I am trying to establish a pipeline to analyse confocal images of Cells and Nuclei. What I would like as an outcome of my pipeline is: Determine cell boundaries, identify nuclei inside one cell, count and quantify nuclei signal within each cell, and quantify nuclear morphology. All of this I was able to do after watching a few tutorials online. However, my issue is counting and identifying nuclei separately rather than having the total of nuclei, and the mean shape morphological parameters. I would like to have separate reads for each nucleus; like in Image J for example, after you analyse your particles every nucleus will be assigned a number, and for every number their will be an output reading generated in the excel sheet of readouts that gives information about each nucleus separately. This is what I am trying to to with cellprofiler. If anyone is aware of a method to do so or is aware of an available plugin that can help me do that please share with me.
The help is very much appreciated from everyone!
Thanks guys and have a nice day!