Hi, I am new to Cellprofiler and want to know if an automated solution for analysis is possible. Let me tell you a little bit about my IHC assay. I am doing a co-localization assay using 10-12 different proteins of interest. We stain the tissue sections, scan the slides, destain and remove the antibodies, then repeat for the next set of proteins. The hard part is manually aligning the images. So far I have thought about applying the ColorToGray module on each image and then performing an alignment on the greyscale images, but this would mean performing an alignment on ~30 images and I’m not sure how to do this.
Sorry for the confusing explanation. I would appreciate any help.