A general illumination correction method for optical microscopy.

Last update: Sep 7, 2022

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Overview

CIDRE

About

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

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.

Installation

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.

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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.

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

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Comments

Turn the ImageJ plugin sources into a full-fledged Maven project

Maven projects are the easiest way to import Java projects into IDEs such as Eclipse, Netbeans or IntelliJ. Please see ImageJ's page on Maven for more information why this is a good idea ;-)

opened by dscho 3
Minor changes

Hello Kevin,

I made these changes a while ago when giving Cidre a test run. They just make it a little to run for a first time user. I tested them about a year ago. It looks like the code hasn't change much since then, so they should continue to work. Not tested them now.

Rob

opened by raacampbell 0

java.lang.ArrayIndexOutOfBoundsException

Hi, I cloned the repo and built the ImageJ plugin, and when testing a set of 96 files, got this error in the model building step:

Exception in thread "Thread-4" java.lang.ArrayIndexOutOfBoundsException: -25
    at Cidre_Plugin.getEntropy(Cidre_Plugin.java:1211)
    at Cidre_Plugin.preprocessData(Cidre_Plugin.java:1403)
    at Cidre_Plugin.loadImages(Cidre_Plugin.java:828)
    at Cidre_Plugin.access$200(Cidre_Plugin.java:60)
    at Cidre_Plugin$2.run(Cidre_Plugin.java:634)

The files were TIFs, converted from Cellomics C01 format with CellProfiler's SaveImages module. Thanks, Harri

opened by hajaalin 5

Owner

Kevin Smith

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