The evaluation of the spot patterns is the most demanding part of the 2-D electrophoresis technique, and the images would be analyzed comparatively and automatically. 2-D gel patterns are compared to detect qualitative and/or quantitative protein expression changes between individual samples or different populations. Imaging analysis of 2-D gels can provide various types of information for the detection of novel, missing, or modified proteins; quantification of protein spots; determine of pI and Mr values of protein spots; enzyme digest and mass spectrometry detection.

For the evaluation and comparison of the complex 2-D patterns, the gel images have to be converted into digital data with a scanner or camera for further analysis with computer software. In imaging analysis, usually a pixel format of 100 mm is applied for scanning, higher pixel resolution does not improve imaging analysis and the image files will become too big to be processed in a reasonable time and take up a lot of space on the hard disk.