arXiv subjects

Siyuan Mei

Publications and source records attributed to Siyuan Mei.

At least 19 recordsLinked to original sources

arXiv2026

Robustness and Stability Analysis of Differentiable Shift-Variant FBP for Cone-Beam CT under Challenging Acquisition Settings

The differentiable shift-variant filtered backprojection (SV-FBP) framework enables data-driven estimation of redundancy weights for cone-beam CT reconstruction under general source trajectories, removing the need for analytically derived weighting schemes. In this work, we present a systematic study of the robustness and adaptability of differentiable SV-FBP under challenging acquisition settings. We show that the framework remains stable across highly irregular and discontinuous trajectories, indicating that reconstruction performance is largely insensitive to trajectory ordering or continuity. Instead, the spatial distribution of sampling points plays a more dominant role. Under sparse-view conditions, differentiable SV-FBP achieves competitive reconstruction quality while providing an order-of-magnitude reduction in computation time compared to iterative reconstruction methods at moderate sampling densities. However, we identify a clear transition regime under severe undersampling, where the absence of iterative data consistency leads to performance degradation. Furthermore, we demonstrate that the framework remains applicable to non-planar multi-isocenter geometries, such as Lissajous-saddle trajectories, without requiring architectural modifications. These findings provide new insights into the behavior and limitations of the differentiable SV-FBP model and highlight it as a flexible and efficient solution for non-standard and robotic CBCT acquisition scenarios.

eess.IV↗

arXiv2026

WING: A Window-Prior-Based Generative Network with Gated Inception for Cross-Modality CT Synthesis

Generating CT volumes from MRI and CBCT can improve treatment planning in adaptive radiotherapy while avoiding additional radiation exposure. However, direct regression of CT intensities is challenged by the inherently high dynamic range and long-tailed distributions, thereby averaging out sparse yet clinically important structures. To alleviate this issue, we reformulate the regression target into multiple windowed representations, leveraging the inductive prior that CT intensities are structure-deterministic and window-separable. These windowed views exhibit smoother distributions and admit structured fusion back to the full-range CT. Building on this reformulation, we introduce WING, a WINdow-prior-based Generative network comprising: 1) a new Gated Inception Generator to produce multi-window predictions, enabling multi-shape kernel interactions to capture cross-modality correspondence; 2) a Fuse-and-Refine Transformer to aggregate the windowed outputs and learn residuals for detail refinement; and 3) a joint adversarial training objective to enhance window-conditioned realism. Extensive experiments demonstrate that our compact WING achieves state-of-the-art performance on the MRI-to-CT and CBCT-to-CT benchmarks, while supporting multi-anatomy synthesis with a single model.

cs.CV↗

arXiv2026

Detail Consistent Stage-Wise Distillation for Efficient 3D MRI Segmentation

Deploying high-performing 3D medical image segmenters (e.g., nnU-Net) is often limited by memory footprint and inference latency. Compression is therefore necessary, but compact 3D encoders tend to lose fine structural cues (small lesions and sharp boundaries) as downsampling repeats across multi-resolution stages. We propose Detail Consistent Distillation (DCD), a stage-wise distillation framework that preserves structural detail across scales by aligning teacher-student features in a wavelet-decomposed representation. At each encoder stage, DCD distills directional detail components in the wavelet domain while leaving the coarse approximation comparatively unconstrained, avoiding over-regularization of global semantics. DCD is used only during training and introduces no inference-time overhead. Experiments on the BraTS 2024 and ISLES 2022 benchmarks demonstrate that our approach achieves superior performance in MRI segmentation using 3D multi-modal data. Code and implementation details for DCD are publicly available at https://github.com/ClinicaAlpha/DCD-3D-MedSeg.

