Daily Papers

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

The Segment Anything Model (SAM) represents a state-of-the-art research advancement in natural image segmentation, achieving impressive results with input prompts such as points and bounding boxes. However, our evaluation and recent research indicate that directly applying the pretrained SAM to medical image segmentation does not yield satisfactory performance. This limitation primarily arises from significant domain gap between natural images and medical images. To bridge this gap, we introduce SAM-Med2D, the most comprehensive studies on applying SAM to medical 2D images. Specifically, we first collect and curate approximately 4.6M images and 19.7M masks from public and private datasets, constructing a large-scale medical image segmentation dataset encompassing various modalities and objects. Then, we comprehensively fine-tune SAM on this dataset and turn it into SAM-Med2D. Unlike previous methods that only adopt bounding box or point prompts as interactive segmentation approach, we adapt SAM to medical image segmentation through more comprehensive prompts involving bounding boxes, points, and masks. We additionally fine-tune the encoder and decoder of the original SAM to obtain a well-performed SAM-Med2D, leading to the most comprehensive fine-tuning strategies to date. Finally, we conducted a comprehensive evaluation and analysis to investigate the performance of SAM-Med2D in medical image segmentation across various modalities, anatomical structures, and organs. Concurrently, we validated the generalization capability of SAM-Med2D on 9 datasets from MICCAI 2023 challenge. Overall, our approach demonstrated significantly superior performance and generalization capability compared to SAM.

Segment Anything Model (SAM) has achieved impressive results for natural image segmentation with input prompts such as points and bounding boxes. Its success largely owes to massive labeled training data. However, directly applying SAM to medical image segmentation cannot perform well because SAM lacks medical knowledge -- it does not use medical images for training. To incorporate medical knowledge into SAM, we introduce SA-Med2D-20M, a large-scale segmentation dataset of 2D medical images built upon numerous public and private datasets. It consists of 4.6 million 2D medical images and 19.7 million corresponding masks, covering almost the whole body and showing significant diversity. This paper describes all the datasets collected in SA-Med2D-20M and details how to process these datasets. Furthermore, comprehensive statistics of SA-Med2D-20M are presented to facilitate the better use of our dataset, which can help the researchers build medical vision foundation models or apply their models to downstream medical applications. We hope that the large scale and diversity of SA-Med2D-20M can be leveraged to develop medical artificial intelligence for enhancing diagnosis, medical image analysis, knowledge sharing, and education. The data with the redistribution license is publicly available at https://github.com/OpenGVLab/SAM-Med2D.

Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each new set of imaging data and task can be labor intensive and inconsistent among annotators. We present CUTS, an unsupervised deep learning framework for medical image segmentation. CUTS operates in two stages. For each image, it produces an embedding map via intra-image contrastive learning and local patch reconstruction. Then, these embeddings are partitioned at dynamic granularity levels that correspond to the data topology. CUTS yields a series of coarse-to-fine-grained segmentations that highlight features at various granularities. We applied CUTS to retinal fundus images and two types of brain MRI images to delineate structures and patterns at different scales. When evaluated against predefined anatomical masks, CUTS improved the dice coefficient and Hausdorff distance by at least 10% compared to existing unsupervised methods. Finally, CUTS showed performance on par with Segment Anything Models (SAM, MedSAM, SAM-Med2D) pre-trained on gigantic labeled datasets.

Segment Anything Model (SAM) has demonstrated impressive performance on a wide range of natural image segmentation tasks. However, its performance significantly deteriorates when directly applied to medical domain, due to the remarkable differences between natural images and medical images. Some researchers have attempted to train SAM on large scale medical datasets. However, poor zero-shot performance is observed from the experimental results. In this context, inspired by the superior performance of U-Net-like models in medical image segmentation, we propose SAMUNet, a new foundation model which incorporates U-Net to the original SAM, to fully leverage the powerful contextual modeling ability of convolutions. To be specific, we parallel a convolutional branch in the image encoder, which is trained independently with the vision Transformer branch frozen. Additionally, we employ multi-scale fusion in the mask decoder, to facilitate accurate segmentation of objects with different scales. We train SAM-UNet on SA-Med2D-16M, the largest 2-dimensional medical image segmentation dataset to date, yielding a universal pretrained model for medical images. Extensive experiments are conducted to evaluate the performance of the model, and state-of-the-art result is achieved, with a dice similarity coefficient score of 0.883 on SA-Med2D-16M dataset. Specifically, in zero-shot segmentation experiments, our model not only significantly outperforms previous large medical SAM models across all modalities, but also substantially mitigates the performance degradation seen on unseen modalities. It should be highlighted that SAM-UNet is an efficient and extensible foundation model, which can be further fine-tuned for other downstream tasks in medical community. The code is available at https://github.com/Hhankyangg/sam-unet.