I am a new user to cell profiler and I have been trying to measure the area taken up by my primary objects (nuclei) and plot the area that they take up in a histogram. As such I expect the area values to be relatively similar to each other. Yet I am unable to tell the histogram to plot the area of each nuclei instead I can only seemingly plot the number of objects and their x or y coordinates but not the area, any help would be appreciated.
Hi Andrew and welcome! To do this, you would need to add to your pipeline these modules:
- MeasureObjectsSizeShape (missing for you is my guess?)
Then to show the values you can use the DisplayHistogram, choosing the Area feature, and DisplayDataOnImage might help as well to show individual objects’ area on a particular image.
Feel free to post your pipeline and a sample image set here if you need more help.