cs.CV↗

arXiv2026

Speech-Guided Multimodal Learning for Vocal Tract Segmentation in Real-Time MRI

Segmenting vocal tract articulators in real-time MRI (rtMRI) is a challenging dynamic image segmentation problem characterized by low contrast, rapid motion, and limited spatial resolution. However, while rtMRI acquisitions may provide synchronized acoustic signals, existing methods discard this information, and the few multimodal approaches that incorporate audio cannot be deployed when audio is unavailable. We propose a three-stage framework that leverages acoustic and phonological supervision during training while requiring only the rtMRI image at inference: phonological representations are converted into spatial bounding-box priors for articulator localization, visual and acoustic encoders are aligned via dual-level cross-modal contrastive pretraining, and the learned representations are fused through a cross-attention decoder, effectively transferring multimodal knowledge into a single-modality inference pipeline. Evaluated on 75-Speaker~Annot-16 and USC-TIMIT datasets, our method outperforms existing unimodal and multimodal methods, demonstrating that multimodal supervision provides transferable benefits for precise and clinically deployable vocal tract segmentation.

cs.CV↗

arXiv2026

Generating synthetic computed tomography for radiotherapy: SynthRAD2025 challenge report

Radiation therapy (RT) requires precise dose delivery over multiple fractions, with CT fundamental for treatment planning due to its electron density information. Repeated CT acquisitions impose radiation exposure and logistical burdens, MRI lacks electron density, and cone-beam CT (CBCT) requires correction for dose calculation. Synthetic CT (sCT) generation addresses these by converting MRI or CBCT into CT-equivalent images with accurate Hounsfield Unit (HU) values, enabling MRI-only RT and CBCT-based adaptive workflows. Building on SynthRAD2023, SynthRAD2025 benchmarked sCT methods on 2,362 patients from five European centers across head and neck, thorax, and abdomen. Two tasks: MRI-to-CT (890 cases) and CBCT-to-CT (1,472 cases), evaluated via image similarity (MAE, PSNR, MS-SSIM), segmentation (Dice, HD95), and dosimetric metrics from photon and proton plans. With 803 participants and 12/13 valid submissions, Task 1 top performance reached MAE $64.8\pm21.3$ HU, PSNR $\sim$30 dB, MS-SSIM $\sim$0.936, Dice 0.79, photon $\gamma_{2\%/2\text{mm}}>98\%$, proton $\gamma\approx85\%$. Task 2 improved: MAE $48.3\pm13.4$ HU, PSNR 32.6 dB, MS-SSIM 0.968, Dice 0.86, photon $\gamma>99\%$, proton $\gamma\approx89\%$. Strong image--segmentation correlations ($\rho=0.78$--$0.79$) but moderate dose correlations confirmed image quality is insufficient as a dosimetric surrogate. Head-and-neck cases were most consistent; thoracic and abdominal cases showed greater variability. Residual errors at tissue interfaces propagate along beam paths, affecting proton dose more than photon. SynthRAD2025 demonstrates that deep learning yields clinically relevant sCTs, especially for CBCT-to-CT, while identifying persistent MRI-to-CT challenges and underscoring dose-based evaluation as essential for clinical validation.

physics.med-ph↗

arXiv2026

Generative Drifting for Conditional Medical Image Generation

Conditional medical image generation plays an important role in many clinically relevant imaging tasks. However, existing methods still face a fundamental challenge in balancing inference efficiency, patient-specific fidelity, and distribution-level plausibility, particularly in high-dimensional 3D medical imaging. In this work, we propose GDM, a generative drifting framework that reformulates deterministic medical image prediction as a multi-objective learning problem to jointly promote distribution-level plausibility and patient-specific fidelity while retaining one-step inference. GDM extends drifting to 3D medical imaging through an attractive-repulsive drift that minimizes the discrepancy between the generator pushforward and the target distribution. To enable stable drifting-based learning in 3D volumetric data, GDM constructs a multi-level feature bank from a medical foundation encoder to support reliable affinity estimation and drifting field computation across complementary global, local, and spatial representations. In addition, a gradient coordination strategy in the shared output space improves optimization balance under competing distribution-level and fidelity-oriented objectives. We evaluate the proposed framework on two representative tasks, MRI-to-CT synthesis and sparse-view CT reconstruction. Experimental results show that GDM consistently outperforms a wide range of baselines, including GAN-based, flow-matching-based, and SDE-based generative models, as well as supervised regression methods, while improving the balance among anatomical fidelity, quantitative reliability, perceptual realism, and inference efficiency. These findings suggest that GDM provides a practical and effective framework for conditional 3D medical image generation.

