This is a 3D composite image after z-stack imaging. Any idea why there are repetitions in the z-plane like those seen in this kidney slice image. This can be seen more clearly from the side looking into the volume.
A bit more about the imaging being done and the workflow for processing them would help. Can you post a couple of the individual slices, preferably sequential? ( Its just hard to tell where the image data is coming from after its been composited together. )
There are a lot of places where the image registration process can go wrong. Sloppy technique or dodgy equipment, resulting in tilted images, changing the optical center of the images, drift, changes in rotation or translation can occur, and the software may just not be trying to correct these.
Or failures in the software, where it focuses on the wrong image data to perform the registration. It may be focusing on high contrast garbage rather than low contrast subject. Or incorrect settings, like forgetting to check the "align the images properly" check box ... somewhat joking, somewhat "OMG, I need more coffee" moments.
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