Imaging Software


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No CLARITY-specific image software is necessary for visualization and analysis of clarified tissue. There are several different open source (free) and commercial software programs available.


2-D Image Analysis

Image J

  • Free, open source software with multiple plugins available for download (many customized for specific analysis techniques)
  • User friendly; simple, but powerful
  • Can use macros to automate analysis
  • Not ideal for 3-D image viewing


  • Free, open source distribution of Image J with many bundled plugins, an updating system, and a coherent menu structure

3-D Image Analysis


  • Useful for 3-D image visualization, analysis, and creating movies (software used in original CLARITY Nature article)
  • Fast and user-friendly; many step-by-step tutorials available in the software and online
  • High cost: one-time license fee


  • Similar 3-D image processing capabilities as Imaris
  • Interface more flexible, but not as user-friendly, as Imaris
  • Allows user to write programs
  • High cost: yearly license fee

Vaa 3D

  • Free, open source software with downloadable plugins, similar to Image J
  • Good 3-D image processing