Correcting image rotation

Welcome

Finally, your scan is finished! You can't wait to see the results... Quickly checking the reconstruction settings before launching the reconstruction... Just a few more minutes... Done! You open the dataset in Dataviewer and start scrolling through the slices. Wait a minute... I did fine-tune the misalignment right!? What is going on here? The central slices look fine, but the top and bottom slices are misaligned... Now what!?

Learn how to correct image rotation in the last Bruker microCT Academy newsletter of this year. Bruker microCT is wishing you all happy holidays and hope you will join us again in 2018!

Alignment is a complex issue in tomography. Consider the axis of rotation, the virtual line around which the object rotates in 3D space during the scan. If this line could be projected by the x-rays onto the camera it would make a vertical line image. In a perfectly aligned scan, this projected line would correspond exactly to the midline of the camera. In this case the misalignment is zero. Yet, in practice, every scan requires a test of alignment, and in most cases a misalignment or “post-alignment” compensation needs to be added. Failure to make this compensation, or applying the wrong value, leads to artefacts. Normally only one post-alignment value is needed for one scan. Sometimes an alignment problem means that the post-alignment correction needed for best image quality is different at the top and bottom of scans.

In this case, the response should be to perform the alignment test on your scanner, using the supplied alignment pin, which includes a parameter of “image rotation” which should fix this problem. However, a scan affected by this problem of a top-bottom difference can be “rescued” at reconstruction by a special option available in the “engineering mode” of NRecon. This special option is called “Image rotation” and is called “Image rotation” and is described in “MN069-Correcting image rotation”.

Bruker microCT Academy 2017 issue 6 mouse fibula a
Bruker microCT Academy 2017 issue 6 mouse fibula b

Cross-sectional slices through a mouse fibula. While the central image is nicely aligned (Left), slices towards the top of the scan are not (Right). Yet, all cross-sections were generated from the same scan, using the same misalignment value.

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