CAMLD: Contrast-Agnostic Medical Landmark Detection with Consistency-Based Regularization

Anatomical landmark detection in medical images is essential for various clinical and research applications, including disease diagnosis and surgical planning. However, manual landmark annotation is time-consuming and requires significant expertise. Existing deep learning (DL) methods often require large amounts of well-annotated data, which are costly to acquire. In this paper, we introduce CAMLD, a novel self-supervised DL framework for anatomical landmark detection in unlabeled scans with varying contrasts by using only a single reference example. To achieve this, we employed an inter-subject landmark consistency loss with an image registration loss while introducing a 3D convolution-based contrast augmentation strategy to promote model generalization to new contrasts. Additionally, we utilize an adaptive mixed loss function to schedule the contributions of different sub-tasks for optimal outcomes. We demonstrate the proposed method with the intricate task of MRI-based 3D brain landmark detection. With comprehensive experiments on four diverse clinical and public datasets, including both T1w and T2w MRI scans at different MRI field strengths, we demonstrate that CAMLD outperforms the state-of-the-art methods in terms of mean radial errors (MREs) and success detection rates (SDRs). Our framework provides a robust and accurate solution for anatomical landmark detection, reducing the need for extensively annotated datasets and generalizing well across different imaging contrasts. Our code will be publicly available at: https://github.com/HealthX-Lab/CAMLD.

Reliability of deep learning models for anatomical landmark detection: The role of inter-rater variability

Automated detection of anatomical landmarks plays a crucial role in many diagnostic and surgical applications. Progresses in deep learning (DL) methods have resulted in significant performance enhancement in tasks related to anatomical landmark detection. While current research focuses on accurately localizing these landmarks in medical scans, the importance of inter-rater annotation variability in building DL models is often overlooked. Understanding how inter-rater variability impacts the performance and reliability of the resulting DL algorithms, which are crucial for clinical deployment, can inform the improvement of training data construction and boost DL models' outcomes. In this paper, we conducted a thorough study of different annotation-fusion strategies to preserve inter-rater variability in DL models for anatomical landmark detection, aiming to boost the performance and reliability of the resulting algorithms. Additionally, we explored the characteristics and reliability of four metrics, including a novel Weighted Coordinate Variance metric to quantify landmark detection uncertainty/inter-rater variability. Our research highlights the crucial connection between inter-rater variability, DL-models performances, and uncertainty, revealing how different approaches for multi-rater landmark annotation fusion can influence these factors.

Comparative Analysis of Diffusion Generative Models in Computational Pathology

Diffusion Generative Models (DGM) have rapidly surfaced as emerging topics in the field of computer vision, garnering significant interest across a wide array of deep learning applications. Despite their high computational demand, these models are extensively utilized for their superior sample quality and robust mode coverage. While research in diffusion generative models is advancing, exploration within the domain of computational pathology and its large-scale datasets has been comparatively gradual. Bridging the gap between the high-quality generation capabilities of Diffusion Generative Models and the intricate nature of pathology data, this paper presents an in-depth comparative analysis of diffusion methods applied to a pathology dataset. Our analysis extends to datasets with varying Fields of View (FOV), revealing that DGMs are highly effective in producing high-quality synthetic data. An ablative study is also conducted, followed by a detailed discussion on the impact of various methods on the synthesized histopathology images. One striking observation from our experiments is how the adjustment of image size during data generation can simulate varying fields of view. These findings underscore the potential of DGMs to enhance the quality and diversity of synthetic pathology data, especially when used with real data, ultimately increasing accuracy of deep learning models in histopathology. Code is available from https://github.com/AtlasAnalyticsLab/Diffusion4Path

BiomedCoOp: Learning to Prompt for Biomedical Vision-Language Models

Recent advancements in vision-language models (VLMs), such as CLIP, have demonstrated substantial success in self-supervised representation learning for vision tasks. However, effectively adapting VLMs to downstream applications remains challenging, as their accuracy often depends on time-intensive and expertise-demanding prompt engineering, while full model fine-tuning is costly. This is particularly true for biomedical images, which, unlike natural images, typically suffer from limited annotated datasets, unintuitive image contrasts, and nuanced visual features. Recent prompt learning techniques, such as Context Optimization (CoOp) intend to tackle these issues, but still fall short in generalizability. Meanwhile, explorations in prompt learning for biomedical image analysis are still highly limited. In this work, we propose BiomedCoOp, a novel prompt learning framework that enables efficient adaptation of BiomedCLIP for accurate and highly generalizable few-shot biomedical image classification. Our approach achieves effective prompt context learning by leveraging semantic consistency with average prompt ensembles from Large Language Models (LLMs) and knowledge distillation with a statistics-based prompt selection strategy. We conducted comprehensive validation of our proposed framework on 11 medical datasets across 9 modalities and 10 organs against existing state-of-the-art methods, demonstrating significant improvements in both accuracy and generalizability. The code will be publicly available at https://github.com/HealthX-Lab/BiomedCoOp.

Ensemble Learning for Microbubble Localization in Super-Resolution Ultrasound

Super-resolution ultrasound (SR-US) is a powerful imaging technique for capturing microvasculature and blood flow at high spatial resolution. However, accurate microbubble (MB) localization remains a key challenge, as errors in localization can propagate through subsequent stages of the super-resolution process, affecting overall performance. In this paper, we explore the potential of ensemble learning techniques to enhance MB localization by increasing detection sensitivity and reducing false positives. Our study evaluates the effectiveness of ensemble methods on both in vivo and simulated outputs of a Deformable DEtection TRansformer (Deformable DETR) network. As a result of our study, we are able to demonstrate the advantages of these ensemble approaches by showing improved precision and recall in MB detection and offering insights into their application in SR-US.

