arXiv subjects

J. Webster Stayman

Publications and source records attributed to J. Webster Stayman.

At least 19 recordsLinked to original sources

arXiv2025

CTorch: PyTorch-Compatible GPU-Accelerated Auto-Differentiable Projector Toolbox for Computed Tomography

This work introduces CTorch, a PyTorch-compatible, GPU-accelerated, and auto-differentiable projector toolbox designed to handle various CT geometries with configurable projector algorithms. CTorch provides flexible scanner geometry definition, supporting 2D fan-beam, 3D circular cone-beam, and 3D non-circular cone-beam geometries. Each geometry allows view-specific definitions to accommodate variations during scanning. Both flat- and curved-detector models may be specified to accommodate various clinical devices. CTorch implements four projector algorithms: voxel-driven, ray-driven, distance-driven (DD), and separable footprint (SF), allowing users to balance accuracy and computational efficiency based on their needs. All the projectors are primarily built using CUDA C for GPU acceleration, then compiled as Python-callable functions, and wrapped as PyTorch network module. This design allows direct use of PyTorch tensors, enabling seamless integration into PyTorch's auto-differentiation framework. These features make CTorch an flexible and efficient tool for CT imaging research, with potential applications in accurate CT simulations, efficient iterative reconstruction, and advanced deep-learning-based CT reconstruction.

physics.med-ph↗

arXiv2025

Differentiable Forward and Back-Projector for Rigid Motion Estimation in X-ray Imaging

Objective: In this work, we propose a framework for differentiable forward and back-projector that enables scalable, accurate, and memory-efficient gradient computation for rigid motion estimation tasks. Methods: Unlike existing approaches that rely on auto-differentiation or that are restricted to specific projector types, our method is based on a general analytical gradient formulation for forward/backprojection in the continuous domain. A key insight is that the gradients of both forward and back-projection can be expressed directly in terms of the forward and back-projection operations themselves, providing a unified gradient computation scheme across different projector types. Leveraging this analytical formulation, we develop a discretized implementation with an acceleration strategy that balances computational speed and memory usage. Results: Simulation studies illustrate the numerical accuracy and computational efficiency of the proposed algorithm. Experiments demonstrates the effectiveness of this approach for multiple X-ray imaging tasks we conducted. In 2D/3D registration, the proposed method achieves ~8x speedup over an existing differentiable forward projector while maintaining comparable accuracy. In motion-compensated analytical reconstruction and cone-beam CT geometry calibration, the proposed method enhances image sharpness and structural fidelity on real phantom data while showing significant efficiency advantages over existing gradient-free and gradient-based solutions. Conclusion: The proposed differentiable projectors enable effective and efficient gradient-based solutions for X-ray imaging tasks requiring rigid motion estimation.

physics.med-ph↗

arXiv2025

Volumetric Material Decomposition Using Spectral Diffusion Posterior Sampling with a Compressed Polychromatic Forward Model

We have previously introduced Spectral Diffusion Posterior Sampling (Spectral DPS) as a framework for accurate one-step material decomposition by integrating analytic spectral system models with priors learned from large datasets. This work extends the 2D Spectral DPS algorithm to 3D by addressing potentially limiting large-memory requirements with a pre-trained 2D diffusion model for slice-by-slice processing and a compressed polychromatic forward model to ensure accurate physical modeling. Simulation studies demonstrate that the proposed memory-efficient 3D Spectral DPS enables material decomposition of clinically significant volume sizes. Quantitative analysis reveals that Spectral DPS outperforms other deep-learning algorithms, such as InceptNet and conditional DDPM in contrast quantification, inter-slice continuity, and resolution preservation. This study establishes a foundation for advancing one-step material decomposition in volumetric spectral CT.

