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ChromosomeJ

Outline

Reference

Software

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Download

ChrmsmJ.jar

Plugin for ImageJ

[Version 09.10.2014]

ChromosomeJ

Chromosome segmentation tool

Written by Ricard Delgado-Gonzalo and Virginie Uhlmann at the Biomedical Image Group (BIG), EPFL, Switzerland

Outline

ChromosomeJ is an efficient and user-friendly tool for the segmentation of images containing chromosomes or, more generally, rod-shaped elements, that are "spread" on microscopic slides. The algorithm allows the user to automatically extract the profile of each chromosome and to sort the collection of profiles in a karyotype image (see Figure 1A-B). The method has been incorporated in a plug-in for ImageJ, which is a free open-source multiplatform Java image-processing software. The plug-in is independent of any imaging hardware and, thanks to ImageJ, any common file format may be used as input.

Outline of ChromosomeJ capabilities.

Figure 1. Outline of ChromosomeJ capabilities.

Reference

Software

ImageJ prerequirement

The software provided here is a plugin for ImageJ, a general purpose image-processing and image-analysis package. ImageJ has a public domain licence; it runs on several plateforms: Unix, Linux, Windows, Mac OS 9 and Mac OS X. It doesn't take more than a couple of minutes to install.

Download and install

To install the plugin download the ChromosomeJ.jar file and put it in the plugins folder of ImageJ (ImageJ/plugins/). ChromosomeJ also requires some external libraries that have been regrouped in the following archive file. The archive should be uncompressed, and the elements it contains should be placed into the jars folder of the plugins folder of ImageJ (ImageJ/plugins/jars/).

User manual

Conditions of use

You'll be free to use this software for research purposes, but you must not transmit and distribute it without our consent. In addition, you undertake to include a citation to the associated papers whenever you present or publish results that are based on it. EPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology.

Related work

© 2014 EPFL • webmaster.big@epfl.ch • 03.11.2014