cs.CV↗

arXiv2025

GANeXt: A Fully ConvNeXt-Enhanced Generative Adversarial Network for MRI- and CBCT-to-CT Synthesis

The synthesis of computed tomography (CT) from magnetic resonance imaging (MRI) and cone-beam CT (CBCT) plays a critical role in clinical treatment planning by enabling accurate anatomical representation in adaptive radiotherapy. In this work, we propose GANeXt, a 3D patch-based, fully ConvNeXt-powered generative adversarial network for unified CT synthesis across different modalities and anatomical regions. Specifically, GANeXt employs an efficient U-shaped generator constructed from stacked 3D ConvNeXt blocks with compact convolution kernels, while the discriminator adopts a conditional PatchGAN. To improve synthesis quality, we incorporate a combination of loss functions, including mean absolute error (MAE), perceptual loss, segmentation-based masked MAE, and adversarial loss and a combination of Dice loss and cross-entropy for multi-head segmentation discriminator. For both tasks, training is performed with a batch size of 8 using two separate AdamW optimizers for the generator and discriminator, each equipped with a warmup and cosine decay scheduler, with learning rates of $5\times10^{-4}$ and $1\times10^{-3}$, respectively. Data preprocessing includes deformable registration, foreground cropping, percentile normalization for the input modality, and linear normalization of the CT to the range $[-1024, 1000]$. Data augmentation involves random zooming within $(0.8, 1.3)$ (for MRI-to-CT only), fixed-size cropping to $32\times160\times192$ for MRI-to-CT and $32\times128\times128$ for CBCT-to-CT, and random flipping. During inference, we apply a sliding-window approach with $0.8$ overlap and average folding to reconstruct the full-size sCT, followed by inversion of the CT normalization. After joint training on all regions without any fine-tuning, the final models are selected at the end of 3000 epochs for MRI-to-CT and 1000 epochs for CBCT-to-CT using the full training dataset.

cs.CV↗

arXiv2025

BigReg: An Efficient Registration Pipeline for High-Resolution X-Ray and Light-Sheet Fluorescence Microscopy

Recently, X-ray microscopy (XRM) and light-sheet fluorescence microscopy (LSFM) have emerged as pivotal tools in preclinical research, particularly for studying bone remodeling diseases such as osteoporosis. These modalities offer micrometer-level resolution, and their integration allows for a complementary examination of bone microstructures which is essential for analyzing functional changes. However, registering high-resolution volumes from these independently scanned modalities poses substantial challenges, especially in real-world and reference-free scenarios. This paper presents BigReg, a fast, two-stage pipeline designed for large-volume registration of XRM and LSFM data. The first stage involves extracting surface features and applying two successive point cloud-based methods for coarse alignment. The subsequent stage refines this alignment using a modified cross-correlation technique, achieving precise volumetric registration. Evaluations using expert-annotated landmarks and augmented test data demonstrate that BigReg approaches the accuracy of landmark-based registration with a landmark distance (LMD) of 8.36\,\textmu m\,$\pm$\,0.12\,\textmu m and a landmark fitness (LM fitness) of 85.71\%\,$\pm$\,1.02\%. Moreover, BigReg can provide an optimal initialization for mutual information-based methods which otherwise fail independently, further reducing LMD to 7.24\,\textmu m\,$\pm$\,0.11\,\textmu m and increasing LM fitness to 93.90\%\,$\pm$\,0.77\%. Ultimately, key microstructures, notably lacunae in XRM and bone cells in LSFM, are accurately aligned, enabling unprecedented insights into the pathology of osteoporosis.

