Tumor Detection, Segmentation and Classification Challenge on Automated 3D Breast Ultrasound: The TDSC-ABUS Challenge

Breast cancer is one of the most common causes of death among women worldwide. Early detection helps in reducing the number of deaths. Automated 3D Breast Ultrasound (ABUS) is a newer approach for breast screening, which has many advantages over handheld mammography such as safety, speed, and higher detection rate of breast cancer. Tumor detection, segmentation, and classification are key components in the analysis of medical images, especially challenging in the context of 3D ABUS due to the significant variability in tumor size and shape, unclear tumor boundaries, and a low signal-to-noise ratio. The lack of publicly accessible, well-labeled ABUS datasets further hinders the advancement of systems for breast tumor analysis. Addressing this gap, we have organized the inaugural Tumor Detection, Segmentation, and Classification Challenge on Automated 3D Breast Ultrasound 2023 (TDSC-ABUS2023). This initiative aims to spearhead research in this field and create a definitive benchmark for tasks associated with 3D ABUS image analysis. In this paper, we summarize the top-performing algorithms from the challenge and provide critical analysis for ABUS image examination. We offer the TDSC-ABUS challenge as an open-access platform at https://tdsc-abus2023.grand-challenge.org/ to benchmark and inspire future developments in algorithmic research.

MedFILIP: Medical Fine-grained Language-Image Pre-training

Medical vision-language pretraining (VLP) that leverages naturally-paired medical image-report data is crucial for medical image analysis. However, existing methods struggle to accurately characterize associations between images and diseases, leading to inaccurate or incomplete diagnostic results. In this work, we propose MedFILIP, a fine-grained VLP model, introduces medical image-specific knowledge through contrastive learning, specifically: 1) An information extractor based on a large language model is proposed to decouple comprehensive disease details from reports, which excels in extracting disease deals through flexible prompt engineering, thereby effectively reducing text complexity while retaining rich information at a tiny cost. 2) A knowledge injector is proposed to construct relationships between categories and visual attributes, which help the model to make judgments based on image features, and fosters knowledge extrapolation to unfamiliar disease categories. 3) A semantic similarity matrix based on fine-grained annotations is proposed, providing smoother, information-richer labels, thus allowing fine-grained image-text alignment. 4) We validate MedFILIP on numerous datasets, e.g., RSNA-Pneumonia, NIH ChestX-ray14, VinBigData, and COVID-19. For single-label, multi-label, and fine-grained classification, our model achieves state-of-the-art performance, the classification accuracy has increased by a maximum of 6.69\%. The code is available in https://github.com/PerceptionComputingLab/MedFILIP.

Efficient MedSAMs: Segment Anything in Medical Images on Laptop

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.

Improving Representation of High-frequency Components for Medical Foundation Models

Foundation models have recently attracted significant attention for their impressive generalizability across diverse downstream tasks. However, these models are demonstrated to exhibit great limitations in representing high-frequency components and fine-grained details. In many medical imaging tasks, the precise representation of such information is crucial due to the inherently intricate anatomical structures, sub-visual features, and complex boundaries involved. Consequently, the limited representation of prevalent foundation models can result in significant performance degradation or even failure in these tasks. To address these challenges, we propose a novel pretraining strategy, named Frequency-advanced Representation Autoencoder (Frepa). Through high-frequency masking and low-frequency perturbation combined with adversarial learning, Frepa encourages the encoder to effectively represent and preserve high-frequency components in the image embeddings. Additionally, we introduce an innovative histogram-equalized image masking strategy, extending the Masked Autoencoder approach beyond ViT to other architectures such as Swin Transformer and convolutional networks. We develop Frepa across nine medical modalities and validate it on 32 downstream tasks for both 2D images and 3D volume data. Without fine-tuning, Frepa can outperform other self-supervised pretraining methods and, in some cases, even surpasses task-specific trained models. This improvement is particularly significant for tasks involving fine-grained details, such as achieving up to a +15% increase in DSC for retina vessel segmentation and a +7% increase in IoU for lung nodule detection. Further experiments quantitatively reveal that Frepa enables superior high-frequency representations and preservation in the embeddings, underscoring its potential for developing more generalized and universal medical image foundation models.

