Image segmentation

IdentifySecondaryObjects identifies objects (e.g., cells) using objects identified by another module (e.g., nuclei) as a starting point.

This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works on both binary and gray-scale data. Output can be pushed to the swimming pool for other plug-ins to further exploit the extracted objects.

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.

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