Dear Cell Profiler Team
I am new to the software so please forgive me if my pipeline (attached) is naive.
I am trying to measure neurite length using cell profiler.
I have four stains: DAPI, neurofilament (647 wavelength), map2 (568, dendritic), SMI312 (488, supposedly axonal).
My pipeline doesn't appear to be working at all and I have fiddled with it a lot now. I am at the moment concentrating on the "dendritic" read-out but ideally I would like to calculate lengths for dendritic, axonal and neurofilament.
My other problem is that the DAPI nuclear staining is not clean in my system, and there is a lot of debris not attached to a neurite that needs to be filtered out.
Any help would be much appreciated! I am attaching one czi file and my pipeline as it stands.
Many thanks indeed!