I have installed cell profiler on my computer since two weeks, my objective is to determine with DAPI nuclei pictures the DNA content of my cells to evaluate their cell cycle (like you already published in GenomeBiology2006 Figure 2C). So, I was wondering if there is any way I can found the directive how to use cellprofiler to obtain these datas, such as an explanation chart.
here is the scheme i am using for a similar job:
on top of that, you can add overlay of segmented cells with DAPI picture to check if the segmentation is correctly executed.
obviously, the crucial part is the second module and the type of algorithm and parameters that will suit the best your images.
module 3 will give you intensity values (mean intensity, integrated intensity…)
and between modules 3 and 4, you can also add a module ClassifyObject to determine which cell belongs to a specific cell cycle stage
lastly, in module 4, you can export data for whole images (so you get averaged values) and specified objects (nucleus in your case).
Hope that helps.
Laurent, thanks for your great post! Delphine, I would follow Laurent’s example. Just to add to the comments, you will want to plot the Integrated Intensity of your DAPI nuclei. If these are ‘normal’ nuclei, there should be 2 peeks (2N and 4N only). If these nuclei are somehow treated with chemicals to inhibit cell division (or become polyploid), you will likely see more peaks.