Table 3.

Overview of useful plugins for image analysis using ImageJ.

Plugin name	Operation	Function
Cell counter	Plugins → Particle Analyses → Cell Counter	Manual counting of up to 3 different cell types in a single image (e.g., vessels, tracheids).
Multi measure	Plugins → ROI → Multi Measure	Manual measuring of multiple distances, lengths, polygons, etc., which can be burnt into your image.
Threshold	Image → Adjust → Threshold	Automatic selection of structures of interest based on their grey values.
Analyze particles	Analyze → Analyze Particles	Automatic counting of cells of a certain size or shape. A threshold for size and shape can be set prior to measuring.