A general illumination correction method for optical microscopy.
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CIDRE is a retrospective illumination correction method for optical microscopy. It is designed to correct collections of images by building a model of the illumination distortion directly from the image data. Larger image collections provide more robust corrections. Details of the method are described in

  1. K. Smith, Y. Li, F. Ficcinini, G. Csucs, A. Bevilacqua, and P. Horvath
    CIDRE: An Illumination Correction Method for Optical Microscopy, Nature Methods, Early Online Access 16 March 2015, doi:10.1038/NMETH.3323


This project contains several folders:

  • matlab a standalone Matlab implementation of CIDRE with a GUI interface.

  • compiled a compiled executable of the Matlab standalone that runs without a Matlab installation.

  • imagej an ImageJ plugin implementation of CIDRE.


To install the ImageJ plugin, simply copy Cidre_Plugin.jar to the plugins folder of your ImageJ or Fiji installation. For instructions on how to use the Matlab implementation, add the CIDRE/matlab folder to your path and type help cidre.


Copyright © 2015 Kevin Smith, ETH Zurich (Swiss Federal Institute of Technology Zurich), Switzerland. All rights reserved.

CIDRE is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 (or higher) as published by the Free Software Foundation. See LICENSE.md. This program is distributed 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.

Creative Commons License
CIDRE uses minFunc by Mark Schmidt which is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.