ITK-SNAP is a software application used to segment structures in 3D medical images. It is an interactive software application that allows users to navigate three-dimensional medical images, manually delineate anatomical regions of interest, and perform automatic image segmentation. The software was designed with the audience of clinical and basic science researchers in mind, and emphasis has been placed on having a user-friendly interface and maintaining a limited feature set to prevent feature creep. ITK-SNAP is most frequently used to work with magnetic resonance imaging (MRI), cone-beam computed tomography (CBCT) and computed tomography (CT) data sets.

ITK-SNAP is the product of a decade-long collaboration between Paul Yushkevich, Ph.D., of the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania, and Guido Gerig, Ph.D., of the Scientific Computing and Imaging Institute (SCI) at the University of Utah, whose vision was to create a tool that would be dedicated to a specific function, segmentation, and would be easy to use and learn. ITK-SNAP is free, open-source, and multi-platform.

ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, ITK-SNAP offers many supporting utilities. Some of the core advantages of ITK-SNAP include:

  • Linked cursor for seamless 3D navigation
  • Manual segmentation in three orthogonal planes at once
  • A modern graphical user interface based on Qt
  • Support for many different 3D image formats, including NIfTI and DICOM
  • Support for concurrent, linked viewing, and segmentation of multiple images
  • Support for color, multi-channel, and time-variant images
  • 3D cut-plane tool for fast post-processing of segmentation results
  • Extensive tutorial and video documentation

Compared to other, larger open-source image analysis tools, ITK-SNAP design focuses specifically on the problem of image segmentation, and extraneous or unrelated features are kept to a minimum. The design also emphasizes interaction and ease of use, with the bulk of the development effort dedicated to the user interface.

ITK is a parent toolkit for ITK-SNAP. ITK is a C++ libary that implements a multitude of image processing techniques. SNAP is one of the end-user applications bundled with ITK.

ITK-SNAP 3.2 was the first major release of ITK-SNAP in several years, and is funded by the NIH grant R01 EB014346. Version 3.2 includes an almost complete rewrite of the software, along with new features focused on multi-modality image support.


Official Website: Main Page, Sourceforge, Wikipedia, Omictools Page, NITRC Page

Download: Main Page, Github, Sourceforge, Source Code

Documentation: v3.x page, v2.x page, Tutorials, Videos, YouTube Channel

References: Main paper, Google scholar citations of ITK-SNAP paper


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