobserver variability. In this paper, we present a new unsupervised segmentation method for prostate cancer detection, using fuzzy Markov random fields (fuzzy MRFs) for the segmentation of multispectral MR prostate images. Typically, both hard and fuzzy MRF models have two groups of parameters to be estimated: the MRF parameters and class parameters for each pixel in the image. To date, these two parameters have been treated separately, and estimated in an alternating fashion. In this paper, we develop a new method to estimate the parameters defining the Markovian distribution of the measured data, while performing the data clustering simultaneously. We perform computer simulations on synthetic test images and multispectral MR prostate datasets to demonstrate the efficacy and efficiency of the proposed method and also provide a comparison with some of the commonly used methods.

Analysis of penalized likelihood image reconstruction for dynamic PET quantification

Quantification of tracer kinetics using dynamic positron emission tomography (PET) provides important information for understanding the physiological and biochemical processes in humans and animals. A common procedure is to reconstruct a sequence of dynamic images first, and then apply kinetic analysis to the time activity curve of a region of interest derived from the reconstructed images. Obviously, the choice of image reconstruction method and its parameters affect the accuracy of the time activity curve and hence the estimated kinetic parameters. This paper analyzes the effects of penalized likelihood image reconstruction on tracer kinetic parameter estimation. Approximate theoretical expressions are derived to study the bias, variance, and ensemble mean squared error of the estimated kinetic parameters. Computer simulations show that these formulae predict correctly the changes of these statistics as functions of the regularization parameter. It is found that the choice of the regularization parameter has a significant impact on kinetic parameter estimation, indicating proper selection of image reconstruction parameters is important for dynamic PET. A practical method has been developed to use the theoretical formulae to guide the selection of the regularization parameter in dynamic PET image reconstruction.

Bayesian motion recovery framework for myocardial phase-contrast velocity MRI

Detailed assessment of myocardial motion provides a key indicator of ventricular function, enabling the early detection and assessment of a range of cardiac abnormalities. Existing techniques for myocardial contractility analysis are complicated by a combination of factors including resolution, acquisition time, and consistency of quantification results. Phase-contrast velocity MRI is a technique that provides instantaneous, in vivo measurement of tissue velocity on a per-voxel basis. It allows for the direct derivation of contractile indices with minimal post-processing. For this method to be clinically useful, SNR and image artifacts need to be addressed. The purpose of this paper is to present a Maximum a posteriori (MAP) restoration technique for high quality myocardial motion recovery. It employs an accurate noise modeling scheme and a generalized Gaussian Markov random field prior tailored for the myocardial morphology. The quality of the proposed method is evaluated with both simulated myocardial velocity data with known ground truth and in vivo phase-contrast MR velocity acquisitions from a group of normal subjects.

A 2D approach to tomographic image reconstruction using a Hopfield-type neural network

OBJECTIVE

In this paper a new approach to tomographic image reconstruction from projections is developed and investigated.

METHOD

To solve the reconstruction problem a special neural network which resembles a Hopfield net is proposed. The reconstruction process is performed during the minimizing of the energy function in this network. To improve the performance of the reconstruction process an entropy term is incorporated into energy expression.

RESULT AND CONCLUSION

The approach presented in this paper significantly decreases the complexity of the reconstruction problem.

Unsupervised Bayesian convex deconvolution based on a field with an explicit partition function

This paper proposes a non-Gaussian Markov field with a special feature: an explicit partition function. To the best of our knowledge, this is an original contribution. Moreover, the explicit expression of the partition function enables the development of an unsupervised edge-preserving convex deconvolution method. The method is fully Bayesian, and produces an estimate in the sense of the posterior mean, numerically calculated by means of a Monte-Carlo Markov chain technique. The approach is particularly effective and the computational practicability of the method is shown on a simple simulated example.

