We considered 2D image analysis to be one of the big bottlenecks in 2D gel proteomics. SameSpots has completely changed that. 2D gel analysis is now easy and we do much more 2D experiments.
Automatic Alignment
The simplest (and the recommended) way to align your images is to use Automatic Alignment. If you have gels that are clearly resolved then this should be all you need. In these circumstances, the automated process is often as good as an expert aligning manually.
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After performing automatic alignment, you should review the alignment on each of your images before moving on to spot detection.
