Auto PHLIP-ML automatically removes extraneous images from CLSM stacks. This iterative operation removes bias in the Otsu threshold calcualtion. Auto PHLIP-ML integrates with the image analysis program PHLIP by automatically creating the PHLIP-ML file.
Auto PHLIP is working perfectly fine, now that I have managed to install it correctly (maybe this is clear to everybody except me, but make sure to install it by clicking on the setup.exe, not the installer). It's straight forward to use, but I can't say anything about it's internal workings as I don't know anything about programming. Just glad that it works and does what I need!