Deep learning-driven pulmonary arteries and veins segmentation reveals demography-associated pulmonary vasculature anatomy

Pulmonary artery-vein segmentation is crucial for diagnosing pulmonary diseases and surgical planning, and is traditionally achieved by Computed Tomography Pulmonary Angiography (CTPA). However, concerns regarding adverse health effects from contrast agents used in CTPA have constrained its clinical utility. In contrast, identifying arteries and veins using non-contrast CT, a conventional and low-cost clinical examination routine, has long been considered impossible. Here we propose a High-abundant Pulmonary Artery-vein Segmentation (HiPaS) framework achieving accurate artery-vein segmentation on both non-contrast CT and CTPA across various spatial resolutions. HiPaS first performs spatial normalization on raw CT scans via a super-resolution module, and then iteratively achieves segmentation results at different branch levels by utilizing the low-level vessel segmentation as a prior for high-level vessel segmentation. We trained and validated HiPaS on our established multi-centric dataset comprising 1,073 CT volumes with meticulous manual annotation. Both quantitative experiments and clinical evaluation demonstrated the superior performance of HiPaS, achieving a dice score of 91.8% and a sensitivity of 98.0%. Further experiments demonstrated the non-inferiority of HiPaS segmentation on non-contrast CT compared to segmentation on CTPA. Employing HiPaS, we have conducted an anatomical study of pulmonary vasculature on 10,613 participants in China (five sites), discovering a new association between pulmonary vessel abundance and sex and age: vessel abundance is significantly higher in females than in males, and slightly decreases with age, under the controlling of lung volumes (p < 0.0001). HiPaS realizing accurate artery-vein segmentation delineates a promising avenue for clinical diagnosis and understanding pulmonary physiology in a non-invasive manner.

Unsupervised Decomposition Networks for Bias Field Correction in MR Image

Bias field, which is caused by imperfect MR devices or imaged objects, introduces intensity inhomogeneity into MR images and degrades the performance of MR image analysis methods. Many retrospective algorithms were developed to facilitate the bias correction, to which the deep learning-based methods outperformed. However, in the training phase, the supervised deep learning-based methods heavily rely on the synthesized bias field. As the formation of the bias field is extremely complex, it is difficult to mimic the true physical property of MR images by synthesized data. While bias field correction and image segmentation are strongly related, the segmentation map is precisely obtained by decoupling the bias field from the original MR image, and the bias value is indicated by the segmentation map in reverse. Thus, we proposed novel unsupervised decomposition networks that are trained only with biased data to obtain the bias-free MR images. Networks are made up of: a segmentation part to predict the probability of every pixel belonging to each class, and an estimation part to calculate the bias field, which are optimized alternately. Furthermore, loss functions based on the combination of fuzzy clustering and the multiplicative bias field are also devised. The proposed loss functions introduce the smoothness of bias field and construct the soft relationships among different classes under intra-consistency constraints. Extensive experiments demonstrate that the proposed method can accurately estimate bias fields and produce better bias correction results. The code is available on the link: https://github.com/LeongDong/Bias-Decomposition-Networks.

Efficient automatic segmentation for multi-level pulmonary arteries: The PARSE challenge

Efficient automatic segmentation of multi-level (i.e. main and branch) pulmonary arteries (PA) in CTPA images plays a significant role in clinical applications. However, most existing methods concentrate only on main PA or branch PA segmentation separately and ignore segmentation efficiency. Besides, there is no public large-scale dataset focused on PA segmentation, which makes it highly challenging to compare the different methods. To benchmark multi-level PA segmentation algorithms, we organized the first \textbf{P}ulmonary \textbf{AR}tery \textbf{SE}gmentation (PARSE) challenge. On the one hand, we focus on both the main PA and the branch PA segmentation. On the other hand, for better clinical application, we assign the same score weight to segmentation efficiency (mainly running time and GPU memory consumption during inference) while ensuring PA segmentation accuracy. We present a summary of the top algorithms and offer some suggestions for efficient and accurate multi-level PA automatic segmentation. We provide the PARSE challenge as open-access for the community to benchmark future algorithm developments at \url{https://parse2022.grand-challenge.org/Parse2022/}.

