Dear CellProfiler forum,
My hope is that I will be able to use CellProfiler to automatically align matching sets of 2 images from a single tissue sample. The images are core biopsies that come from a breast cancer tissue microarray slide that was first stained with immunofluorescence (with an anbitody against CK8):
This stain is then washed off and the slide is stained with hematoxylin and eosin and imaged (ideally with the exact same physical parameters as the first time):
Since the images come from the exact same tissue slice, the alignment should only require rotation and translation (with no issues involving morphing of the tissue). Following alignment of the images, I would like to output 2 aligned images, which could then be used to outline the CK8 stain on the HE image. So far, I have tried a very simple CP pipeline (using a pipeline with the align module, which is attached). This pipeline does not seem to be altering the images at all (the reported shift is 0). I wonder if I am running it incorrectly, if there are other pre-processing steps I should complete prior to running align, or should I go with a different strategy altogether.
Any help is greatly appreciated!
Pipeline_CP_Posting.mat (882 Bytes)