Revision as of 06:20, 30 April 2018 by Gcardone (talk | contribs)

MyofribilJ (ImageJ/Fiji)
Author Giovanni Cardone and Maria Spletter
Maintainer Giovanni Cardone
Source on GitHub
Initial release November 2017
Category Analysis, Scripting, Plugins


The MyofibrilJ plugin provides two scripts to analyse fibril morphology. Given a fluorescence image of muscle fibers, the scripts measure myofibrils dimensions and sarcomere length. The scripts were initially developed for the analysis of both longitudinal and cross sections of myofibrils stained with rhodamine-phalloidin.


Two distinct commands are provided to analyse either cross-sections or longitudinal sections of fibers. In both cases:

  • open one or more images to analyse, all of them displaying either longitudinal or cross sections of fibrils
  • for each multi-channel or stack image, display the slice and the channel of interest. Optionally, draw a ROI to focus on a portion of the image (recommended to exclude empty regions)
  • launch the script suitable for the images displayed

The script will process all the images and generate a table with results, along with some control images

analyse myofibrils lengthwise

analyse myofibrils crosswise


Longitudinal sections

The sarcomere length is estimated by means of Fourier analysis. Because of the periodic nature of sarcomere organization, the position of the periodic peaks on the horizontal axis of the Fourier transformed imaged is strictly related to the lenght of sarcomeres. The width of the fibrils is estimated in two different manners. One estimate is obtained from the autocorrelation image, by measuring the position of the first minimum in its vertical intensity profile. Furthermore, the width of the cross-profile of multiple fibrils is measured in the original image and combined to provide an additional average width.

Cross sections

An initial estimate of the diameter of the fibrils is obtained by finding the first minimum in the radial average profile of the autocorrelation image, while their position is determined by examining the peak intensities. This estimate is used to determine the optimal crop area around all the cross-sections in the image. All of the detected fibrils cross sections are then cropped from the image, the size of the crop being proportional to the the initial diameter estimate, and combined to obtain a noise-free average representation of the fibril section. The diameter is estimated from this average as the full width of its radial profile, where the intensity is 26% of the maximum range. In addition to their diameter, the level of clustering of the fibrils is characterized by nearest neighbor analysis and summarized by the Nearest Neighbor Index (NNI).



The easiest way to install MyofibrilJ is by first adding the update site, by clicking the Add update site button in the site management dialog button and filling in the name of your choice for the site and for the URL, and then by subscribing to it.


This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.