Quantification of nucleus


Thanks again for creating a pipeline for us to quantitate cytoplasmic foci! It is working pretty good for us! ! A new problem we encounter is that we have to count the cells in one image to average the number of foci in each cell.

The following is the image of cell nucleus counterstained with DAPI

Is it feasible to create another pipeline to count these nucleus? Your help will be highly appreciated!!




Hi Shangli,

You can do this in the same pipeline! If you have images of nuclei and of your foci, you can have one pipeline that loads both images, identifies both the nucleus and the foci, and get quantitation for both. Better yet, you can also identify “cells” (arbitrary rings around nucleus) and correlate these to your foci to automatically get average foci/cell! Here is what I would do:

LoadImages (load Foci and Nuclei image)
IdentifyPrimAutomatic (Identify your Nuclei)
IdentifySecondary (Identify Cells around Nuclei using Distance - N)
METHOD OF IDENTIFYING FOCI (I showed you two methods, so use the one which works better here)
Relate (Have foci be the children of Cells)

Now when you analyze your images, the relate module will calculate how many foci are in each cell. You can make these cells expand as far as you want from each nucleus, to cover all of the foci. When you export your data using the data tool “ExportData”, the image output file will contain a field which is the average foci per cell.

Give it a try and if you run in to problems, please ask for help.