cs.CV↗

arXiv2025

Learning Wavelet-Sparse FDK for 3D Cone-Beam CT Reconstruction

Cone-Beam Computed Tomography (CBCT) is essential in medical imaging, and the Feldkamp-Davis-Kress (FDK) algorithm is a popular choice for reconstruction due to its efficiency. However, FDK is susceptible to noise and artifacts. While recent deep learning methods offer improved image quality, they often increase computational complexity and lack the interpretability of traditional methods. In this paper, we introduce an enhanced FDK-based neural network that maintains the classical algorithm's interpretability by selectively integrating trainable elements into the cosine weighting and filtering stages. Recognizing the challenge of a large parameter space inherent in 3D CBCT data, we leverage wavelet transformations to create sparse representations of the cosine weights and filters. This strategic sparsification reduces the parameter count by $93.75\%$ without compromising performance, accelerates convergence, and importantly, maintains the inference computational cost equivalent to the classical FDK algorithm. Our method not only ensures volumetric consistency and boosts robustness to noise, but is also designed for straightforward integration into existing CT reconstruction pipelines. This presents a pragmatic enhancement that can benefit clinical applications, particularly in environments with computational limitations.

eess.IV↗

arXiv2025

Filter2Noise: A Framework for Interpretable and Zero-Shot Low-Dose CT Image Denoising

Noise in low-dose computed tomography (LDCT) can obscure important diagnostic details. While deep learning offers powerful denoising, supervised methods require impractical paired data, and self-supervised alternatives often use opaque, parameter-heavy networks that limit clinical trust. We propose Filter2Noise (F2N), a novel self-supervised framework for interpretable, zero-shot denoising from a single LDCT image. Instead of a black-box network, its core is an Attention-Guided Bilateral Filter, a transparent, content-aware mathematical operator. A lightweight attention module predicts spatially varying filter parameters, making the process transparent and allowing interactive radiologist control. To learn from a single image with correlated noise, we introduce a multi-scale self-supervised loss coupled with Euclidean Local Shuffle (ELS) to disrupt noise patterns while preserving anatomical integrity. On the Mayo Clinic LDCT Challenge, F2N achieves state-of-the-art results, outperforming competing zero-shot methods by up to 3.68 dB in PSNR. It accomplishes this with only 3.6k parameters, orders of magnitude fewer than competing models, which accelerates inference and simplifies deployment. By combining high performance with transparency, user control, and high parameter efficiency, F2N offers a trustworthy solution for LDCT enhancement. We further demonstrate its applicability by validating it on clinical photon-counting CT data. Code is available at: https://github.com/sypsyp97/Filter2Noise.

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arXiv2024

Data-Driven Filter Design in FBP: Transforming CT Reconstruction with Trainable Fourier Series

In this study, we introduce a Fourier series-based trainable filter for computed tomography (CT) reconstruction within the filtered backprojection (FBP) framework. This method overcomes the limitation in noise reduction by optimizing Fourier series coefficients to construct the filter, maintaining computational efficiency with minimal increment for the trainable parameters compared to other deep learning frameworks. Additionally, we propose Gaussian edge-enhanced (GEE) loss function that prioritizes the $L_1$ norm of high-frequency magnitudes, effectively countering the blurring problems prevalent in mean squared error (MSE) approaches. The model's foundation in the FBP algorithm ensures excellent interpretability, as it relies on a data-driven filter with all other parameters derived through rigorous mathematical procedures. Designed as a plug-and-play solution, our Fourier series-based filter can be easily integrated into existing CT reconstruction models, making it an adaptable tool for a wide range of practical applications. Code and data are available at https://github.com/sypsyp97/Trainable-Fourier-Series.

eess.IV↗

arXiv2024

A gradient-based approach to fast and accurate head motion compensation in cone-beam CT

