RAW and processed files has misalignment. This is visable when scrolling through images, the images "step" from side to side in the preview.
When starting a new project or reusing a recipe/calibration it is vital that the light source has identical distance, angle and power. When the Focus and Alignment calibration is made the light source needs to be accurate from both sides to ensure that equal contrast is achieved. Also the contrast is important.
The reason is that the MSI software and chessboard target together identifies, calculate and place small green check marks that is used for the MSI software corner detection. If the chessboard has to little or different contrast or lightning from side to side, this corner detection will fail. And the fail will result in the misaligment of the images in the project. Those corners are used for calculating the filter refraction compensation - used for alignment. Below are samples showing different corner detection and thereby eventual misalignment. Note that the images below are screendump from the project calibration images (calibration_images\alignment) and that you will be able to see the small green check marks if you zoom into the images.
1. This is a chessboard corner from the left side of an alignment calibration image (450 nm blue) - this has good contrast for the corner detection:
2. This is a chessboard corner from the right side of the 450 nm blue alignment calibration image - which does not have sufficient contrast for a high quality corner detection:
3. Here is an example of a major detection error from 620 nm orange red:
The solution to misaligned images are simply to redo the Focus and Alignment calibration for the images that are affected.