Measuring intensity of many individuals


I am trying to measure the intensity of some plants that I have treated with D-luciferin containing a promoter:LUC construct. So I have some pictures with several plants that have different intensities and I am able to measure that but I am unable to output the intensity of each individual with location tag so that I know which is which. Is that possible? It seems like it should be fairly simple but at the moment I cannot figure it out…
I have been working on a pipeline but I have been playing around and it is a bit messy but I will upload it anyways.
I will also upload a picture but this is a fairly bad example as the plants are saturated but it is just a test to get this pipeline ready. I do have pictures that are not saturated to work with (just saying so there is no confusion).


PS - If I missed adding something please just ask…


Luciferase test analysis 2.cppipe (7.96 KB)

Ok so nobody is helping me out but I managed to make a pretty nice pipeline.
There are 2 problems:

  1. I still cannot figure out with object is connect to which object number.
    I have turned them into colour spaces so each has a different colour
    But that information is not output into the spreadsheet
    Is there any way to get that information out

  2. I have some plants with some pretty low signals that are not picked up with my identifyPrimary/secondaryObjects
    Is there any method that is more sensitive

I will post my new pipeline. Again it is a bit messy, only because I am trying out a couple of things and I haven’t had time to clean it up, but the important values, I believe, are the object number and the Intensity values

It would be nice with some help, if it is possible…

Luciferase_pipeline_1.cppipe (31.4 KB)


I’m not on the Cellprofiler team or anything but I might be able to help with your location tag problem.

  1. Select the “DisplayDataOnImage” module.
  2. Choose the objects you want to locate.
  3. For “Category”, choose “Number”.
  4. For “Measurement”, choose “Object_Number”.

This should give you an image that displays each object’s respective number on top of the object. The number should correspond to the object number shown for each object in your exported spreadsheet.

Hope this helps.


Ok thanks I will try that now


So it seems to work really well in terms of placing the number on the picture, however the pictures do not save to my computer. I cannot find them anywhere.
Do I need to add something else to the pipeline in order for that to work properly?
I have to analyze quite a number of pictures so it would not be great if I had to do it one at a time and save the picture, but if there is no other way I suppose I have no choice


First, Vahid is right, namely that you need a DisplayDataOnImage module to add the object number (or whichever measurement you choose) to your image.

And to answer your last question, i.e. to save this image, you need to explicitly add a SaveImages module and save the image that you named in DisplayDataOnImage. Please see the attached pipeline in which I added onto one of your pipelines. The reason we do it this way is that CellProfiler is designed to work in high-throughput, and it would be prohibitive to save all the intermediate steps/images, and so we require the user to explicitly name the images that they want to save.

Hope that helps!

DL_display_pipe.cppipe (9.71 KB)

Thanks that was helpful. I just need to tweak it a bit to include lower intensities I guess but that will depend on which promoter I use anyways.