Alignment Views
The alignment views are designed to make finding and fixing any alignment problems as easy as possible. Each view shows a combination of the same two images - the alignment target and the image being aligned.
Whole Image
The images are shown overlaid in different colours - the alignment target shown in purple and the image being aligned shown in green. The two colours combine to a shade of grey. This gives an overall indication of where the two images are well aligned (grey areas) and where they are not well aligned (areas where the different colours can still be seen).
The other three views focus on the area inside the orange rectangle in the Whole Image view.
Vector Editing
Before alignment
After alignment
This shows the images overlaid in the same way as the Whole Image view. Circles show where alignment vectors have been placed.
Transition
Before alignment
After alignment
This view alternates between the images with a smooth transition. When the images are not well aligned you will see the protein spots 'moving'. After alignment this movement will be removed. Some of the spots will appear to 'pulse' where there is an expression change between the images.
Checkerboard
Before alignment
After alignment
The checkerboard is created by drawing a section from each image in alternating squares. When the images are not aligned the edges between the squares can be seen. After alignment these edges become less clear and the view should start to take on the appearance of one continuous image.
