Donghang Lyu

Jun Ma, Feifei Li, Sumin Kim et al.

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

Ruochen Gao, Donghang Lyu, Marius Staring

Medical imaging is essential for the diagnosis and treatment of diseases, with medical image segmentation as a subtask receiving high attention. However, automatic medical image segmentation models are typically task-specific and struggle to handle multiple scenarios, such as different imaging modalities and regions of interest. With the introduction of the Segment Anything Model (SAM), training a universal model for various clinical scenarios has become feasible. Recently, several Medical SAM (MedSAM) methods have been proposed, but these models often rely on heavy image encoders to achieve high performance, which may not be practical for real-world applications due to their high computational demands and slow inference speed. To address this issue, a lightweight version of the MedSAM (LiteMedSAM) can provide a viable solution, achieving high performance while requiring fewer resources and less time. In this work, we introduce Swin-LiteMedSAM, a new variant of LiteMedSAM. This model integrates the tiny Swin Transformer as the image encoder, incorporates multiple types of prompts, including box-based points and scribble generated from a given bounding box, and establishes skip connections between the image encoder and the mask decoder. In the \textit{Segment Anything in Medical Images on Laptop} challenge (CVPR 2024), our approach strikes a good balance between segmentation performance and speed, demonstrating significantly improved overall results across multiple modalities compared to the LiteMedSAM baseline provided by the challenge organizers. Our proposed model achieved a DSC score of \textbf{0.8678} and an NSD score of \textbf{0.8844} on the validation set. On the final test set, it attained a DSC score of \textbf{0.8193} and an NSD score of \textbf{0.8461}, securing fourth place in the challenge.

Donghang Lyu, Ruochen Gao, Marius Staring

Medical image segmentation involves partitioning medical images into meaningful regions, with a focus on identifying anatomical structures and lesions. It has broad applications in healthcare, and deep learning methods have enabled significant advancements in automating this process. Recently, the introduction of the Segmentation Anything Model (SAM), the first foundation model for segmentation task, has prompted researchers to adapt it for the medical domain to improve performance across various tasks. However, SAM's large model size and high GPU requirements hinder its scalability and development in the medical domain. In this work, we propose MCP-MedSAM, a powerful and lightweight medical SAM model designed to be trainable on a single A100 GPU with 40GB of memory within one day while delivering superior segmentation performance. Recognizing the significant internal differences between modalities and the need for direct segmentation target information within bounding boxes, we introduce two kinds of prompts: the modality prompt and the content prompt. After passing through the prompt encoder, their embedding representations can further improve the segmentation performance by incorporating more relevant information without adding significant training overhead. Additionally, we adopt an effective modality-based data sampling strategy to address data imbalance between modalities, ensuring more balanced performance across all modalities. Our method was trained and evaluated using a large-scale challenge dataset, compared to top-ranking methods on the challenge leaderboard, MCP-MedSAM achieved superior performance while requiring only one day of training on a single GPU. The code is publicly available at \textcolor{blue}{https://github.com/dong845/MCP-MedSAM}.}

Donghang Lyu, Chinmay Rao, Marius Staring et al.

Cardiac magnetic resonance imaging (CMR) is vital for diagnosing heart diseases, but long scan time remains a major drawback. To address this, accelerated imaging techniques have been introduced by undersampling k-space, which reduces the quality of the resulting images. Recent deep learning advancements aim to speed up scanning while preserving quality, but adapting to various sampling modes and undersampling factors remains challenging. Therefore, building a universal model is a promising direction. In this work, we introduce UPCMR, a universal unrolled model designed for CMR reconstruction. This model incorporates two kinds of learnable prompts, undersampling-specific prompt and spatial-specific prompt, and integrates them with a UNet structure in each block. Overall, by using the CMRxRecon2024 challenge dataset for training and validation, the UPCMR model highly enhances reconstructed image quality across all random sampling scenarios through an effective training strategy compared to some traditional methods, demonstrating strong adaptability potential for this task.

Donghang Lyu, Marius Staring, Hildo Lamb et al.

In recent years, deep learning has attracted increasing attention in the field of Cardiac MRI (CMR) reconstruction due to its superior performance over traditional methods, particularly in handling higher acceleration factors, highlighting its potential for real-world clinical applications. However, current deep learning methods remain limited in generalizability. CMR scans exhibit wide variability in image contrast, sampling patterns, scanner vendors, anatomical structures, and disease types. Most existing models are designed to handle only a single or narrow subset of these variations, leading to performance degradation when faced with distribution shifts. Therefore, it is beneficial to develop a unified model capable of generalizing across diverse CMR scenarios. To this end, we propose CRUNet-MR-Univ, a foundation model that leverages spatio-temporal correlations and prompt-based priors to effectively handle the full diversity of CMR scans. Our approach consistently outperforms baseline methods across a wide range of settings, highlighting its effectiveness and promise.

Donghang Lyu, Marius Staring, Mariya Doneva et al.

Cardiac Magnetic Resonance (CMR) imaging is a non-invasive method for assessing cardiac structure, function, and blood flow. Cine MRI extends this by capturing heart motion, providing detailed insights into cardiac mechanics. To reduce scan time and breath-hold discomfort, fast acquisition techniques have been utilized at the cost of lowering image quality. Recently, Implicit Neural Representation (INR) methods have shown promise in unsupervised reconstruction by learning coordinate-to-value mappings from undersampled data, enabling high-quality image recovery. However, current existing INR methods primarily focus on using coordinate-based positional embeddings to learn the mapping, while overlooking the feature representations of the target point and its neighboring context. In this work, we propose KP-INR, a dual-branch INR method operating in k-space for cardiac cine MRI reconstruction: one branch processes the positional embedding of k-space coordinates, while the other learns from local multi-scale k-space feature representations at those coordinates. By enabling cross-branch interaction and approximating the target k-space values from both branches, KP-INR can achieve strong performance on challenging Cartesian k-space data. Experiments on the CMRxRecon2024 dataset confirms its improved performance over baseline models and highlights its potential in this field.