I’m trying to use cellprofiler to identify some yeast cells and measure the ratio of intensity from the nucleus / cytoplasm. Unfortunately the images are grayscale, so I don’t have different colours for nuclei… The images (e.g. im2.tif which is attached) have also a bad contrast and I can’t identify the cells very well in the first place. Could you please help me with a pipeline which can improve the detection of these cells? Is there a way to measure the intensity from the nucleus/cytoplasm if I have only primary objects (whole cells)?
Another unrelated question that I have: is it possible to integrate the cellprofiler modules in Matlab? I know that the first versions of cellprofiler used Matlab code.