Filter2Noise: Interpretable Self-Supervised Single-Image Denoising for Low-Dose CT with Attention-Guided Bilateral Filtering

Effective denoising is crucial in low-dose CT to enhance subtle structures and low-contrast lesions while preventing diagnostic errors. Supervised methods struggle with limited paired datasets, and self-supervised approaches often require multiple noisy images and rely on deep networks like U-Net, offering little insight into the denoising mechanism. To address these challenges, we propose an interpretable self-supervised single-image denoising framework -- Filter2Noise (F2N). Our approach introduces an Attention-Guided Bilateral Filter that adapted to each noisy input through a lightweight module that predicts spatially varying filter parameters, which can be visualized and adjusted post-training for user-controlled denoising in specific regions of interest. To enable single-image training, we introduce a novel downsampling shuffle strategy with a new self-supervised loss function that extends the concept of Noise2Noise to a single image and addresses spatially correlated noise. On the Mayo Clinic 2016 low-dose CT dataset, F2N outperforms the leading self-supervised single-image method (ZS-N2N) by 4.59 dB PSNR while improving transparency, user control, and parametric efficiency. These features provide key advantages for medical applications that require precise and interpretable noise reduction. Our code is demonstrated at https://github.com/sypsyp97/Filter2Noise.git .

seg2med: a segmentation-based medical image generation framework using denoising diffusion probabilistic models

In this study, we present seg2med, an advanced medical image synthesis framework that uses Denoising Diffusion Probabilistic Models (DDPM) to generate high-quality synthetic medical images conditioned on anatomical masks from TotalSegmentator. The framework synthesizes CT and MR images from segmentation masks derived from real patient data and XCAT digital phantoms, achieving a Structural Similarity Index Measure (SSIM) of 0.94 +/- 0.02 for CT and 0.89 +/- 0.04 for MR images compared to ground-truth images of real patients. It also achieves a Feature Similarity Index Measure (FSIM) of 0.78 +/- 0.04 for CT images from XCAT. The generative quality is further supported by a Fr\'echet Inception Distance (FID) of 3.62 for CT image generation. Additionally, seg2med can generate paired CT and MR images with consistent anatomical structures and convert images between CT and MR modalities, achieving SSIM values of 0.91 +/- 0.03 for MR-to-CT and 0.77 +/- 0.04 for CT-to-MR conversion. Despite the limitations of incomplete anatomical details in segmentation masks, the framework shows strong performance in cross-modality synthesis and multimodal imaging. seg2med also demonstrates high anatomical fidelity in CT synthesis, achieving a mean Dice coefficient greater than 0.90 for 11 abdominal organs and greater than 0.80 for 34 organs out of 59 in 58 test cases. The highest Dice of 0.96 +/- 0.01 was recorded for the right scapula. Leveraging the TotalSegmentator toolkit, seg2med enables segmentation mask generation across diverse datasets, supporting applications in clinical imaging, data augmentation, multimodal synthesis, and diagnostic algorithm development.

Compressibility Analysis for the differentiable shift-variant Filtered Backprojection Model

The differentiable shift-variant filtered backprojection (FBP) model enables the reconstruction of cone-beam computed tomography (CBCT) data for any non-circular trajectories. This method employs deep learning technique to estimate the redundancy weights required for reconstruction, given knowledge of the specific trajectory at optimization time. However, computing the redundancy weight for each projection remains computationally intensive. This paper presents a novel approach to compress and optimize the differentiable shift-variant FBP model based on Principal Component Analysis (PCA). We apply PCA to the redundancy weights learned from sinusoidal trajectory projection data, revealing significant parameter redundancy in the original model. By integrating PCA directly into the differentiable shift-variant FBP reconstruction pipeline, we develop a method that decomposes the redundancy weight layer parameters into a trainable eigenvector matrix, compressed weights, and a mean vector. This innovative technique achieves a remarkable 97.25% reduction in trainable parameters without compromising reconstruction accuracy. As a result, our algorithm significantly decreases the complexity of the differentiable shift-variant FBP model and greatly improves training speed. These improvements make the model substantially more practical for real-world applications.

