ImageJ is powerful software for micro-measurement and atomic force microscopy (AFM) analysis. It is used in the California State University scientific community, and in many, many others...
From the ImageJ website:
Runs Everywhere: ImageJ is written in Java, which allows it to run on Linux, Mac OS X and Windows, in both 32-bit and 64-bit modes.
User Community: ImageJ has a large and knowledgeable worldwide user community. More than 1700 users and developers subscribe to the ImageJ mailing list.
Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM), however it can be generally used for any other height field and image analysis, for instance for analysis of profilometry data (learn more about Gwyddion features).
Gwyddion is Free and Open Source software, covered by GNU General Public License. It aims to provide multiplatform modular program for 2D data analysis that could be easily extended by modules and plug-ins. Moreover, the status of free software enables to provide source codes to developers and users, which makes the further program improvement easier.
Gwyddion works on GNU/Linux, Microsoft Windows, Mac OS X and FreeBSD operating systems on common architectures, all systems can be used also for developement. Its graphical user interface is based on Gtk+ and port to other systems supported by Gtk+ should be possible.