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Manuscript Title: JChainsAnalyser: an ImageJ-based stand-alone application for the study of magneto-rheological fluids.
Authors: P. Domínguez-García, M.A. Rubio
Program title: JChainsAnalyser
Catalogue identifier: AEDT_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 180(2009)1956
Programming language: Java 2.
Computer: Any computer with Java Runtime Environment (JRE) installed.
Operating system: Any OS with Java Runtime Environment (JRE) installed.
RAM: Typically, 3.3 Mb.
Keywords: magneto-rheological fluid, magnetic colloids, aggregation, ImageJ, java.
PACS: 61.43.HV, 82.70.Dd, 83.80.Gv.
Classification: 23.

External routines: ImageJ, ij-imageIO, jdom, L2FProd

Nature of problem:
The video-microscopy technique usually produces quite a big quantity of images to analyse. Although ImageJ gives the required filters and methods for image analysis, it fails when a large number of images is used. Moreover, an adequate combination of filters is needed for the segmentation and binarization of this kind of images.

Solution method:
JChainsAnalyser filters and analyses any quantity of MRF images automatically, so the application can be run on a desktop computer or using a cluster of processors. It can be run in a desktop computer using the GUI (graphical user interface) or by a command-line interface. JChainsAnalyser uses XML files to define input/output data and Java to ensure portability between operating systems. It also utilizes an image algorithm based on the application of different and adaptative ImageJ's filters.

Running time:
The test run provided takes only a few seconds.