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%.

Reference-Free Multi-Modality Volume Registration of X-Ray Microscopy and Light-Sheet Fluorescence Microscopy

Recently, X-ray microscopy (XRM) and light-sheet fluorescence microscopy (LSFM) have emerged as two pivotal imaging tools in preclinical research on bone remodeling diseases, offering micrometer-level resolution. Integrating these complementary modalities provides a holistic view of bone microstructures, facilitating function-oriented volume analysis across different disease cycles. However, registering such independently acquired large-scale volumes is extremely challenging under real and reference-free scenarios. This paper presents a fast two-stage pipeline for volume registration of XRM and LSFM. The first stage extracts the surface features and employs two successive point cloud-based methods for coarse alignment. The second stage fine-tunes the initial alignment using a modified cross-correlation method, ensuring precise volumetric registration. Moreover, we propose residual similarity as a novel metric to assess the alignment of two complementary modalities. The results imply robust gradual improvement across the stages. In the end, all correlating microstructures, particularly lacunae in XRM and bone cells in LSFM, are precisely matched, enabling new insights into bone diseases like osteoporosis which are a substantial burden in aging societies.

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.

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}.

Deep Learning Computed Tomography based on the Defrise and Clack Algorithm

This study presents a novel approach for reconstructing cone beam computed tomography (CBCT) for specific orbits using known operator learning. Unlike traditional methods, this technique employs a filtered backprojection type (FBP-type) algorithm, which integrates a unique, adaptive filtering process. This process involves a series of operations, including weightings, differentiations, the 2D Radon transform, and backprojection. The filter is designed for a specific orbit geometry and is obtained using a data-driven approach based on deep learning. The approach efficiently learns and optimizes the orbit-related component of the filter. The method has demonstrated its ability through experimentation by successfully learning parameters from circular orbit projection data. Subsequently, the optimized parameters are used to reconstruct images, resulting in outcomes that closely resemble the analytical solution. This demonstrates the potential of the method to learn appropriate parameters from any specific orbit projection data and achieve reconstruction. The algorithm has demonstrated improvement, particularly in enhancing reconstruction speed and reducing memory usage for handling specific orbit reconstruction.

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, inherent in conventional FBP methods, by optimizing Fourier series coefficients to construct the filter. This method enables robust performance across different resolution scales and maintains 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 a versatile tool for a wide range of practical applications. Our research presents a robust and scalable method that expands the utility of FBP in both medical and scientific imaging.

ViSTA: Vision and Scene Text Aggregation for Cross-Modal Retrieval

Visual appearance is considered to be the most important cue to understand images for cross-modal retrieval, while sometimes the scene text appearing in images can provide valuable information to understand the visual semantics. Most of existing cross-modal retrieval approaches ignore the usage of scene text information and directly adding this information may lead to performance degradation in scene text free scenarios. To address this issue, we propose a full transformer architecture to unify these cross-modal retrieval scenarios in a single $\textbf{Vi}$sion and $\textbf{S}$cene $\textbf{T}$ext $\textbf{A}$ggregation framework (ViSTA). Specifically, ViSTA utilizes transformer blocks to directly encode image patches and fuse scene text embedding to learn an aggregated visual representation for cross-modal retrieval. To tackle the modality missing problem of scene text, we propose a novel fusion token based transformer aggregation approach to exchange the necessary scene text information only through the fusion token and concentrate on the most important features in each modality. To further strengthen the visual modality, we develop dual contrastive learning losses to embed both image-text pairs and fusion-text pairs into a common cross-modal space. Compared to existing methods, ViSTA enables to aggregate relevant scene text semantics with visual appearance, and hence improve results under both scene text free and scene text aware scenarios. Experimental results show that ViSTA outperforms other methods by at least $\bf{8.4}\%$ at Recall@1 for scene text aware retrieval task. Compared with state-of-the-art scene text free retrieval methods, ViSTA can achieve better accuracy on Flicker30K and MSCOCO while running at least three times faster during the inference stage, which validates the effectiveness of the proposed framework.