thank you for bringing up this important topic. The interpolation is intentional, it ensures that the scaling in the directions dxy and dz is identical, which is necessary for some of our parameter calculation procedures. To avoid issues with the downstream analysis, we chose the interpolation to be mandatory, so unfortunately, you cannot avoid it without skewing your quantification results.
That being said, if you do not care so much about the quantification, or you´re willing to work through the details of which parameters are affected by the scaling, you can trick BiofilmQ into using the raw data. If you set the dz scaling equal to the dxy, there will be no need for interpolation. However, note that any scaling-related parameter - volumina, distances, range-depended parameters - will not be correctly calculated. Some are just off by a factor, but there are also a few that cannot be recovered. If you choose this work-around, I would be happy to assist you in making sure that you don´t introduce errors into your analysis, but I do not recommend that you try this by yourself.
I would also like to learn more about the reasons, why would prefer to not apply the interpolation. As you might know, BiofilmQ is still in its beta, and we are constantly working on improvements, so your feedback is very helpful to us.
So, what are the main issues you see with the interpolation? And would you, for example, like to be able to switch it off, even if that would result in less parameters being available for calculation for this particular data set?
I apologize for not being able to help more and am very much looking forward to your reply. Thank you for helping us improve our software