This is my first post on this board. I have been using cellprofiler for several month now, I have a fairly specific question regarding nuclei identification. I have a set of images consisting of cell that have been immunostained for a nuclei specific protein (see attached image), I need to calculate the area of the nuclei based on this signal. I am using the attached pipelines to generate this data.
I am having the following problem. If the identification parameter of object size is set to be between 10,40 pixels, the program seems to break up the nuclei into small pieces. If the parameter is set as 20,60 pixels (very close to what the measured size is) the program does not identify many nuclei, and tends to merge the ones it does identify. I tried running several different identification algorithms, and no luck, OTSU adaptive seems to be the best. What would be the recommended setting for this type of images? Would it be possible to train the software to recognize my objects? Should I do more image processing to improve my results?
Nuclei_id_2060_w_figsPIPE.mat (956 Bytes)
Nuclei_id_1040_w_figsPIPE.mat (956 Bytes)