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

3-D Image Analysis

Imaris

• 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

Amira

• 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