arXiv subjects

Fuxin Fan

Publications and source records attributed to Fuxin Fan.

At least 19 recordsLinked to original sources

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.

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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.

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arXiv2026

Cut to the Mix: Simple Data Augmentation Outperforms Elaborate Ones in Limited Organ Segmentation Datasets

Multi-organ segmentation is a widely applied clinical routine and automated organ segmentation tools dramatically improve the pipeline of the radiologists. Recently, deep learning (DL) based segmentation models have shown the capacity to accomplish such a task. However, the training of the segmentation networks requires large amount of data with manual annotations, which is a major concern due to the data scarcity from clinic. Working with limited data is still common for researches on novel imaging modalities. To enhance the effectiveness of DL models trained with limited data, data augmentation (DA) is a crucial regularization technique. Traditional DA (TDA) strategies focus on basic intra-image operations, i.e. generating images with different orientations and intensity distributions. In contrast, the interimage and object-level DA operations are able to create new images from separate individuals. However, such DA strategies are not well explored on the task of multi-organ segmentation. In this paper, we investigated four possible inter-image DA strategies: CutMix, CarveMix, ObjectAug and AnatoMix, on two organ segmentation datasets. The result shows that CutMix, CarveMix and AnatoMix can improve the average dice score by 4.9, 2.0 and 1.9, compared with the state-of-the-art nnUNet without DA strategies. These results can be further improved by adding TDA strategies. It is revealed in our experiments that Cut-Mix is a robust but simple DA strategy to drive up the segmentation performance for multi-organ segmentation, even when CutMix produces intuitively 'wrong' images. Our implementation is publicly available for future benchmarks.

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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.

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arXiv2025

FIND-Net -- Fourier-Integrated Network with Dictionary Kernels for Metal Artifact Reduction

Metal artifacts, caused by high-density metallic implants in computed tomography (CT) imaging, severely degrade image quality, complicating diagnosis and treatment planning. While existing deep learning algorithms have achieved notable success in Metal Artifact Reduction (MAR), they often struggle to suppress artifacts while preserving structural details. To address this challenge, we propose FIND-Net (Fourier-Integrated Network with Dictionary Kernels), a novel MAR framework that integrates frequency and spatial domain processing to achieve superior artifact suppression and structural preservation. FIND-Net incorporates Fast Fourier Convolution (FFC) layers and trainable Gaussian filtering, treating MAR as a hybrid task operating in both spatial and frequency domains. This approach enhances global contextual understanding and frequency selectivity, effectively reducing artifacts while maintaining anatomical structures. Experiments on synthetic datasets show that FIND-Net achieves statistically significant improvements over state-of-the-art MAR methods, with a 3.07% MAE reduction, 0.18% SSIM increase, and 0.90% PSNR improvement, confirming robustness across varying artifact complexities. Furthermore, evaluations on real-world clinical CT scans confirm FIND-Net's ability to minimize modifications to clean anatomical regions while effectively suppressing metal-induced distortions. These findings highlight FIND-Net's potential for advancing MAR performance, offering superior structural preservation and improved clinical applicability. Code is available at https://github.com/Farid-Tasharofi/FIND-Net

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arXiv2025

Novel-view X-ray Projection Synthesis through Geometry-Integrated Deep Learning

X-ray imaging plays a crucial role in the medical field, providing essential insights into the internal anatomy of patients for diagnostics, image-guided procedures, and clinical decision-making. Traditional techniques often require multiple X-ray projections from various angles to obtain a comprehensive view, leading to increased radiation exposure and more complex clinical processes. This paper explores an innovative approach using the DL-GIPS model, which synthesizes X-ray projections from new viewpoints by leveraging a single existing projection. The model strategically manipulates geometry and texture features extracted from an initial projection to match new viewing angles. It then synthesizes the final projection by merging these modified geometry features with consistent texture information through an advanced image generation process. We demonstrate the effectiveness and broad applicability of the DL-GIPS framework through lung imaging examples, highlighting its potential to revolutionize stereoscopic and volumetric imaging by minimizing the need for extensive data acquisition.

