PDE-based algorithm to reduce noise in grey-scale image, while keeping and reinforcing linear or planar structures in 2D or 3D images respectively (Hessian based anisotropic filter) or keeping sharp edges between objects (gradient based anisotropic filter).

If you use these filters, please cite the following article: Yuchen Long, Ibrahim Cheddadi, Gabriella Mosca, Vincent Mirabet, Mathilde Dumond, Annamaria Kiss, Jan Traas, Christophe Godin, Arezki Boudaoud Cellular Heterogeneity in Pressure and Growth Emerges from Tissue Topology and Geometry. Curr Biol. 2020 Apr 20;30(8):1504-1516.e8. doi: 10.1016

The "AniFilters" tools

- ani2D --> anisotropic filter reinforcing linear structures in 2D
- ani3D --> anisotropic filter in 3D (.inr, .inr.gz files)
- ani3D-tiff --> same as ani3D for tiff files


Move into a directory where you want to install the filters, having the path say "path_to_softs", then download

cd path_to_softs
svn checkout http://forge.cbp.ens-lyon.fr/svn/anifilters


Before compiling, please make sure you have the following packages installed :
- libx11-xcb-dev
- libtiff5-dev


cd anifilters

The binaries will be in the anifilters/bin folder. Add this folder to your PATH by adding in your .bashrc file

export PATH=$PATH:path_to_softs/anifilters/bin

For more detailed information on the method and usage please see the Wiki.


You may want to test the Hessian based anisotropic filter

cd data
ani3D t3_cut.inr.gz 0.2 3 1 10 50

The result is written in your current directory.