physics.med-ph↗

arXiv2024

Multi-Material Decomposition Using Spectral Diffusion Posterior Sampling

Many spectral CT applications require accurate material decomposition. Existing material decomposition algorithms are often susceptible to significant noise magnification or, in the case of one-step model-based approaches, hampered by slow convergence rates and large computational requirements. In this work, we proposed a novel framework - spectral diffusion posterior sampling (spectral DPS) - for one-step reconstruction and multi-material decomposition, which combines sophisticated prior information captured by one-time unsupervised learning and an arbitrary analytic physical system model. Spectral DPS is built upon a general DPS framework for nonlinear inverse problems. Several strategies developed in previous work, including jumpstart sampling, Jacobian approximation, and multi-step likelihood updates are applied facilitate stable and accurate decompositions. The effectiveness of spectral DPS was evaluated on a simulated dual-layer and a kV-switching spectral system as well as on a physical cone-beam CT (CBCT) test bench. In simulation studies, spectral DPS improved PSNR by 27.49% to 71.93% over baseline DPS and by 26.53% to 57.30% over MBMD, depending on the the region of interest. In physical phantom study, spectral DPS achieved a <1% error in estimating the mean density in a homogeneous region. Compared with baseline DPS, spectral DPS effectively avoided generating false structures in the homogeneous phantom and reduced the variability around edges. Both simulation and physical phantom studies demonstrated the superior performance of spectral DPS for stable and accurate material decomposition.

physics.med-ph↗

arXiv2024

Deep Learning CT Image Restoration using System Blur and Noise Models

The restoration of images affected by blur and noise has been widely studied and has broad potential for applications including in medical imaging modalities like computed tomography (CT). Although the blur and noise in CT images can be attributed to a variety of system factors, these image properties can often be modeled and predicted accurately and used in classical restoration approaches for deconvolution and denoising. In classical approaches, simultaneous deconvolution and denoising can be challenging and often represent competing goals. Recently, deep learning approaches have demonstrated the potential to enhance image quality beyond classic limits; however, most deep learning models attempt a blind restoration problem and base their restoration on image inputs alone without direct knowledge of the image noise and blur properties. In this work, we present a method that leverages both degraded image inputs and a characterization of the system blur and noise to combine modeling and deep learning approaches. Different methods to integrate these auxiliary inputs are presented. Namely, an input-variant and a weight-variant approach wherein the auxiliary inputs are incorporated as a parameter vector before and after the convolutional block, respectively, allowing easy integration into any CNN architecture. The proposed model shows superior performance compared to baseline models lacking auxiliary inputs. Evaluations are based on the average Peak Signal-to-Noise Ratio (PSNR), selected examples of good and poor performance for varying approaches, and an input space analysis to assess the effect of different noise and blur on performance. Results demonstrate the efficacy of providing a deep learning model with auxiliary inputs, representing system blur and noise characteristics, to enhance the performance of the model in image restoration tasks.

physics.med-ph↗

arXiv2024

Strategies for CT Reconstruction using Diffusion Posterior Sampling with a Nonlinear Model

Diffusion Posterior Sampling(DPS) methodology is a novel framework that permits nonlinear CT reconstruction by integrating a diffusion prior and an analytic physical system model, allowing for one-time training for different applications. However, baseline DPS can struggle with large variability, hallucinations, and slow reconstruction. This work introduces a number of strategies designed to enhance the stability and efficiency of DPS CT reconstruction. Specifically, jumpstart sampling allows one to skip many reverse time steps, significantly reducing the reconstruction time as well as the sampling variability. Additionally, the likelihood update is modified to simplify the Jacobian computation and improve data consistency more efficiently. Finally, a hyperparameter sweep is conducted to investigate the effects of parameter tuning and to optimize the overall reconstruction performance. Simulation studies demonstrated that the proposed DPS technique achieves up to 46.72% PSNR and 51.50% SSIM enhancement in a low-mAs setting, and an over 31.43% variability reduction in a sparse-view setting. Moreover, reconstruction time is sped up from >23.5 s/slice to <1.5 s/slice. In a physical data study, the proposed DPS exhibits robustness on an anthropomorphic phantom reconstruction which does not strictly follow the prior distribution. Quantitative analysis demonstrates that the proposed DPS can accommodate various dose levels and number of views. With 10% dose, only a 5.60% and 4.84% reduction of PSNR and SSIM was observed for the proposed approach. Both simulation and phantom studies demonstrate that the proposed method can significantly improve reconstruction accuracy and reduce computational costs, greatly enhancing the practicality of DPS CT reconstruction.

eess.IV↗

arXiv2024

CT Reconstruction using Diffusion Posterior Sampling conditioned on a Nonlinear Measurement Model