AIDA: an adaptive image deconvolution algorithm with application to multi-frame and three-dimensional data

We describe an adaptive image deconvolution algorithm (AIDA) for myopic deconvolution of multi-frame and three-dimensional data acquired through astronomical and microscopic imaging. AIDA is a reimplementation and extension of the MISTRAL method developed by Mugnier and co-workers and shown to yield object reconstructions with excellent edge preservation and photometric precision [J. Opt. Soc. Am. A21, 1841 (2004)]. Written in Numerical Python with calls to a robust constrained conjugate gradient method, AIDA has significantly improved run times over the original MISTRAL implementation. Included in AIDA is a scheme to automatically balance maximum-likelihood estimation and object regularization, which significantly decreases the amount of time and effort needed to generate satisfactory reconstructions. We validated AIDA using synthetic data spanning a broad range of signal-to-noise ratios and image types and demonstrated the algorithm to be effective for experimental data from adaptive optics-equipped telescope systems and wide-field microscopy.

Estimating optimal parameters for MRF stereo from a single image pair

This paper presents a novel approach for estimating the parameters for MRF-based stereo algorithms. This approach is based on a new formulation of stereo as a maximum a posterior (MAP) problem in which both a disparity map and MRF parameters are estimated from the stereo pair itself. We present an iterative algorithm for the MAP estimation that alternates between estimating the parameters while fixing the disparity map and estimating the disparity map while fixing the parameters. The estimated parameters include robust truncation thresholds for both data and neighborhood terms, as well as a regularization weight. The regularization weight can be either a constant for the whole image or spatially-varying, depending on local intensity gradients. In the latter case, the weights for intensity gradients are also estimated. Our approach works as a wrapper for existing stereo algorithms based on graph cuts or belief propagation, automatically tuning their parameters to improve performance without requiring the stereo code to be modified. Experiments demonstrate that our approach moves a baseline belief propagation stereo algorithm up six slots in the Middlebury rankings.

High-resolution diffusion MRI

This paper presents a magnetic resonance imaging method that can provide high-resolution images characterizing water diffusion in biological tissues. These images contain information about tissue microstructure, thereby providing a useful means to monitor physiological changes. The proposed method overcomes the long-standing problem of limited signal-to-noise ratio with diffusion MRI by using penalized maximum-likelihood reconstruction. Experiments performed on a mouse brain illustrate the ability of the technique to elucidate high resolution structural detail that would not be visible using other non-invasive approaches.

Estimation of kinetic model parameters in fluorescence optical diffusion tomography

We present a technique for reconstructing the spatially dependent dynamics of a fluorescent contrast agent in turbid media. The dynamic behavior is described by linear and nonlinear parameters of a compartmental model or some other model with a deterministic functional form. The method extends our previous work in fluorescence optical diffusion tomography by parametrically reconstructing the time-dependent fluorescent yield. The reconstruction uses a Bayesian framework and parametric iterative coordinate descent optimization, which is closely related to Gauss-Seidel methods. We demonstrate the method with a simulation study.

Direct reconstruction of kinetic parameter images from dynamic PET data

Our goal in this paper is the estimation of kinetic model parameters for each voxel corresponding to a dense three-dimensional (3-D) positron emission tomography (PET) image. Typically, the activity images are first reconstructed from PET sinogram frames at each measurement time, and then the kinetic parameters are estimated by fitting a model to the reconstructed time-activity response of each voxel. However, this "indirect" approach to kinetic parameter estimation tends to reduce signal-to-noise ratio (SNR) because of the requirement that the sinogram data be divided into individual time frames. In 1985, Carson and Lange proposed, but did not implement, a method based on the expectation-maximization (EM) algorithm for direct parametric reconstruction. The approach is "direct" because it estimates the optimal kinetic parameters directly from the sinogram data, without an intermediate reconstruction step. However, direct voxel-wise parametric reconstruction remained a challenge due to the unsolved complexities of inversion and spatial regularization. In this paper, we demonstrate and evaluate a new and efficient method for direct voxel-wise reconstruction of kinetic parameter images using all frames of the PET data. The direct parametric image reconstruction is formulated in a Bayesian framework, and uses the parametric iterative coordinate descent (PICD) algorithm to solve the resulting optimization problem. The PICD algorithm is computationally efficient and is implemented with spatial regularization in the domain of the physiologically relevant parameters. Our experimental simulations of a rat head imaged in a working small animal scanner indicate that direct parametric reconstruction can substantially reduce root-mean-squared error (RMSE) in the estimation of kinetic parameters, as compared to indirect methods, without appreciably increasing computation.

