Is there any pipelines for calculating viral plaque size by using cell profiler?

Hi, I would like to ask for a good pipeline for calculating viral plaques size by using cell profiler. I am currently using vero cells and try to get an optimized method to measure the plaque sizes after viral infection and stained with cyrstal virolet. Would you mind to share any opinion or pipeline that I can use? thank you

In general, a sample image would help as not everyone will be familiar with your instrument, methods, image background, etc.

Dear Research_Associate,

Thank you for your reply. Please find the picture as attached.

Thank You

A1_01_1_74_Bright Field_001.tif (2.1 MB)

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Dear xevirothtim,

It would also be great if you tell which is your plaque region in your sample image. For example, is this your region of interest,

Do you mean area of the region as plaque size?

Regards,
Lakshmi
Fujfilm Wako Automation (Consultant)
www.wakoautomation.com

Dear Lakshmi,

Thank you very much for your reply,

Exactly, I have tons of picture to analyze. It is really time consuming if I should draw one by one the region. Do you have any idea to automate this by using cell profiler?

Thank You
Tim

That looks like something where the Weka pixel classifier plugin/Ilastik/some sort of pixel classifier might help. You might check out other topics on the forum, there are quite a few on those topics and some decent video guides.

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Dear Xevirothtim,

I don’t think there is an existing pipeline. You might have to make one. I tried the quick segmentation with your sample in cell profiler just based on thresholding. If your intensity/values are in the same range then might work. Is this is what you expect?


Then this just works with Indentify primary object module. This could definitely be better with little playing around with parameters is the module.

The other way is definitely you could try Weka pixel classifier.

Hope this helps.

Regards,
Lakshmi
Fujfilm Wako Automation (Consultant)
www.wakoautomation.com

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Hi Lakshmi,
Thank you again. Yes, definitely something like that. However, I am still new to this platform. Would you mind to share on how you do it? Or else can I consult with you privately?

Thank You

Thank You Research_Associate,

I will noted your input. But, it will be helpful to share the thread which are you referring to in the forum.

Best

Hi Xevirothtim,

I am fine sharing here. This contains just a module with the parameters set in based on your sample image. In case required you might need to add saving the output module and measurement module. This gives you segmentation. In case you need help in complete pipeline let me know.
plaque_trial.cpproj (672.7 KB)
Regards,

Lakshmi
Fujfilm Wako Automation (Consultant)
www.wakoautomation.com

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