I was wondering if there was a way to output the area of the h2ax foci. I see a column for the integrated intensity, but I was also wondering if I can just see the area.
Do you have a MeasureObjectSizeShape module in your pipeline? If you don’t and you add one it will add area measurements (among others) to your results output.
The measurement part of the CellProfiler manual has all the details of which modules return which measurements:
As Laura explained you have to include MeasureObjectSizeShape module in your pipeline to get separate Area column. However, if you need only Area but not other SizeShape measurements, I think you can extract it from intensity measurements. I believe, in your spreadsheet you have not only integrated intensity, but also Mean intensity, which is basically integrated intensity divided by area in pixels
- IntegratedIntensity: The sum of the pixel intensities within an object.
- MeanIntensity: The average pixel intensity within an object.
Thus simple math helps you to extract area of the h2ax foci from only intensity measurements.