PatternJ is an ImageJ/Fiji macro toolset for the automated analysis of repeated patterns.
This tool is described in the following manuscript:
by Mélina Baheux Blin, Vincent Loreau, Frank Schnorrer, Pierre Mangeol
Please cite this reference if you plan to publish with PatternJ
PatternJ was developed to help researchers extract automatically pattern features from their images obtained with fluorescence microscopy as well as electron or bright-field microscopy. Typical images it can analyze automatically include sarcomeric patterns, actin rings in neurons, somites in developing vertebrates, etc...
From a given image, it can extract the position of pre-defined patterns with sub-pixel precision.
With PatternJ 2.0 comes the analysis of time-lapse series and ROI lists.
Above is one example of what it can achieve (a Drosophila muscle sarcomeric pattern).
Download the lastest version of PatternJ here.
(currently PatternJ 2.0a, March 2025)
To install and use PatternJ, read our user manual or follow the video below.
You can use one of our example files or your own image (or image series).
Mac users, please follow step 3 of the installation found in the user manual (recapitulated from minute 1:55 in the video below).