Evaluating Detection Thresholds: The Impact of False Positives and Negatives on Super-Resolution Ultrasound Localization Microscopy

Super-resolution ultrasound imaging with ultrasound localization microscopy (ULM) offers a high-resolution view of microvascular structures. Yet, ULM image quality heavily relies on precise microbubble (MB) detection. Despite the crucial role of localization algorithms, there has been limited focus on the practical pitfalls in MB detection tasks such as setting the detection threshold. This study examines how False Positives (FPs) and False Negatives (FNs) affect ULM image quality by systematically adding controlled detection errors to simulated data. Results indicate that while both FP and FN rates impact Peak Signal-to-Noise Ratio (PSNR) similarly, increasing FP rates from 0\% to 20\% decreases Structural Similarity Index (SSIM) by 7\%, whereas same FN rates cause a greater drop of around 45\%. Moreover, dense MB regions are more resilient to detection errors, while sparse regions show high sensitivity, showcasing the need for robust MB detection frameworks to enhance super-resolution imaging.

MedCLIP-SAMv2: Towards Universal Text-Driven Medical Image Segmentation

Segmentation of anatomical structures and pathological regions in medical images is essential for modern clinical diagnosis, disease research, and treatment planning. While significant advancements have been made in deep learning-based segmentation techniques, many of these methods still suffer from limitations in data efficiency, generalizability, and interactivity. As a result, developing precise segmentation methods that require fewer labeled datasets remains a critical challenge in medical image analysis. Recently, the introduction of foundation models like CLIP and Segment-Anything-Model (SAM), with robust cross-domain representations, has paved the way for interactive and universal image segmentation. However, further exploration of these models for data-efficient segmentation in medical imaging is still needed and highly relevant. In this paper, we introduce MedCLIP-SAMv2, a novel framework that integrates the CLIP and SAM models to perform segmentation on clinical scans using text prompts, in both zero-shot and weakly supervised settings. Our approach includes fine-tuning the BiomedCLIP model with a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss, and leveraging the Multi-modal Information Bottleneck (M2IB) to create visual prompts for generating segmentation masks from SAM in the zero-shot setting. We also investigate using zero-shot segmentation labels within a weakly supervised paradigm to enhance segmentation quality further. Extensive testing across four diverse segmentation tasks and medical imaging modalities (breast tumor ultrasound, brain tumor MRI, lung X-ray, and lung CT) demonstrates the high accuracy of our proposed framework. Our code is available at https://github.com/HealthX-Lab/MedCLIP-SAMv2.

Uncertainty Decomposition and Error Margin Detection of Homodyned-K Distribution in Quantitative Ultrasound

Homodyned K-distribution (HK-distribution) parameter estimation in quantitative ultrasound (QUS) has been recently addressed using Bayesian Neural Networks (BNNs). BNNs have been shown to significantly reduce computational time in speckle statistics-based QUS without compromising accuracy and precision. Additionally, they provide estimates of feature uncertainty, which can guide the clinician's trust in the reported feature value. The total predictive uncertainty in Bayesian modeling can be decomposed into epistemic (uncertainty over the model parameters) and aleatoric (uncertainty inherent in the data) components. By decomposing the predictive uncertainty, we can gain insights into the factors contributing to the total uncertainty. In this study, we propose a method to compute epistemic and aleatoric uncertainties for HK-distribution parameters ($\alpha$ and $k$) estimated by a BNN, in both simulation and experimental data. In addition, we investigate the relationship between the prediction error and both uncertainties, shedding light on the interplay between these uncertainties and HK parameters errors.

Denoising Plane Wave Ultrasound Images Using Diffusion Probabilistic Models

Ultrasound plane wave imaging is a cutting-edge technique that enables high frame-rate imaging. However, one challenge associated with high frame-rate ultrasound imaging is the high noise associated with them, hindering their wider adoption. Therefore, the development of a denoising method becomes imperative to augment the quality of plane wave images. Drawing inspiration from Denoising Diffusion Probabilistic Models (DDPMs), our proposed solution aims to enhance plane wave image quality. Specifically, the method considers the distinction between low-angle and high-angle compounding plane waves as noise and effectively eliminates it by adapting a DDPM to beamformed radiofrequency (RF) data. The method underwent training using only 400 simulated images. In addition, our approach employs natural image segmentation masks as intensity maps for the generated images, resulting in accurate denoising for various anatomy shapes. The proposed method was assessed across simulation, phantom, and in vivo images. The results of the evaluations indicate that our approach not only enhances image quality on simulated data but also demonstrates effectiveness on phantom and in vivo data in terms of image quality. Comparative analysis with other methods underscores the superiority of our proposed method across various evaluation metrics. The source code and trained model will be released along with the dataset at: http://code.sonography.ai

Vision Mamba for Classification of Breast Ultrasound Images

Mamba-based models, VMamba and Vim, are a recent family of vision encoders that offer promising performance improvements in many computer vision tasks. This paper compares Mamba-based models with traditional Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) using the breast ultrasound BUSI and B datasets. Our evaluation, which includes multiple runs of experiments and statistical significance analysis, demonstrates that Mamba-based architectures frequently outperform CNN and ViT models with statistically significant results. These Mamba-based models effectively capture long-range dependencies while maintaining inductive biases, making them suitable for applications with limited data.