A Bayesian filtering technique for SAR interferometric phase fields

SAR interferograms are affected by a strong noise component which often prevents correct phase unwrapping and always impairs the phase reconstruction accuracy. To obtain satisfactory performance, most filtering techniques exploit prior information by means of ad hoc, empirical strategies. In this paper, we recast phase filtering as a Bayesian estimation problem in which the image prior is modeled as a suitable Markov random field, and the filtered phase field is the configuration with maximum a posteriori probability. Assuming the image to be residue free and generally smooth, a two-component MRF model is adopted, where the first component penalizes residues, while the second one penalizes discontinuities. Constrained aimulated annealing is then used to find the optimal solution. The experimental analysis shows that, by gradually adjusting the MRF parameters, the algorithm filters out most of the high-frequency noise and, in the limit, eliminates all residues, allowing for a trivial phase unwrapping. Given a limited processing time, the algorithm is still able to eliminate most residues, paving the way for the successful use of any subsequent phase unwrapping technique.

Fluorescence optical diffusion tomography using multiple-frequency data

A method is presented for fluorescence optical diffusion tomography in turbid media using multiple-frequency data. The method uses a frequency-domain diffusion equation model to reconstruct the fluorescent yield and lifetime by means of a Bayesian framework and an efficient, nonlinear optimizer. The method is demonstrated by using simulations and laboratory experiments to show that reconstruction quality can be improved in certain problems through the use of more than one frequency. A broadly applicable mutual information performance metric is also presented and used to investigate the advantages of using multiple modulation frequencies compared with using only one.

Unsupervised robust nonparametric estimation of the hemodynamic response function for any fMRI experiment

This paper deals with the estimation of the blood oxygen level-dependent response to a stimulus, as measured in functional magnetic resonance imaging (fMRI) data. A precise estimation is essential for a better understanding of cerebral activations. The most recent works have used a nonparametric framework for this estimation, considering each brain region as a system characterized by its impulse response, the so-called hemodynamic response function (HRF). However, the use of these techniques has remained limited since they are not well-adapted to real fMRI data. Here, we develop a threefold extension to previous works. We consider asynchronous event-related paradigms, account for different trial types and integrate several fMRI sessions into the estimation. These generalizations are simultaneously addressed through a badly conditioned observation model. Bayesian formalism is used to model temporal prior information of the underlying physiological process of the brain hemodynamic response. By this way, the HRF estimate results from a tradeoff between information brought by the data and by our prior knowledge. This tradeoff is modeled with hyperparameters that are set to the maximum-likelihood estimate using an expectation conditional maximization algorithm. The proposed unsupervised approach is validated on both synthetic and real fMRI data, the latter originating from a speech perception experiment.

Ordered subsets Bayesian tomographic reconstruction using 2-D smoothing splines as priors

The ordered subsets expectation maximization (OS-EM) algorithm has enjoyed considerable interest for accelerating the well-known EM algorithm for emission tomography. The OS principle has also been applied to several regularized EM algorithms, such as nonquadratic convex minimization-based maximum a posteriori (MAP) algorithms. However, most of these methods have not been as practical as OS-EM due to their complex optimization methods and difficulties in hyperparameter estimation. We note here that, by relaxing the requirement of imposing sharp edges and using instead useful quadratic spline priors, solutions are much easier to compute, and hyperparameter calculation becomes less of a problem. In this work, we use two-dimensional smoothing splines as priors and apply a method of iterated conditional modes for the optimization. In this case, step sizes or line-search algorithms necessary for gradient-based descent methods are avoided. We also accelerate the resulting algorithm using the OS approach and propose a principled way of scaling smoothing parameters to retain the strength of smoothing for different subset numbers. Our experimental results show that the OS approach applied to our quadratic MAP algorithms provides a considerable acceleration while retaining the advantages of quadratic spline priors.

Fluorescence optical diffusion tomography

A nonlinear, Bayesian optimization scheme is presented for reconstructing fluorescent yield and lifetime, the absorption coefficient, and the diffusion coefficient in turbid media, such as biological tissue. The method utilizes measurements at both the excitation and the emission wavelengths to reconstruct all unknown parameters. The effectiveness of the reconstruction algorithm is demonstrated by simulation and by application to experimental data from a tissue phantom containing the fluorescent agent Indocyanine Green.

