Imaging Software
From CLARITY Wiki
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.
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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