How to measure lines width and lengths by cell profiler

If you see actins in this picture, I hope to analyze the average length, width and even orientation of the actins. How to do with cell profiler, what modules I need to add to the pipeline.C5-2_z44_ch02.tiff (1.0 MB)

Hi Xiang,

After finding the actin fibers by using “IdentifyingPrimaryObjects” module, you can then measure the detected objects by “MeasureObjectSizeShape” module.

Here are some resources that can help you:
Documentation: http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html#measureobjectsizeshape
Take a look at the Measurements made by this module under MeasureObjectSizeShape section.

Examples: https://cellprofiler.org/examples/
and tutorials: https://cellprofiler.org/tutorials/

1 Like

Thanks. But how to identify those fibers, they are too thin and small. I use identifyprimaryobjectives, but the result seems not ideal. Any setting I should change for the module?

It would be helpful if you could upload your pipeline, as well as explain in a bit more detail what “the results are not ideal” are, so we could better figure out how to optimize your workflow!

hi, I upload the pipeline and a picture. The goal is to analyze fiber numbers, length and orientations. But the identified objectives can be 3 or 4 actin bunched together, or circular fibers, which are hard to measure. I hope the pipeline can identify the linear fibers one by one clearly and, if it can, try to remove the very circular signal but leave the almost linear part.
C5-2_z44_ch02.tiff (1.0 MB)
Xiang stress fiber.cpproj (647.7 KB)
I do appreciate if you could help me!

Hi @xxl,
@bcimini

Checked your pipeline. Based on my understanding, you are interested in only linear objects.
In your pipeline I have just added on module called “DisplayDataonImage” & tried to display the parameter i.e.in this case I tried eccentricity since it gives a measure of circularity of object. Based on the values displayed on the objects I choose the same parameter cutoff to remove the object. This remove few circular (semi) objects, may you might have to play around with cutoff to optimise better. you can also explore formfactor. You could also use more than one parameter in filter objects. I have tried using area to remove very small ones.
Regarding the parameters explore check out here.
PFA modified pipeline & screenshot.

Xiang stress fiber_new.cpproj (653.0 KB)
Hope this helps.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

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