Initial in vivo experience with steady-state subzone-based MR elastography of the human breast

PURPOSE

To describe initial in vivo experiences with a subzone-based, steady-state MR elastography (MRE) method. This sparse collection of in vivo results is intended to shed light on some of the strengths and weaknesses of existing clinical MRE approaches and to indicate important areas of future research.

MATERIALS AND METHODS

Elastic property reconstruction results are compared with data compiled from the limited existing body of published studies in breast elasticity. Mechanical parameter distributions are also investigated in terms of their implications for the nature of biological soft tissue. Additionally, a derivation of the statistical variance of the elastic parameter reconstruction is given and the resulting confidence intervals (CIs) for different parameter solutions are examined.

RESULTS

By comparison with existing estimates of the elastic properties of breast tissue, the subzone-based, steady-state MRE method is seen to produce reasonable estimates for the mechanical properties of in vivo tissue.

CONCLUSION

MRE shows potential as an effective way to determine the elastic properties of breast tissue, and may be of significant clinical interest.

Statistical regularization in linearized microwave imaging through MRF-based MAP estimation: hyperparameter estimation and image computation

The application of a Markov random fields (MRF) based maximum a posteriori (MAP) estimation method for microwave imaging is presented in this paper. The adopted MRF family is the so-called Gaussian-MRF (GMRF), whose energy function is quadratic. In order to implement the MAP estimation, first, the MRF hyperparameters are estimated by means of the expectation-maximization (EM) algorithm, extended in this case to complex and nonhomogeneous images. Then, it is implemented by minimizing a cost function whose gradient is fully analytically evaluated. Thanks to the quadratic nature of the energy function of the MRF, well posedness and efficiency of the proposed method can be simultaneously guaranteed. Numerical results, also performed on real data, show the good performance of the method, also when compared with conventional techniques like Tikhonov regularization.

Source-detector calibration in three-dimensional Bayesian optical diffusion tomography

Optical diffusion tomography is a method for reconstructing three-dimensional optical properties from light that passes through a highly scattering medium. Computing reconstructions from such data requires the solution of a nonlinear inverse problem. The situation is further complicated by the fact that while reconstruction algorithms typically assume exact knowledge of the optical source and detector coupling coefficients, these coupling coefficients are generally not available in practical measurement systems. A new method for estimating these unknown coupling coefficients in the three-dimensional reconstruction process is described. The joint problem of coefficient estimation and three-dimensional reconstruction is formulated in a Bayesian framework, and the resulting estimates are computed by using a variation of iterative coordinate descent optimization that is adapted for this problem. Simulations show that this approach is an accurate and efficient method for simultaneous reconstruction of absorption and diffusion coefficients as well as the coupling coefficients. A simple experimental result validates the approach.

Multiscale Bayesian segmentation using a trainable context model

Multiscale Bayesian approaches have attracted increasing attention for use in image segmentation. Generally, these methods tend to offer improved segmentation accuracy with reduced computational burden. Existing Bayesian segmentation methods use simple models of context designed to encourage large uniformly classified regions. Consequently, these context models have a limited ability to capture the complex contextual dependencies that are important in applications such as document segmentation. We propose a multiscale Bayesian segmentation algorithm which can effectively model complex aspects of both local and global contextual behavior. The model uses a Markov chain in scale to model the class labels that form the segmentation, but augments this Markov chain structure by incorporating tree based classifiers to model the transition probabilities between adjacent scales. The tree based classifier models complex transition rules with only a moderate number of parameters. One advantage to our segmentation algorithm is that it can be trained for specific segmentation applications by simply providing examples of images with their corresponding accurate segmentations. This makes the method flexible by allowing both the context and the image models to be adapted without modification of the basic algorithm. We illustrate the value of our approach with examples from document segmentation in which test, picture and background classes must be separated.