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arXiv2025

A Category-Fragment Segmentation Framework for Pelvic Fracture Segmentation in X-ray Images

Pelvic fractures, often caused by high-impact trauma, frequently require surgical intervention. Imaging techniques such as CT and 2D X-ray imaging are used to transfer the surgical plan to the operating room through image registration, enabling quick intraoperative adjustments. Specifically, segmenting pelvic fractures from 2D X-ray imaging can assist in accurately positioning bone fragments and guiding the placement of screws or metal plates. In this study, we propose a novel deep learning-based category and fragment segmentation (CFS) framework for the automatic segmentation of pelvic bone fragments in 2D X-ray images. The framework consists of three consecutive steps: category segmentation, fragment segmentation, and post-processing. Our best model achieves an IoU of 0.91 for anatomical structures and 0.78 for fracture segmentation. Results demonstrate that the CFS framework is effective and accurate.

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arXiv2025

Benchmark of Segmentation Techniques for Pelvic Fracture in CT and X-ray: Summary of the PENGWIN 2024 Challenge

The segmentation of pelvic fracture fragments in CT and X-ray images is crucial for trauma diagnosis, surgical planning, and intraoperative guidance. However, accurately and efficiently delineating the bone fragments remains a significant challenge due to complex anatomy and imaging limitations. The PENGWIN challenge, organized as a MICCAI 2024 satellite event, aimed to advance automated fracture segmentation by benchmarking state-of-the-art algorithms on these complex tasks. A diverse dataset of 150 CT scans was collected from multiple clinical centers, and a large set of simulated X-ray images was generated using the DeepDRR method. Final submissions from 16 teams worldwide were evaluated under a rigorous multi-metric testing scheme. The top-performing CT algorithm achieved an average fragment-wise intersection over union (IoU) of 0.930, demonstrating satisfactory accuracy. However, in the X-ray task, the best algorithm achieved an IoU of 0.774, which is promising but not yet sufficient for intra-operative decision-making, reflecting the inherent challenges of fragment overlap in projection imaging. Beyond the quantitative evaluation, the challenge revealed methodological diversity in algorithm design. Variations in instance representation, such as primary-secondary classification versus boundary-core separation, led to differing segmentation strategies. Despite promising results, the challenge also exposed inherent uncertainties in fragment definition, particularly in cases of incomplete fractures. These findings suggest that interactive segmentation approaches, integrating human decision-making with task-relevant information, may be essential for improving model reliability and clinical applicability.

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arXiv2024

Task-Specific Data Preparation for Deep Learning to Reconstruct Structures of Interest from Severely Truncated CBCT Data

Cone-beam computed tomography (CBCT) is widely used in interventional surgeries and radiation oncology. Due to the limited size of flat-panel detectors, anatomical structures might be missing outside the limited field-of-view (FOV), which restricts the clinical applications of CBCT systems. Recently, deep learning methods have been proposed to extend the FOV for multi-slice CT systems. However, in mobile CBCT system with a smaller FOV size, projection data is severely truncated and it is challenging for a network to restore all missing structures outside the FOV. In some applications, only certain structures outside the FOV are of interest, e.g., ribs in needle path planning for liver/lung cancer diagnosis. Therefore, a task-specific data preparation method is proposed in this work, which automatically let the network focus on structures of interest instead of all the structures. Our preliminary experiment shows that Pix2pixGAN with a conventional training has the risk to reconstruct false positive and false negative rib structures from severely truncated CBCT data, whereas Pix2pixGAN with the proposed task-specific training can reconstruct all the ribs reliably. The proposed method is promising to empower CBCT with more clinical applications.

