Aligning your images

In order to achieve the best possible results from your analysis, it's important that your images are aligned accurately. The alignment views try to make this process as easy as possible.

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.

After performing automatic alignment, you should review the alignment on each of your images before moving on to spot detection.

Reviewing Alignment

The simplest way to review your alignment is to click the Show Aligned button, and then look for movement in the Transition view. You can use the arrow keys to move the focus area in the Whole Image view.

If you find any areas that need the alignment improving, you can right-click on the incorrect alignment vectors to delete them. If you need to add any new alignment vectors, you can click and drag with the left button (see how to perform manual alignment below).

Manual Alignment

If the automatic alignment can't align some of your images accurately, you can help the process by adding manual alignment vectors to those images. You can use the "Remove Vectors" button on the toolbar to clear the automatic alignment before doing any manual alignment. The manual alignment can then be used as a starting point for the automatic alignment. It is possible to align your images entirely manually, but this is time consuming and can lead to overly subjective results.

To perform manual alignment, follow these steps

1. Press (and hold) the left mouse button on the green spot that you want to align.
2. Drag that spot over the equivalent purple reference image spot.
3. Release the mouse button to add the alignment vector.
4. Repeat for any other spots you want to manually align.

You usually only need to align a few spots manually. Once some are aligned, the automatic alignment will use those as a starting point. This is usually enough to give you a high level of alignment.

See Also: Why do I need to align my gels?