Diffusion models have been demonstrated as powerful deep learning tools for image generation in CT reconstruction and restoration. Recently, diffusion posterior sampling, where a score-based diffusion prior is combined with a likelihood model, has been used to produce high quality CT images given low-quality measurements. This technique is attractive since it permits a one-time, unsupervised training of a CT prior; which can then be incorporated with an arbitrary data model. However, current methods rely on a linear model of x-ray CT physics to reconstruct or restore images. While it is common to linearize the transmission tomography reconstruction problem, this is an approximation to the true and inherently nonlinear forward model. We propose a new method that solves the inverse problem of nonlinear CT image reconstruction via diffusion posterior sampling. We implement a traditional unconditional diffusion model by training a prior score function estimator, and apply Bayes rule to combine this prior with a measurement likelihood score function derived from the nonlinear physical model to arrive at a posterior score function that can be used to sample the reverse-time diffusion process. This plug-and-play method allows incorporation of a diffusion-based prior with generalized nonlinear CT image reconstruction into multiple CT system designs with different forward models, without the need for any additional training. We develop the algorithm that performs this reconstruction, including an ordered-subsets variant for accelerated processing and demonstrate the technique in both fully sampled low dose data and sparse-view geometries using a single unsupervised training of the prior.

physics.med-ph↗

arXiv2024

CT Material Decomposition using Spectral Diffusion Posterior Sampling

In this work, we introduce a new deep learning approach based on diffusion posterior sampling (DPS) to perform material decomposition from spectral CT measurements. This approach combines sophisticated prior knowledge from unsupervised training with a rigorous physical model of the measurements. A faster and more stable variant is proposed that uses a jumpstarted process to reduce the number of time steps required in the reverse process and a gradient approximation to reduce the computational cost. Performance is investigated for two spectral CT systems: dual-kVp and dual-layer detector CT. On both systems, DPS achieves high Structure Similarity Index Metric Measure(SSIM) with only 10% of iterations as used in the model-based material decomposition(MBMD). Jumpstarted DPS (JSDPS) further reduces computational time by over 85% and achieves the highest accuracy, the lowest uncertainty, and the lowest computational costs compared to classic DPS and MBMD. The results demonstrate the potential of JSDPS for providing relatively fast and accurate material decomposition based on spectral CT data.

eess.IV↗

arXiv2023

How to Trust Your Diffusion Model: A Convex Optimization Approach to Conformal Risk Control

Score-based generative modeling, informally referred to as diffusion models, continue to grow in popularity across several important domains and tasks. While they provide high-quality and diverse samples from empirical distributions, important questions remain on the reliability and trustworthiness of these sampling procedures for their responsible use in critical scenarios. Conformal prediction is a modern tool to construct finite-sample, distribution-free uncertainty guarantees for any black-box predictor. In this work, we focus on image-to-image regression tasks and we present a generalization of the Risk-Controlling Prediction Sets (RCPS) procedure, that we term $K$-RCPS, which allows to $(i)$ provide entrywise calibrated intervals for future samples of any diffusion model, and $(ii)$ control a certain notion of risk with respect to a ground truth image with minimal mean interval length. Differently from existing conformal risk control procedures, ours relies on a novel convex optimization approach that allows for multidimensional risk control while provably minimizing the mean interval length. We illustrate our approach on two real-world image denoising problems: on natural images of faces as well as on computed tomography (CT) scans of the abdomen, demonstrating state of the art performance.

stat.ML↗

arXiv2023

A Joint Processing Strategy for Image Quality Improvement in 3D Digital Subtraction Angiography

Three-dimensional digital subtraction angiography (3D-DSA) is a widely adopted technique for clinical evaluation of contrast-enhanced vasculatures. The distribution of a contrast agent such as iodine is often estimated via temporal subtraction. Advancements in spectral imaging technologies such as photon counting detectors offer new opportunities to improve DSA image quality. In this work, we propose a novel joint processing strategy to achieve an iodine image using two-bin spectral measurements from a photon counting detector acquired both the pre- and post-contrast injection. Simulation studies were performed using a digital phantom with iodine-enhanced vessels. The proposed method was compared with temporal subtraction and conventional spectral imaging using just the post-contrast measurements. Imaging performance was evaluated in terms of noise-resolution tradeoffs. Preliminary findings have shown measurably improved image quality given by joint processing, reducing noise by 40% and 70% compared to temporal subtraction and conventional spectral imaging, respectively.

physics.med-ph↗

arXiv2023

Fourier Diffusion Models: A Method to Control MTF and NPS in Score-Based Stochastic Image Generation

