ITKSNAP

ITK-SNAP is a free, open-source software application used for the segmentation and visualization of three-dimensional medical images. Developed by the University of Pennsylvania, it is built upon the Insight Toolkit (ITK) and Visualization Toolkit (VTK) libraries. The primary purpose of ITK-SNAP is to assist researchers and clinicians in segmenting anatomical structures from medical imaging modalities such as MRI, CT scans, and PET scans.

The software provides a user-friendly graphical interface that allows for manual segmentation, where users can trace boundaries of structures. It also incorporates semi-automatic segmentation tools, including region growing and level sets, which help automate parts of the segmentation process by leveraging image intensity and gradient information. ITK-SNAP supports various image formats commonly used in medical imaging, including DICOM and NIfTI.

A key feature of ITK-SNAP is its advanced 3D visualization capabilities. Users can view segmented structures and their corresponding original images in multiple orthogonal planes and 3D reconstructions. This facilitates a comprehensive understanding of the spatial relationships between different anatomical parts. The software is widely used in academic research for tasks such as creating atlases, quantifying tumor volumes, and analyzing brain structures. Its open-source nature allows for community contributions and extensions.