Parallelizable Bayesian tomography algorithms with rapid, guaranteed convergence

Bayesian tomographic reconstruction algorithms generally require the efficient optimization of a functional of many variables. In this setting, as well as in many other optimization tasks, functional substitution (FS) has been widely applied to simplify each step of the iterative process. The function to be minimized is replaced locally by an approximation having a more easily manipulated form, e.g., quadratic, but which maintains sufficient similarity to descend the true functional while computing only the substitute. We provide two new applications of FS methods in iterative coordinate descent for Bayesian tomography. The first is a modification of our coordinate descent algorithm with one-dimensional (1-D) Newton-Raphson approximations to an alternative quadratic which allows convergence to be proven easily. In simulations, we find essentially no difference in convergence speed between the two techniques. We also present a new algorithm which exploits the FS method to allow parallel updates of arbitrary sets of pixels using computations similar to iterative coordinate descent. The theoretical potential speed up of parallel implementations is nearly linear with the number of processors if communication costs are neglected.

Gradient-based iterative image reconstruction scheme for time-resolved optical tomography

Currently available tomographic image reconstruction schemes for optical tomography (OT) are mostly based on the limiting assumptions of small perturbations and a priori knowledge of the optical properties of a reference medium. Furthermore, these algorithms usually require the inversion of large, full, ill-conditioned Jacobian matrixes. In this work a gradient-based iterative image reconstruction (GIIR) method is presented that promises to overcome current limitations. The code consists of three major parts: 1) A finite-difference, time-resolved, diffusion forward model is used to predict detector readings based on the spatial distribution of optical properties; 2) An objective function that describes the difference between predicted and measured data; 3) An updating method that uses the gradient of the objective function in a line minimization scheme to provide subsequent guesses of the spatial distribution of the optical properties for the forward model. The reconstruction of these properties is completed, once a minimum of this objective function is found. After a presentation of the mathematical background, two- and three-dimensional reconstruction of simple heterogeneous media as well as the clinically relevant example of ventricular bleeding in the brain are discussed. Numerical studies suggest that intraventricular hemorrhages can be detected using the GIIR technique, even in the presence of a heterogeneous background.

Approximate maximum likelihood hyperparameter estimation for Gibbs priors

The parameters of the prior, the hyperparameters, play an important role in Bayesian image estimation. Of particular importance for the case of Gibbs priors is the global hyperparameter, beta, which multiplies the Hamiltonian. Here we consider maximum likelihood (ML) estimation of beta from incomplete data, i.e., problems in which the image, which is drawn from a Gibbs prior, is observed indirectly through some degradation or blurring process. Important applications include image restoration and image reconstruction from projections. Exact ML estimation of beta from incomplete data is intractable for most image processing. Here we present an approximate ML estimator that is computed simultaneously with a maximum a posteriori (MAP) image estimate. The algorithm is based on a mean field approximation technique through which multidimensional Gibbs distributions are approximated by a separable function equal to a product of one-dimensional (1-D) densities. We show how this approach can be used to simplify the ML estimation problem. We also show how the Gibbs-Bogoliubov-Feynman (GBF) bound can be used to optimize the approximation for a restricted class of problems. We present the results of a Monte Carlo study that examines the bias and variance of this estimator when applied to image restoration.

A unified approach to statistical tomography using coordinate descent optimization

Over the past years there has been considerable interest in statistically optimal reconstruction of cross-sectional images from tomographic data. In particular, a variety of such algorithms have been proposed for maximum a posteriori (MAP) reconstruction from emission tomographic data. While MAP estimation requires the solution of an optimization problem, most existing reconstruction algorithms take an indirect approach based on the expectation maximization (EM) algorithm. We propose a new approach to statistically optimal image reconstruction based on direct optimization of the MAP criterion. The key to this direct optimization approach is greedy pixel-wise computations known as iterative coordinate decent (ICD). We propose a novel method for computing the ICD updates, which we call ICD/Newton-Raphson. We show that ICD/Newton-Raphson requires approximately the same amount of computation per iteration as EM-based approaches, but the new method converges much more rapidly (in our experiments, typically five to ten iterations). Other advantages of the ICD/Newton-Raphson method are that it is easily applied to MAP estimation of transmission tomograms, and typical convex constraints, such as positivity, are easily incorporated.