This plugin helps keeping track of microscopes' performances by extracting 4 relevant estimators out of standardized images, acquired from test samples.


Fabrice P. Cordelières, Bordeaux Imaging Center (France). Fabrice.Cordelieres at gmail dot com

Cédric Matthews, CNRS - IBDML - UMR 6216,Marseille (France). cedric.matthews at

This plugin has been created as part of the metrology workgroup work, within the framework of the "French technological network for multidimensional fluorescence microscopies" (RT- MFM), supported by the Mission ressources et compétences technologiques du CNRS" (MRCT)”.


This plugin allows measuring relevant parameters which helps testing, following and comparing microscopes performances. This is achieved by extracting four indicators out of standardized images, acquired from standardized samples: the estimation of the detector sensitivity , the evaluation of the field illumination homogeneity, the system resolution, and finally the characterization of its spectral registration.


This plugin is composed of five parts:

  • Generate CV report
  • Generate field illumination report
  • Generate PSF report
  • Generate axial resolution report
  • Generate co-alignement report

Please refer to the plugin's manual for more details.


When using the “MetroloJ” plugin for publication, please refer to Cédric Matthews and Fabrice P. Cordelieres, €œMetroloJ : an ImageJ plugin to help monitor microscopes'€™ health, in ImageJ User & Developer Conference 2010 proceedings, to this webpage and of course to ImageJ, as explained in the FAQ section, on ImageJ’s website. A copy of your paper being sent to both our e-mail address would also be greatly appreciated !


Simply download metroloj_.jar to the Plugins folder of ImageJ, use the “Help/Update Menus” function to refresh the plugins' menu.

Reports are generated as pdf files, using currently the iText library v2.1.4 (Newer versions are available from iText website, but are not yet compatible with MetroloJ) which should be downloaded to the Plugins folder of ImageJ.

If you get an error message stating "java.lang.NoClassDefFoundError: com/lowagie/textDocumentationException...", it means you are missing the iText library v2.1.4. Download it and save it to your plugins' folder.



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; either version 3 of the License, or (at your option) any later version. 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. You should have received a copy of the GNU General Public License along with this program. If not, see

Copyright (C) 2011 Fabrice P. Cordelières/Cédric Matthews


22/04/11: First public release

06/07/17: Correction of a bug in the field illumination report where wrong intensity was reported for the bottom-right corner

plugin/analysis/metroloj/start.txt · Last modified: 2018/04/10 15:03 by fab
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