Using a Consistent Image Orientation

Scan all gel images using the same orientation. A common trick is to cut off one corner of the gel. Cut off the low mW, low pI corner. Make sure that this corner becomes the lower left corner in the image for every gel you scan. This has the added advantage that your images will have the orientation that is usually required by the proteomics journals (pI increasing from left to right, mW decreasing from top to bottom).

If you need to rotate or flip the image it is recommended to use the software that came with your scanner for this. General purpose image processing software (such as Adobe Photoshop) may not preserve the vendor specific grayscale calibration information in the image file.