Dear Viviana

Open2dprot is an open source tool and it works good:  http://open2dprot.sourceforge.net/Flicker/

Best

Prash 

Great! Thanks for your answer. I'll try it out and let you know how it works out...

Pleasure

Have you considered to use ImageJ? http://imagej.net/Welcome It is a universal platform for image analysis with numerous plugins that can be adapted to your problem. It is free, open source, platform independent and has a very active user group, which is eager to help you. I have used it to align CT and MRI images and works fine in this respect.

As Harrie recomendatios, use ImageJ.

Dear Viviana,

in addition to my previous link:

http://www.la-press.com/image-analysis-workflow-for-2-d-electrophoresis-gels-based-on-imagej-article-a2928

Hope this works

Regards,

Harrie