Dear Christos. Thank you. You also have and interesting data sets.

Here is a download link for ImageJ, developed open source by the NIH. I believe it has  C+-like macro language abilities.

http://rsb.info.nih.gov/ij/index.html

Thank you Cedric.

Please consider OpenCV C++ library.

https://ru.wikipedia.org/wiki/OpenCV

If your work includes also 3D images, in addition to OpenCV I would suggest ITK.

http://itk.org/

Try our software that can be downloaded from http://www.medinfo.cs.ucy.ac.cy/. Go under downloads-->toolboxes and Download the Image Despeckle Filtering (IDF) Toolbox. 

Dear Christos. Thank you. You also have and interesting data sets.

Dear Vyacheslav,

Check the Below links

1. CVIP toolbox

http://cviptools.ece.siue.edu/

2.  Lispix Image processing toolbox

http://www.nist.gov/lispix/

3. Fiji J

http://fiji.sc/Fiji

4. ImageMagick

http://www.imagemagick.org/index.php

Hope this Helps!

Try OpenCV

If it is medical image processing, you might give a try to this one, too:

http://www.mevislab.de/

Ajay, Juan, Mauro thanks for the help.