Semi-automated

The grayscale watershed segmentation is useful to segment particles in contact when the model of shape is unknown a priori.

This plugin copies the pixel size from the calibration of one image or stack to a second image or stack. This allows one to copy the spatial calibration from one stack to another.

A second dialog allows to enter the scale factors.

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.