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arXiv2024

Enhancing Cross-Modality Synthesis: Subvolume Merging for MRI-to-CT Conversion

Providing more precise tissue attenuation information, synthetic computed tomography (sCT) generated from magnetic resonance imaging (MRI) contributes to improved radiation therapy treatment planning. In our study, we employ the advanced SwinUNETR framework for synthesizing CT from MRI images. Additionally, we introduce a three-dimensional subvolume merging technique in the prediction process. By selecting an optimal overlap percentage for adjacent subvolumes, stitching artifacts are effectively mitigated, leading to a decrease in the mean absolute error (MAE) between sCT and the labels from 52.65 HU to 47.75 HU. Furthermore, implementing a weight function with a gamma value of 0.9 results in the lowest MAE within the same overlap area. By setting the overlap percentage between 50% and 70%, we achieve a balance between image quality and computational efficiency.

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arXiv2024

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.

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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

Generating Synthetic Computed Tomography for Radiotherapy: SynthRAD2023 Challenge Report

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>97.3%/97.0%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

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arXiv2024

AnatoMix: Anatomy-aware Data Augmentation for Multi-organ Segmentation

Multi-organ segmentation in medical images is a widely researched task and can save much manual efforts of clinicians in daily routines. Automating the organ segmentation process using deep learning (DL) is a promising solution and state-of-the-art segmentation models are achieving promising accuracy. In this work, We proposed a novel data augmentation strategy for increasing the generalizibility of multi-organ segmentation datasets, namely AnatoMix. By object-level matching and manipulation, our method is able to generate new images with correct anatomy, i.e. organ segmentation mask, exponentially increasing the size of the segmentation dataset. Initial experiments have been done to investigate the segmentation performance influenced by our method on a public CT dataset. Our augmentation method can lead to mean dice of 76.1, compared with 74.8 of the baseline method.

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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.

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arXiv2024

A 2D Sinogram-Based Approach to Defect Localization in Computed Tomography

The rise of deep learning has introduced a transformative era in the field of image processing, particularly in the context of computed tomography. Deep learning has made a significant contribution to the field of industrial Computed Tomography. However, many defect detection algorithms are applied directly to the reconstructed domain, often disregarding the raw sensor data. This paper shifts the focus to the use of sinograms. Within this framework, we present a comprehensive three-step deep learning algorithm, designed to identify and analyze defects within objects without resorting to image reconstruction. These three steps are defect segmentation, mask isolation, and defect analysis. We use a U-Net-based architecture for defect segmentation. Our method achieves the Intersection over Union of 92.02% on our simulated data, with an average position error of 1.3 pixels for defect detection on a 512-pixel-wide detector.

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arXiv2022

Metal-conscious Embedding for CBCT Projection Inpainting

The existence of metallic implants in projection images for cone-beam computed tomography (CBCT) introduces undesired artifacts which degrade the quality of reconstructed images. In order to reduce metal artifacts, projection inpainting is an essential step in many metal artifact reduction algorithms. In this work, a hybrid network combining the shift window (Swin) vision transformer (ViT) and a convolutional neural network is proposed as a baseline network for the inpainting task. To incorporate metal information for the Swin ViT-based encoder, metal-conscious self-embedding and neighborhood-embedding methods are investigated. Both methods have improved the performance of the baseline network. Furthermore, by choosing appropriate window size, the model with neighborhood-embedding could achieve the lowest mean absolute error of 0.079 in metal regions and the highest peak signal-to-noise ratio of 42.346 in CBCT projections. At the end, the efficiency of metal-conscious embedding on both simulated and real cadaver CBCT data has been demonstrated, where the inpainting capability of the baseline network has been enhanced.

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arXiv2022

Metal Inpainting in CBCT Projections Using Score-based Generative Model

During orthopaedic surgery, the inserting of metallic implants or screws are often performed under mobile C-arm systems. Due to the high attenuation of metals, severe metal artifacts occur in 3D reconstructions, which degrade the image quality greatly. To reduce the artifacts, many metal artifact reduction algorithms have been developed and metal inpainting in projection domain is an essential step. In this work, a score-based generative model is trained on simulated knee projections and the inpainted image is obtained by removing the noise in conditional resampling process. The result implies that the inpainted images by score-based generative model have more detailed information and achieve the lowest mean absolute error and the highest peak-signal-to-noise-ratio compared with interpolation and CNN based method. Besides, the score-based model can also recover projections with big circlar and rectangular masks, showing its generalization in inpainting task.

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