Ting Ma

Jiesi Hu, Yanwu Yang, Zhiyu Ye et al.

Universal models for medical image segmentation, such as interactive and in-context learning (ICL) models, offer strong generalization but require extensive annotations. Interactive models need repeated user prompts for each image, while ICL relies on dense, pixel-level labels. To address this, we propose Weakly Supervised In-Context Learning (WS-ICL), a new ICL paradigm that leverages weak prompts (e.g., bounding boxes or points) instead of dense labels for context. This approach significantly reduces annotation effort by eliminating the need for fine-grained masks and repeated user prompting for all images. We evaluated the proposed WS-ICL model on three held-out benchmarks. Experimental results demonstrate that WS-ICL achieves performance comparable to regular ICL models at a significantly lower annotation cost. In addition, WS-ICL is highly competitive even under the interactive paradigm. These findings establish WS-ICL as a promising step toward more efficient and unified universal models for medical image segmentation. Our code and model are publicly available at https://github.com/jiesihu/Weak-ICL.

Jiesi Hu, Chenfei Ye, Yanwu Yang et al.

In-context learning (ICL), a type of universal model, demonstrates exceptional generalization across a wide range of tasks without retraining by leveraging task-specific guidance from context, making it particularly effective for the intricate demands of neuroimaging. However, current ICL models, limited to 2D inputs and thus exhibiting suboptimal performance, struggle to extend to 3D inputs due to the high memory demands of ICL. In this regard, we introduce Neuroverse3D, an ICL model capable of performing multiple neuroimaging tasks in 3D (e.g., segmentation, denoising, inpainting). Neuroverse3D overcomes the large memory consumption associated with 3D inputs through adaptive parallel-sequential context processing and a U-shaped fusion strategy, allowing it to handle an unlimited number of context images. Additionally, we propose an optimized loss function to balance multi-task training and enhance focus on anatomical boundaries. Our study incorporates 43,674 3D multi-modal scans from 19 neuroimaging datasets and evaluates Neuroverse3D on 14 diverse tasks using held-out test sets. The results demonstrate that Neuroverse3D significantly outperforms existing ICL models and closely matches task-specific models, enabling flexible adaptation to medical center variations without retraining. The code and model weights are publicly available at https://github.com/jiesihu/Neuroverse3D.

Hongwei Bran Li, Fernando Navarro, Ivan Ezhov et al.

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT; various organs such as the brain, prostate, kidney, and pancreas; and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks.