Unsupervised 3D Medical Image Segmentation With Sparse Radiation Measurement

ObjectiveThree-dimensional medical image segmentation is a central task in medical image analysis. Compared with two-dimensional imaging, it captures organ and lesion morphology more completely and provides detailed structural information, supporting early disease screening, personalized surgical planning, and treatment assessment. With advances in artificial intelligence, three-dimensional segmentation is viewed as a key technique for diagnostic support, precision therapy, and intraoperative navigation. However, methods such as Swinunetr-v2 and UNETR++ depend on extensive voxel-level annotations, which create high annotation costs and restrict clinical use. High-quality segmentation also often requires multi-view projections to recover full volumetric information, increasing radiation exposure and patient burden. Segmentation under sparse radiation measurements is therefore an important challenge. Neural Attenuation Fields (NAF) have recently been introduced for low-dose reconstruction by recovering linear attenuation coefficient fields from sparse views, yet their suitability for three-dimensional segmentation remains insufficiently examined. To address this limitation, a unified framework termed NA-SAM3D is proposed, integrating NAF-based reconstruction with interactive segmentation to enable unsupervised three-dimensional segmentation under sparse-view conditions, reduce annotation dependence, and improve boundary perception.MethodsThe framework is designed in two stages. In the first stage, sparse-view reconstruction is performed with NAF to generate a continuous three-dimensional attenuation coefficient tensor from sparse X-ray projections. Ray sampling and positional encoding are applied to arbitrary three-dimensional points, and the encoded features are forwarded to a Multi-Layer Perceptron (MLP) to predict linear attenuation coefficients that serve as input for segmentation. In the second stage, interactive segmentation is performed. A three-dimensional image encoder extracts high-dimensional features from the attenuation coefficient tensor, and clinician-provided point prompts specify regions of interest. These prompts are embedded into semantic features by an interactive user module and fused with image features to guide the mask decoder in producing initial masks. Because point prompts provide only local positional cues, boundary ambiguity and mask expansion may occur. To address these issues, a Density-Guided Module (DGM) is introduced at the decoder output stage. NAF-derived attenuation coefficients are transformed into a density-aware attention map, which is fused with the initial masks to strengthen tissue-boundary perception and improve segmentation accuracy in complex anatomical regions.Results and DiscussionsNA-SAM3D is evaluated on a self-constructed colorectal cancer dataset comprising 299 patient cases (collected in collaboration with Nanjing Hospital of Traditional Chinese Medicine) and on two public benchmarks: the Lung CT Segmentation Challenge (LCTSC) and the Liver Tumor Segmentation Challenge (LiTS). The results show that NA-SAM3D achieves overall better performance than mainstream unsupervised three-dimensional segmentation methods based on full radiation observation (SAM-MED series) and reaches accuracy comparable to, or in some cases higher than, the fully supervised Swinunetr-v2. Compared with SAM-MED3D, NA-SAM3D increases the Dice on the LCTSC dataset by more than 3%, while HD95 and ASD decrease by 5.29 mm and 1.32 mm, respectively, indicating improved boundary localization and surface consistency. Compared with the sparse-field-based method SA3D, NA-SAM3D achieves higher Dice scores on all three datasets (Table 1). Compared with the fully supervised Swinunetr-v2, NA-SAM3D reduces HD95 by 1.28 mm, and the average Dice is only 0.3% lower. Compared with SA3D, NA-SAM3D increases the average Dice by about 6.6% and reduces HD95 by about 11 mm, further confirming its capacity to restore structural details and boundary information under sparse-view conditions (Table 2). Although the overall performance remains slightly lower than that of the fully supervised UNETR++ model, NA-SAM3D still shows strong competitiveness and good generalization under label-free inference. Qualitative analysis shows that in complex pelvic and intestinal regions, NA-SAM3D produces clearer boundaries and higher contour consistency (Fig. 3). On public datasets, segmentation of the lung and liver also shows superior boundary localization and contour integrity (Fig. 4). Three-dimensional visualization further confirms that in colorectal, lung, and liver regions, NA-SAM3D achieves stronger structural continuity and boundary preservation than SAM-MED2D and SAM-MED3D (Fig. 5). The DGM further enhances boundary sensitivity, increasing Dice and mIoU by 1.20% and 3.31% on the self-constructed dataset, and by 4.49 and 2.39 percentage points on the LiTS dataset (Fig. 6).ConclusionsAn unsupervised three-dimensional medical image segmentation framework, NA-SAM3D, is presented, integrating NAF-based reconstruction with interactive segmentation to achieve high-precision segmentation under sparse radiation measurements. The DGM effectively uses attenuation coefficient priors to enhance boundary recognition in complex lesion regions. Experimental results show that the framework approaches the performance of fully supervised methods under unsupervised inference and yields an average Dice improvement of 2.0%, indicating strong practical value and clinical potential for low-dose imaging and complex anatomical segmentation. Future work will refine the model for additional anatomical regions and assess its practical use in preoperative planning.