Score-based stochastic denoising models have recently been demonstrated as powerful machine learning tools for conditional and unconditional image generation. The existing methods are based on a forward stochastic process wherein the training images are scaled to zero over time and white noise is gradually added such that the final time step is approximately zero-mean identity-covariance Gaussian noise. A neural network is then trained to approximate the time-dependent score function, or the gradient of the logarithm of the probability density, for that time step. Using this score estimator, it is possible to run an approximation of the time-reversed stochastic process to sample new images from the training data distribution. These score-based generative models have been shown to out-perform generative adversarial neural networks using standard benchmarks and metrics. However, one issue with this approach is that it requires a large number of forward passes of the neural network. Additionally, the images at intermediate time steps are not useful, since the signal-to-noise ratio is low. In this work we present a new method called Fourier Diffusion Models which replaces the scalar operations of the forward process with shift-invariant convolutions and the additive white noise with additive stationary noise. This allows for control of MTF and NPS at intermediate time steps. Additionally, the forward process can be crafted to converge to the same MTF and NPS as the measured images. This way, we can model continuous probability flow from true images to measurements. In this way, the sample time can be used to control the tradeoffs between measurement uncertainty and generative uncertainty of posterior estimates. We compare Fourier diffusion models to existing scalar diffusion models and show that they achieve a higher level of performance and allow for a smaller number of time steps.

physics.med-ph↗

arXiv2021

High-Sensitivity Iodine Imaging by Combining Spectral CT Technologies

Spectral CT offers enhanced material discrimination over single-energy systems and enables quantitative estimation of basis material density images. Water/iodine decomposition in contrast-enhanced CT is one of the most widespread applications of this technology in the clinic. However, low concentrations of iodine can be difficult to estimate accurately, limiting potential clinical applications and/or raising injected contrast agent requirements. We seek high-sensitivity spectral CT system designs which minimize noise in water/iodine density estimates. In this work, we present a model-driven framework for spectral CT system design optimization to maximize material separability. We apply this tool to optimize the sensitivity spectra on a spectral CT test bench using a hybrid design which combines source kVp control and k-edge filtration. Following design optimization, we scanned a water/iodine phantom with the hybrid spectral CT system and performed dose-normalized comparisons to two single-technique designs which use only kVp control or only kedge filtration. The material decomposition results show that the hybrid system reduces both standard deviation and crossmaterial noise correlations compared to the designs where the constituent technologies are used individually.

physics.med-ph↗

arXiv2020

Manifold Reconstruction of Differences: A Model-Based Iterative Statistical Estimation Algorithm with a Data-Driven Prior

Manifold learning using deep neural networks been shown to be an effective tool for building sophisticated prior image models that can be applied to noise reduction in low-dose CT. We propose a new iterative CT reconstruction algorithm, called Manifold Reconstruction of Differences (MRoD), which combines physical and statistical models with a data-driven prior based on manifold learning. The MRoD algorithm involves estimating a manifold component, approximating common features among all patients, and the difference component which has the freedom to fit the measured data. By applying a sparsity-promoting penalty to the difference image rather than a hard constraint to the manifold, the MRoD algorithm is able to reconstruct features which are not present in the training data. The difference component itself may be independently useful. While the manifold captures typical patient features (e.g. healthy anatomy), the difference image highlights patient-specific elements (e.g. pathology). In this work, we present a description of an optimization framework which combines trained manifold-based modules with physical modules. We present a simulation study using anthropomorphic lung data showing that the MRoD algorithm can both isolate differences between a particular patient and the typical distribution, but also provide significant noise reduction with less bias than a typical penalized likelihood estimator in composite manifold plus difference reconstructions.

physics.med-ph↗

arXiv2020

Design of Spatial-Spectral Filters for CT Material Decomposition

Spectral CT has shown promise for high-sensitivity quantitative imaging and material decomposition. This work presents a new device called a spatial-spectral filter (SSF) which consists of a tiled array of filter materials positioned near the x-ray source that is used to modulate the spectral shape of the x-ray beam. The filter is moved to obtain projection data that is sparse in each spectral channel. To process this sparse data, we employ a direct model-based material decomposition (MBMD)to reconstruct basis material density images directly from the SSF CT data. To evaluate different possible SSF designs, we define a new Fisher-information-based predictive image quality metric called separability index which characterizes the ability of a spectral CT system to distinguish between the signals from two or more materials. This predictive metric is used to define a system design optimization framework. We have applied this framework to find optimized combinations of filter materials, filter tile widths, and source settings for SSF CT. We conducted simulation-based design optimization study and separability-optimized filter designs are presented for water/iodine imaging and water/iodine/gadolinium/gold imaging for different patient sizes. Finally, we present MBMD results using simulated SSFCT data using the optimized designs to demonstrate the ability to reconstruct basis material density images and to show the benefits of the optimized designs.

