The intensity of each cell

Hi,

I just want to ask a simple question relating to my experiment. I firstly need to identify the cytoplasm of cell by using whole cell stain and DAPI and I have successfully done that by identify primary, secondary and tertiary objects. Then I need to calculate the intensity of cytoplasm of each cell. However, I only can generate the intensity value as a sum of all cytoplasm I outlined. Is there any module I can select to measure and report the intensity of every cell as a list. That will be really helpful because now I have to draw every single cell manually as region of interest on ImageJ which is killing me. I uploaded a picture which is the merge picture of the DAPI and my GFP labelled protein. I want to know the intensity of the cytoplasmic area of each cell, Mean value and the min and max. I have single channel images.

Also, I always get the intensity as a number between 0-1. is there any other range? like 0-4096. My image is 12bits.


Hi,

Yes, you can use MeasureObjectIntensity on the Cytoplasm object (from the TertiaryObjects module). Then use ExportToSpreadsheet and be sure to export the PerObject table (which it does by default). Note that the PerImage table contains means across all objects in an image, which is what I assume you were looking at. If you look at the PerObject table/csv, then there will be one row per object with all the intensities of those objects, including mean, max, min, etc.

Please see this recent answer:
cellprofiler.org/forum/viewtopic … cc07#p8851

David