Utilizing 3D Slicer for pulmonary bronchovascular anatomy reconstruction: a practical workflow and case examples

Current surgical planning relies on conventional two-dimensional (2D) imaging, but this is limited by its inability to fully represent three-dimensional (3D) anatomical relationships. This limitation is particularly evident in thoracic surgery, where accurate visualization of the pulmonary bronchovascular anatomy is essential for planning lung resections in a surgical field that has high anatomical variations and dynamic deformation during surgery. Although 3D reconstruction techniques have been explored to address these limitations, their adoption into routine clinical practice has been constrained by reliance on expensive proprietary software and a lack of detailed, efficient, reproducible workflows. Here, we describe a novel, practical imaging-based approach for generating patient-specific 3D reconstructions of pulmonary anatomy from computed tomography (CT) data using 3D Slicer, an open-source platform for imaging segmentation and 3D modelling. A reproducible step-by-step workflow is presented, detailing segmentation of pulmonary arteries, veins, bronchi, tumour localization, and resection margin assessment, together with common pitfalls, troubleshooting strategies, and factors influencing accuracy and efficiency. The workflow is designed to be intuitive and time-feasible, with model generation achievable within routine pre-operative planning timeframes. The process is demonstrated through two representative cases in which 3D reconstruction altered surgical planning by clarifying ambiguous anatomy, enabling precise pulmonary tumour localization and accurate resection. With the use of 3D reconstruction technology, anatomical understanding and operative precision can be enhanced, supporting more informed surgical decision-making and potentially improving patient outcomes.