Filament_Morphology_Tool
The tool count filaments and measure their areas and forms. It specially measures the geodesic diameter of the objects, counts the branches and measures their lengths.
You can download example images here:
The source code in git-hub can be found here.
You need to have MorpholibJ installed. To install the tool save the file filament_morphology_tool.ijm into the folder macros/toolsets of your FIJI installation.
Select the "filament_morphology_tool" toolset from the >> button of the ImageJ launcher.
- the first button (the one with the image) opens this help page
- the a-button runs the analysis on the active image
- the b-button runs the batch analysis on all images in a folder
-
filament channel: the channel containing the filaments -
filament auto-thresholding method: the auto-thresholding method used to segment the filaments -
filament min. area: the minimum area of filaments, smaller objects are removed -
interpolation length: the interpolation length for the geodesic-diameter
The tool assembles the measurements of ImageJ, AnalyzeSkeleton and the geodesic-diameter from MorpholibJ in one table. The skeletons are analysed one by one to match the order of the particle-analyzer.
Volker Bäcker