Emulsion polydispersity evaluation


Hello. I’m new to the cellprofiler. Here is my problem.
I am trying to get monodisperse emulsion, so I need to get sizes of many droplets from microscope images. So I tried CellProfiler to streamline this process.
The problem is I can’t make it identify them correctly. They are almost perfectly round circles with dark rims and light insides. IdentifyPrimaryObjects usually finds light insides. This is the main obstacle. I want it to identify them as round circles.
Another problem I don’t understand is working with ExportToSpreadsheet. When I open file with Excel all the data is in one column instead of three, divided by comma. I don’t know how to work with it. I export only MajorAxisLength to get the diameter. If possible I would like get mean value from the set of images and a coefficient of variation.
test.zip (1.48 MB)
test.cp (6.4 KB)



The spreadsheet produced by your pipeline on your images seems to open correctly in Excel on my machine. I suggest trying one of the approaches listed here: excel.tips.net/T003002_CSV_File_ … olumn.html. Let us known if this doesn’t work for you.

Also, would you mind posting the spreadsheet that you are getting from CellProfiler, one that is not opening correctly in Excel?



Thank you for answer!
OK, this spreadsheet. I use Office 2010 on Windows 8.
And the main problem is still identifying droplets. I tried IdentifySecondaryObjects but still didn’t get appropriate results.
DefaultOUT_FilteredRound.csv (5.1 KB)



I’m attaching a pipeline which I think will get your closer to what you want. Your pipeline was definitely pointed in the right correction, so I made the following modifications:

  • Some pre-processing to get rid of the background illumination heterogeneity.
  • With your images, trying to identify the full droplet boundary didn’t seem to work well, due to their touching in some cases, but mostly due to the bright “hole” in the center of each droplet. But it was easier to identify the “hole” first,and then expand out to the full droplet after.
  • Using filtering to distinguish the “holes” from everything else, much as you already did.

Also, you will want to remove the scale bar from the images prior to running the pipeline.

2013_02_19.cp (11.4 KB)


I know this discussion was almost 4 years ago. However, I am currently trying to quantify exact the same thing. Simply mix water and oil with surfactant then quantify emulsion polydispersity. I was wondering if any of you could share your experience using CellProfiler? I am happy to share my images, however, they seem to be too big to upload.


Hi, welcome!

You could try uploading images to google drive on a public sharing setting and placing the link here?

But perhaps your best bet is to download not just the pipeline that Mark made above but also the example images because then you can see how it works on someone else’s images before you try it on your own.


For some reason, downloading/uploading files directly from/to the forum are currently not working.

As Anne mentioned, you can upload your example images on Google drive/Dropbox and share with us the links. But we may have to build pipeline from scratch until the downloading functions again.

Sorry for the inconvenience.