Semi-automated

Plugin designed to allow easy semi-automatic tracing of neurons or other filament-like structures (e.g., microtubules, blood vessels) through either 2D images or 3D image stacks. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software.

This plugin is included in Fiji by default.

Enhances the global contrast by equalizing the histogram. This plugin transforms pixel intensities so that they are uniformly distributed over the gray-scale range. It operates on the selected channel of each image of a sequence. This operation is also called "histogram flattening".

A Jython scripting example (but is included as a menu item in Fiji) for screen capturing with certain time delay.

Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite.