Georeference a computed tomography image without changing its proportions in QGIS

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I have several images obtained from a Micro computed tomography (mCT). The scanned elements are human teeth.

In a particular mCT slice, I have introduced a cartesian plot with its X and Y axis. The (0,0) point is placed in a particular anatomical structure. The maximum width of both the X and Y axis is considered to be 100, as I am working with relative values. However, the X axis and the Y axis are not at the same scale.

When I georeference the slice, I open the image as a raster layer and introduce 3 points: the origin (0,0), the X point (100,0) and the Y point (0,100). Notice that although eiter the X point or the Y point have 100 as maximum, because they are expressed in different scales, their real measures on the image are different.

When I apply the transformation according to these three points and see the result on the QGIS mainscreen I notice that the image have been distorted, changing its proportion. The real distance in the georeferenced image between the origin and the other two points is the same (both are 100). However, what I want is to keep the original proportion maintaining the original values of the coordinates of the three points.

Is it possible? And... how?

Thanks



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