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Filament_Morphology_Tool

Volker edited this page May 20, 2021 · 6 revisions

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.

branch_info.png summary_table.png

You can download example images here:

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

Getting started

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.

toolset.png

  • 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

Options

filament_morpho_options.png

  • 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

Method

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.

Literature

  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).

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