Registering two images manually

This procedure will warp an image to match a reference image, using manually-obtained landmark points.

1. Identify a number of points that are landmarks visible in both images. In the example above, 6 protein spots were selected and labeled 1 to 6. The greater number of points that are selected, the more complicated the warping that can be done.
2. Click the ``Image no.'' settings to ensure the desired image numbers are shown.
3. Click on ``Obtain landmarks'' for the reference image and click on each spot. Press Space when finished. Keep a mental note of the order in which the points were clicked.
4. Repeat for the unknown image, making sure to click on the point in the second image that corresponds to a point in the first image.
5. Click ``Edit landmarks'' if desired to check the selected coordinates and edit if necessary.
6. If the unknown image needs to be rotated, click ``Rotate image''. This should be done before any warping. The landmark points will also be rotated, so that the same landmarks can be used for warping.
7. Click ``Calculate vector map''. This will create a new image illustrating the vector map using a color-coding scheme.
8. Click on the image to be unknown to select it.
9. Click ``Warp image'' to perform the warping alignment using the vector map.
10. (optional) Select ``Config..Configure..Main cursor'' and change the cursor to ``multiple crosshairs''. The corresponding spots will now be indicated by crosshair cursors on both images.

Notes

1. If the image is both rotated and warped, rotation should be performed first. Better results are occasionally obtained if new control points are obtained after rotating.
2. Only one point is needed to rotate or warp an image. If a single point is used, the rotation or translation will be constant over the entire image. More points allow correction for more complicated twists and warps.
3. Don't click ``Correlate points'' when using manually-selected control points. Manually selected points are already correlated.
4. Rotation and warping are done independently for greater flexibility. If the image is known not to be rotated, you can click on ``Warp image'' to warp without rotating (and vice versa).
5. The control points are automatically moved to new locations after rotation and warping.
6. Avoid selecting control points for rotation near the exact center of the image, since the image is rotated around the center point. This might cause excessive twisting near the center of the image.