I am using CellProfiler to automatically generate alignments from the same tissue. I am trying to match and align the first hematoxylin stain to an IHC image. However, with the pipeline that I am currently using, sometimes the alignments are inaccurate (see image)
How can I improve my pipeline and make the automatic alignment generations more accurate? When I am going to further analyze these images, the images won’t match and I will be unable to get a good analysis. Is there any other way I can do this using a different software (i.e. Fiji)?