3D Slicer as an image computing platform for the Quantitative Imaging Network

Abstract

Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions.In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams,

Three‐dimensional printing CT‐derived objects with controllable radiopacity

“…First, the pelvis bone was manually separated from surrounding tissues including the femurs, vertebra, and soft tissues using the open‐source 3D Slicer software package (http://www.slicer.org)25 as depicted in Fig. 2.…”

Prior Direct Oral Anticoagulant Therapy is Related to Small Infarct Volume and No Major Artery Occlusion in Patients With Stroke and Non‐Valvular Atrial Fibrillation

“…The infarct volume was assessed semi‐automatically using DWI on admission and image analysis software (3D Slicer, http://www.slicer.org). 3D Slicer, built through support from the National Institutes of Health, is a free open‐source extensible software application for medical image computing and visualization 19. The patients’ Digital Imaging and Communications in Medicine data were imported, and a hyperintense lesion on DWI was semi‐automatically outlined on each slice using segmentation tools within 3D slicer.…”

Dietary Docosahexaenoic Acid Reduces Oscillatory Wall Shear Stress, Atherosclerosis, and Hypertension, Most Likely Mediated via an IL‐1–Mediated Mechanism

“…Projection images (×400) were obtained with a 0.9° rotation step, and these were reconstructed into a 3‐dimensional image that contained a stack of 1024 cross‐sections using NRecon software (Skyscan). The 3‐dimensional image was then triangulated into a high‐resolution STL (standard triangle language) surface, and an intermediate surface mesh comprising 2.2 million triangles was produced using image processing and reconstruction (ImageJ v1.49u36) and image segmentation (3‐dimensional slicer v4.5.037) software. Further mesh manipulation and cleaning were performed using Paraview v4.3.138 and the specialized vascular modeling software @neuFuse v7.3 to produce a high‐resolution mesh comprising 1.3 million triangles.…”