Filament_Morphology_Tool - MontpellierRessourcesImagerie/imagej_macros_and_scripts GitHub Wiki

The tool count filaments and measure their areas and forms. It specially measures the geodesic diameter of the objects and its curvature, counts the branches and measures their lengths.

You can download example images here:

• image01.czi
• image02.czi

The source code in git-hub can be found here.

You need to have MorpholibJ [2] 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 [1] and the geodesic-diameter from MorpholibJ [2] in one table. The skeletons are analysed one by one to match the order of the particle-analyzer. It measures the curvature for each point of a filament and reports the sum, the max., the mean and the stdDev. The interpolation length will influence the measurement of the curvature.

1. Ignacio Arganda-Carreras, Rodrigo Fernandez-Gonzalez, Arrate Munoz-Barrutia, Carlos Ortiz-De-Solorzano, 3D reconstruction of histological sections: Application to mammary gland tissue, Microscopy Research and Technique, Volume 73, Issue 11, pages 1019–1029, October 2010.

2. Legland, D.; Arganda-Carreras, I. & Andrey, P. (2016), MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ, Bioinformatics (Oxford Univ Press) 32(22): 3532-3534, PMID 27412086, doi:10.1093/bioinformatics/btw413 (on Google Scholar).