The state-of-the-art 3D anisotropic intracranial hemorrhage segmentation on non-contrast head CT: The INSTANCE challenge

Automatic intracranial hemorrhage segmentation in 3D non-contrast head CT (NCCT) scans is significant in clinical practice. Existing hemorrhage segmentation methods usually ignores the anisotropic nature of the NCCT, and are evaluated on different in-house datasets with distinct metrics, making it highly challenging to improve segmentation performance and perform objective comparisons among different methods. The INSTANCE 2022 was a grand challenge held in conjunction with the 2022 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). It is intended to resolve the above-mentioned problems and promote the development of both intracranial hemorrhage segmentation and anisotropic data processing. The INSTANCE released a training set of 100 cases with ground-truth and a validation set with 30 cases without ground-truth labels that were available to the participants. A held-out testing set with 70 cases is utilized for the final evaluation and ranking. The methods from different participants are ranked based on four metrics, including Dice Similarity Coefficient (DSC), Hausdorff Distance (HD), Relative Volume Difference (RVD) and Normalized Surface Dice (NSD). A total of 13 teams submitted distinct solutions to resolve the challenges, making several baseline models, pre-processing strategies and anisotropic data processing techniques available to future researchers. The winner method achieved an average DSC of 0.6925, demonstrating a significant growth over our proposed baseline method. To the best of our knowledge, the proposed INSTANCE challenge releases the first intracranial hemorrhage segmentation benchmark, and is also the first challenge that intended to resolve the anisotropic problem in 3D medical image segmentation, which provides new alternatives in these research fields.

Position-prior Clustering-based Self-attention Module for Knee Cartilage Segmentation

The morphological changes in knee cartilage (especially femoral and tibial cartilages) are closely related to the progression of knee osteoarthritis, which is expressed by magnetic resonance (MR) images and assessed on the cartilage segmentation results. Thus, it is necessary to propose an effective automatic cartilage segmentation model for longitudinal research on osteoarthritis. In this research, to relieve the problem of inaccurate discontinuous segmentation caused by the limited receptive field in convolutional neural networks, we proposed a novel position-prior clustering-based self-attention module (PCAM). In PCAM, long-range dependency between each class center and feature point is captured by self-attention allowing contextual information re-allocated to strengthen the relative features and ensure the continuity of segmentation result. The clutsering-based method is used to estimate class centers, which fosters intra-class consistency and further improves the accuracy of segmentation results. The position-prior excludes the false positives from side-output and makes center estimation more precise. Sufficient experiments are conducted on OAI-ZIB dataset. The experimental results show that the segmentation performance of combination of segmentation network and PCAM obtains an evident improvement compared to original model, which proves the potential application of PCAM in medical segmentation tasks. The source code is publicly available from link: https://github.com/LeongDong/PCAMNet

ULTRA: Uncertainty-aware Label Distribution Learning for Breast Tumor Cellularity Assessment

Neoadjuvant therapy (NAT) for breast cancer is a common treatment option in clinical practice. Tumor cellularity (TC), which represents the percentage of invasive tumors in the tumor bed, has been widely used to quantify the response of breast cancer to NAT. Therefore, automatic TC estimation is significant in clinical practice. However, existing state-of-the-art methods usually take it as a TC score regression problem, which ignores the ambiguity of TC labels caused by subjective assessment or multiple raters. In this paper, to efficiently leverage the label ambiguities, we proposed an Uncertainty-aware Label disTRibution leArning (ULTRA) framework for automatic TC estimation. The proposed ULTRA first converted the single-value TC labels to discrete label distributions, which effectively models the ambiguity among all possible TC labels. Furthermore, the network learned TC label distributions by minimizing the Kullback-Leibler (KL) divergence between the predicted and ground-truth TC label distributions, which better supervised the model to leverage the ambiguity of TC labels. Moreover, the ULTRA mimicked the multi-rater fusion process in clinical practice with a multi-branch feature fusion module to further explore the uncertainties of TC labels. We evaluated the ULTRA on the public BreastPathQ dataset. The experimental results demonstrate that the ULTRA outperformed the regression-based methods for a large margin and achieved state-of-the-art results. The code will be available from https://github.com/PerceptionComputingLab/ULTRA