Cone-beam computed tomography (CBCT) systems, with their flexibility, present a promising avenue for direct point-of-care medical imaging, particularly in critical scenarios such as acute stroke assessment. However, the integration of CBCT into clinical workflows faces challenges, primarily linked to long scan duration resulting in patient motion during scanning and leading to image quality degradation in the reconstructed volumes. This paper introduces a novel approach to CBCT motion estimation using a gradient-based optimization algorithm, which leverages generalized derivatives of the backprojection operator for cone-beam CT geometries. Building on that, a fully differentiable target function is formulated which grades the quality of the current motion estimate in reconstruction space. We drastically accelerate motion estimation yielding a 19-fold speed-up compared to existing methods. Additionally, we investigate the architecture of networks used for quality metric regression and propose predicting voxel-wise quality maps, favoring autoencoder-like architectures over contracting ones. This modification improves gradient flow, leading to more accurate motion estimation. The presented method is evaluated through realistic experiments on head anatomy. It achieves a reduction in reprojection error from an initial average of 3mm to 0.61mm after motion compensation and consistently demonstrates superior performance compared to existing approaches. The analytic Jacobian for the backprojection operation, which is at the core of the proposed method, is made publicly available. In summary, this paper contributes to the advancement of CBCT integration into clinical workflows by proposing a robust motion estimation approach that enhances efficiency and accuracy, addressing critical challenges in time-sensitive scenarios.

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arXiv2024

DRACO: Differentiable Reconstruction for Arbitrary CBCT Orbits

This paper introduces a novel method for reconstructing cone beam computed tomography (CBCT) images for arbitrary orbits using a differentiable shift-variant filtered backprojection (FBP) neural network. Traditional CBCT reconstruction methods for arbitrary orbits, like iterative reconstruction algorithms, are computationally expensive and memory-intensive. The proposed method addresses these challenges by employing a shift-variant FBP algorithm optimized for arbitrary trajectories through a deep learning approach that adapts to a specific orbit geometry. This approach overcomes the limitations of existing techniques by integrating known operators into the learning model, minimizing the number of parameters, and improving the interpretability of the model. The proposed method is a significant advancement in interventional medical imaging, particularly for robotic C-arm CT systems, enabling faster and more accurate CBCT reconstructions with customized orbits. Especially this method can also be used for the analytical reconstruction of non-continuous orbits like circular plus arc. The experimental results demonstrate that the proposed method significantly accelerates the reconstruction process compared to conventional iterative algorithms. It achieves comparable or superior image quality, as evidenced by metrics such as the mean squared error (MSE), the peak signal-to-noise ratio (PSNR), and the structural similarity index measure (SSIM). The validation experiments show that the method can handle data from different trajectories, demonstrating its flexibility and robustness across different scan geometries. Our method demonstrates a significant improvement, particularly for the sinusoidal trajectory, achieving a 38.6% reduction in MSE, a 7.7% increase in PSNR, and a 5.0% improvement in SSIM. Furthermore, the computation time for reconstruction was reduced by more than 97%.

cs.CV↗

arXiv2024

On the Influence of Smoothness Constraints in Computed Tomography Motion Compensation

Computed tomography (CT) relies on precise patient immobilization during image acquisition. Nevertheless, motion artifacts in the reconstructed images can persist. Motion compensation methods aim to correct such artifacts post-acquisition, often incorporating temporal smoothness constraints on the estimated motion patterns. This study analyzes the influence of a spline-based motion model within an existing rigid motion compensation algorithm for cone-beam CT on the recoverable motion frequencies. Results demonstrate that the choice of motion model crucially influences recoverable frequencies. The optimization-based motion compensation algorithm is able to accurately fit the spline nodes for frequencies almost up to the node-dependent theoretical limit according to the Nyquist-Shannon theorem. Notably, a higher node count does not compromise reconstruction performance for slow motion patterns, but can extend the range of recoverable high frequencies for the investigated algorithm. Eventually, the optimal motion model is dependent on the imaged anatomy, clinical use case, and scanning protocol and should be tailored carefully to the expected motion frequency spectrum to ensure accurate motion compensation.

