For the ZEN software we developed a special file format called *.czi (Carl Zeiss Image). Besides the image data itself, the image format saves a lot of additional data, for example the date of acquisition, microscope settings, exposure values, size and scale details, contrast procedures which were used. Also, all annotations and measured values are saved with the file.
To learn more about the ZEISS image file format we recommend to visit the ZEISS Microscopy Community forum in the internet (http://forums.zeiss.com/microscopy/community/forum.php). There you can join interesting discussions or download the detailed documentation of the file format.