Endocytic organelles


Hi everyone,
I am using cell profiler to assess the impact of different pharmacological compounds on
endocytic organelles. I am starting to set up a pipeline able to follow these changes. Can you help me in extrapolating this parameter ?


Analyzing the RelateObjects Image

(Note: I split this post into a separate topic)
Thanks – you’ll need to post some example images, and best, try to create your own pipeline before we can help much.


Hi David,

you are right: here are my picture and my pipeline. I would extrapolate two information: 1) the diameter of the vesicles and 2) the distribution or maybe the percentage of perinuclear lysosomes. May you help me in drawing correctly my pipeline ()?lysosomes_structures.cpproj (532.4 KB)

Thanks a lot for your help and this powerful image analysis tool,

lysosomes_structures.cpproj (532.4 KB)


I am still waiting on this as well…I would like to determine the distance from the nuclear edge to each endosome such that I can capture re-localization from the periphery to the peri-nuclear region.


Hi, sorry for the delay. You are very close I think, but in any case try out the attached pipeline!

This one is easy, and you’ve already done it. Just look in your output spreadsheet for the object in question, namely MaskedPuncta (assuming you want only masked puncta sizes). There is a column named “AreaShape_Area” which has the output from the MeasureObjectSizeShape module, and the measurement Area.

For this, I added the module MeasureObjectIntensityDistribution, which was just recently renamed from MeasureObjectRadialDistribution. The output looks like this:

  • First, I upgraded to

** BUT note that the pipeline I attached will only work in the Beta CellProfiler we recently pushed out, as there have been a number of fixes and added visualization in MeasureObjectIntensityDistribution that I thought you’d like. Download it here: cellprofiler.org/releases/

Some notes:

  • I added ColorToGray simply because I only had your color image to work with
  • I duplicated your IdentifyPrimaryObjects and changed a couple parameters, and disabled the original. I don’t think the smoothing is likely necessary and am using the raw DNA as input. I lowered the min diameter which was very close to the bottom nucleus size. I raised the Threshold Correction Factor to make the segmentation tighter around the nuclei
  • I think you were missing too many puncta, so I changed to using Otsu thresholding method, and manually setting some declumping parameters
  • I like your masking
  • Added MeasureObjectIntensityDistribution. There are two ways to set this, scaled or unscaled. I did both as an example. Read the Help for more info.

Hope that helps!

lysosomes_structures_DLogan.cppipe (19.8 KB)


Hello David,
thank you very much for youl helpful support-it’s powerful the pipeline you have attached. I was interrogating your pipeline when I got this advice " pipeline version mismatch (mine is rev1b13225)". I have already updated my Cell Profiler to the latest version (beta Cell Profiler). How can I update my CP version to yours (revb91da8e) ?

Thanks a lot for this powerful cell image analysis tool and looking forward to hearing you,



Hi Alessandro,

Ah, good question, but it turns out to be a very minor, or zero, difference. You must be running Windows, since the Windows beta version is (a git hash of) 1b13225. But I am running Mac and the version is b91da8e but the underlying software is the same version.

So please ignore this warning. It’s an unfortunate byproduct of how we have to build on two different OSes and they get different ‘versions’ even though they are really the same. I’ll see if we can make this a little clearer for users on the next beta version.



Hi David,

I have tried the other CP version (Nightly) and it works. Using the beta version, the pipeline unfortunately failed (it claimed an error about the unability to decipher the last renamed module. Anyway, I am going ahead and interrogating the pipeline with my images. I let you know how it progresses.

Thanks again for your support and I come back to you for other issues :wink:



Ah, ok very good! I’ll see about the error too.


Hi David,
This pipeline works great. I’d like ask you something more: I would graph the percentage of lysosomes which are located in the perinuclear area. Looking at table I get from CP analysis, I have three parameters (e.g. Fraction, Intensity and COV). Which parameter is the most associated with my goal ?

Once again, thank you very much…



thanks this post is useful


Dear David,

I’m trying to set up a pipeline for a similar problem and would love to see your pipeline to know what is the problem with mine. However, I can not download your pipeline with Mac or Windows. Could you maybe repost it? I would really appreciate it. Thank you very much.



We’re having a small problem with forum uploads and downloads at the moment; we hope to have it resolved early next week. Sorry for the inconvenience!