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arXiv2024

Differentiable Score-Based Likelihoods: Learning CT Motion Compensation From Clean Images

Motion artifacts can compromise the diagnostic value of computed tomography (CT) images. Motion correction approaches require a per-scan estimation of patient-specific motion patterns. In this work, we train a score-based model to act as a probability density estimator for clean head CT images. Given the trained model, we quantify the deviation of a given motion-affected CT image from the ideal distribution through likelihood computation. We demonstrate that the likelihood can be utilized as a surrogate metric for motion artifact severity in the CT image facilitating the application of an iterative, gradient-based motion compensation algorithm. By optimizing the underlying motion parameters to maximize likelihood, our method effectively reduces motion artifacts, bringing the image closer to the distribution of motion-free scans. Our approach achieves comparable performance to state-of-the-art methods while eliminating the need for a representative data set of motion-affected samples. This is particularly advantageous in real-world applications, where patient motion patterns may exhibit unforeseen variability, ensuring robustness without implicit assumptions about recoverable motion types.

cs.CV↗

arXiv2024

Segmentation-Guided Knee Radiograph Generation using Conditional Diffusion Models

Deep learning-based medical image processing algorithms require representative data during development. In particular, surgical data might be difficult to obtain, and high-quality public datasets are limited. To overcome this limitation and augment datasets, a widely adopted solution is the generation of synthetic images. In this work, we employ conditional diffusion models to generate knee radiographs from contour and bone segmentations. Remarkably, two distinct strategies are presented by incorporating the segmentation as a condition into the sampling and training process, namely, conditional sampling and conditional training. The results demonstrate that both methods can generate realistic images while adhering to the conditioning segmentation. The conditional training method outperforms the conditional sampling method and the conventional U-Net.

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arXiv2024

Analysing Diffusion Segmentation for Medical Images

Denoising Diffusion Probabilistic models have become increasingly popular due to their ability to offer probabilistic modeling and generate diverse outputs. This versatility inspired their adaptation for image segmentation, where multiple predictions of the model can produce segmentation results that not only achieve high quality but also capture the uncertainty inherent in the model. Here, powerful architectures were proposed for improving diffusion segmentation performance. However, there is a notable lack of analysis and discussions on the differences between diffusion segmentation and image generation, and thorough evaluations are missing that distinguish the improvements these architectures provide for segmentation in general from their benefit for diffusion segmentation specifically. In this work, we critically analyse and discuss how diffusion segmentation for medical images differs from diffusion image generation, with a particular focus on the training behavior. Furthermore, we conduct an assessment how proposed diffusion segmentation architectures perform when trained directly for segmentation. Lastly, we explore how different medical segmentation tasks influence the diffusion segmentation behavior and the diffusion process could be adapted accordingly. With these analyses, we aim to provide in-depth insights into the behavior of diffusion segmentation that allow for a better design and evaluation of diffusion segmentation methods in the future.

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arXiv2024

EAGLE: An Edge-Aware Gradient Localization Enhanced Loss for CT Image Reconstruction

Computed Tomography (CT) image reconstruction is crucial for accurate diagnosis and deep learning approaches have demonstrated significant potential in improving reconstruction quality. However, the choice of loss function profoundly affects the reconstructed images. Traditional mean squared error loss often produces blurry images lacking fine details, while alternatives designed to improve may introduce structural artifacts or other undesirable effects. To address these limitations, we propose Eagle-Loss, a novel loss function designed to enhance the visual quality of CT image reconstructions. Eagle-Loss applies spectral analysis of localized features within gradient changes to enhance sharpness and well-defined edges. We evaluated Eagle-Loss on two public datasets across low-dose CT reconstruction and CT field-of-view extension tasks. Our results show that Eagle-Loss consistently improves the visual quality of reconstructed images, surpassing state-of-the-art methods across various network architectures. Code and data are available at \url{https://github.com/sypsyp97/Eagle_Loss}.

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