physics.med-ph↗

arXiv2020

Multi-Contrast CT Imaging with a Prototype Spatial-Spectral Filter

Spectral CT has great potential for a variety of clinical applications due to the improved material discrimination with respect to conventional CT. Many clinical and preclinical spectral CT systems have two spectral channels for dual-energy CT using strategies such as split-filtration, dual-layer detectors, or kVp-switching. However, there are emerging clinical imaging applications which would require three or more spectral sensitivity channels, for example, multiple exogenous contrast agents in a single scan. Spatial-spectral filters are a new spectral CT technology which use x-ray beam modulation to offer greater spectral diversity. The device consists of an array of k-edge filters which divide the x-ray beam into spectrally varied beamlets. This design allows for an arbitrary number of spectral channels; however, traditional two-step reconstruction-decomposition schemes are typically not effective because the measured data for any individual spectral channel is sparse in the projection domain. Instead, we use a one-step model-based material decomposition algorithm to iteratively estimate material density images directly from spectral CT data. In this work, we present a prototype spatial-spectral filter integrated with an x-ray CT test-bench. The filter is composed of an array of tin, erbium, tantalum, and lead filter tiles which spatially modulate the system spectral sensitivity pattern. After the system was characterized and modeled, we conducted a spectral CT scan of a multi-contrast-enhanced phantom containing water, iodine, and gadolinium solutions. We present the resulting spectral CT data as well as the material density images estimated by model-based material decomposition...

physics.med-ph↗

arXiv2020

Optimized Spatial-Spectral CT for Multi-Material Decomposition

Spectral CT is an emerging modality that uses a data acquisition scheme with varied spectral responses to provide enhanced material discrimination in addition to the structural information of conventional CT. Existing clinical and preclinical designs with this capability include kV-switching, split-filtration, and dual-layer detector systems to provide two spectral channels of projection data. In this work, we examine an alternate design based on a spatial-spectral filter. This source-side filter is made up a linear array of materials that divide the incident x-ray beam into spectrally varied beamlets. This design allows for any number of spectral channels; however, each individual channel is sparse in the projection domain. Model-based iterative reconstruction methods can accommodate such sparse spatial-spectral sampling patterns and allow for the incorporation of advanced regularization. With the goal of an optimized physical design, we characterize the effects of design parameters including filter tile order and filter tile width and their impact on material decomposition performance. We present results of numerical simulations that characterize the impact of each design parameter using a realistic CT geometry and noise model to demonstrate feasibility. Results for filter tile order show little change indicating that filter order is a low-priority design consideration. We observe improved performance for narrower filter widths; however, the performance drop-off is relatively flat indicating that wider filter widths are also feasible designs.

physics.med-ph↗

arXiv2020

Combining Spectral CT Acquisition Methods for High-Sensitivity Material Decomposition

Quantitative estimation of contrast agent concentration is made possible by spectral CT and material decomposition. There are several approaches to modulate the sensitivity of the imaging system to obtain the different spectral channels required for decomposition. Spectral CT technologies that enable this varied sensitivity include source kV-switching, dual-layer detectors, and source-side filtering (e.g., tiled spatial-spectral filters). In this work, we use an advanced physical model to simulate these three spectral CT strategies as well as hybrid acquisitions using all combinations of two or three strategies. We apply model-based material decomposition to a water-iodine phantom with iodine concentrations from 0.1 to 5.0 mg/mL. We present bias-noise plots for the different combinations of spectral techniques and show that combined approaches permit diversity in spectral sensitivity and improve low concentration imaging performance relative to the those strategies applied individually. Better ability to estimate low concentrations of contrast agent has the potential to reduce risks associated with contrast administration (by lowering dosage) or to extend imaging applications into targets with much lower uptake.

physics.med-ph↗

arXiv2020

A Preconditioned Algorithm for Model-Based Iterative CT Reconstruction and Material Decomposition from Spectral CT Data

Model-based material decomposition is a statisticaliterative reconstruction framework where basis material densityimages are estimated directly from spectral CT data. This methoduses a physical model for polyenergetic x-ray transmission andattenuation and therefore it does not typically suffer frombeam-hardening artifacts. However, this estimation is a poorly-conditioned inverse problem due to the strong anticorrelationbetween basis materials. In this work we propose an precondi-tioned optimization algorithm for a nonlinear penalized weightedleast-squares objective function.

physics.med-ph↗