3D Medical Image Segmentation with 3D Modelling

Abstract

Background/Objectives: The segmentation of three-dimensional radiological images constitutes a fundamental task in medical image processing for isolating tumors from complex datasets in computed tomography or magnetic resonance imaging. Precise visualization, volumetry, and treatment monitoring are enabled, which are critical for oncology diagnostics and planning. Volumetric analysis surpasses standard criteria by detecting subtle tumor changes, thereby aiding adaptive therapies. The objective of this study was to develop an enhanced, interactive Graphcut algorithm for 3D DICOM segmentation, specifically designed to improve boundary accuracy and 3D modeling of breast and brain tumors in datasets with heterogeneous tissue intensities. Methods: The standard Graphcut algorithm was augmented with a clustering mechanism (utilizing k = 2-5 clusters) to refine boundary detection in tissues with varying intensities. DICOM datasets were processed into 3D volumes using pixel spacing and slice thickness metadata. User-defined seeds were utilized for tumor and background initialization, constrained by bounding boxes. The method was implemented in Python 3.13 using the PyMaxflow library for graph optimization and pydicom for data transformation. Results: The proposed segmentation method outperformed standard thresholding and region growing techniques, demonstrating reduced noise sensitivity and improved boundary definition. An average Dice Similarity Coefficient (DSC) of 0.92 ± 0.07 was achieved for brain tumors and 0.90 ± 0.05 for breast tumors. These results were found to be comparable to state-of-the-art deep learning benchmarks (typically ranging from 0.84 to 0.95), achieved without the need for extensive pre-training. Boundary edge errors were reduced by a mean of 7.5% through the integration of clustering. Therapeutic changes were quantified accurately (e.g., a reduction from 22,106 mm³ to 14,270 mm³ post-treatment) with an average processing time of 12-15 s per stack. Conclusions: An efficient, precise 3D tumor segmentation tool suitable for diagnostics and planning is presented. This approach is demonstrated to be a robust, data-efficient alternative to deep learning, particularly advantageous in clinical settings where the large annotated datasets required for training neural networks are unavailable.

Keywords: 3D segmentation; DICOM data; Graphcut; image processing; tumor volumetry.