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

Fiji

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