What are alignment vectors?

Alignment Vectors

Alignment vectors are used to connect 'land marks' (e.g. a clearly visible spot) from the image being aligned (shown in green) to the alignment target (shown in purple).

Before placing an alignment vector

After placing an alignment vector

The red alignment vector (shown on the right) connects the green spot on the image being aligned to the purple spot on the alignment target.

Alignment vectors can be automatically calculated. In many cases you will need very few, if any, manual vectors.

Before automatically calculating vectors

After automatically calculating vectors

The blue alignment vectors (shown on the right) are the automatically calculated ones. The single red alignment vector has been placed manually, by clicking and dragging in the vector editing view.

When the alignment is applied, Progenesis SameSpots will try to make the tail of each vector as short as possible, by pulling and stretching the image being aligned. The alignment target (purple image) will remain the same, so the head of the vectors stay in the same place. Any areas containing both green and purple that are overlaid will be combined to show black. You can see this by clicking the "Show aligned" button on the toolbar.

Unaligned (vectors with long tails)

Aligned (vectors with short tails)

When the alignment vectors are consistent with each other (i.e. they don't conflict) the tails will become single dots in the middle of the circle for each vector.