This is a fork of the CIDRE repository. The only modification of the code is concerned the way the images are loaded. It is adjusted to our in-house 2-photon microscopy data.

Details of the CIDRE algorithm 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

• matlab a modified Matlab implementation of CIDRE.

In odre to run CIDRE correction in the Stichit, you need to download this repository and add the folder to the path in the Stitchit pipeline(https://github.com/BaselLaserMouse/StitchIt). An example of use you can see on Stichit fork.

• Rob Campbell for Stichit algorithm.
• Kevin Smith, 2015 for CIDRE.
• And Gus Brown for recurcive directory listing rdir.