Re-orientate images or complete stacks in TrakEM2

After aligning all images in TrakEM2, the object of interest might be positioned in an oblique angle. The orientation can be easily be changed. If the whole stack should be rotateted, make sure that all images are linked ( chain sign in the image bar on the left). If the images are not linked, only the single image in the canvas will be rotated. The latter can be handy if single images are rotated and not perfectly aligned after a first rough alignment.

Make sure that one image is highlighted and press “t” (for transform) or use the drop down menu as shown in the video (Transform –> Transform (affine)). Now the angle can be adapted using the handle in the centre. After hitting the return key (“Enter”) the transformation is applied to all linked images.

angular transformation of an aligned image stack

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