Exporting individual cell informtion

Hello, I am using cellprofiler to measure the total intensity of fluorescence in a set of microscope images. My problem is that most images have more than one cell and when the numbers are exported I have a list that tells me the number of cells in each image and the total fluorescent intensity for all the cells, but these numbers are combined. I would like to use standard deviation or other statistics on my numbers, but I need the individual fluorescent values to do this. Any suggestions?

I attached some samples images (positive and negative) and the pipeline I have been using for this analysis. Thanks!

-Lela




FinalDigitoninQuantify.cp (7.69 KB)

Hi Lela,

You are using MeasureImageIntensity when I beleieve what you want to use is MeasureObjectIntensity. This will measure the per-object intensities, and then you will see these values in the Cells.csv spreadsheet as well as the aggregate statistics in the Image.csv spreadsheet.

Regards,
-Mark