IdentifyPrimaryObjects accurately

Hi all,

I am attempting to get cellProfiler to accurately measure nucleus size and secondly identifysecondaryobject. I am having issues getting this to work effectively. Please see attached image.


Which settings in IdentifyPrimaryObjects do I need to play around with to make the program better capture the data?

Hi!

I would recommend including the original image along with your segmented image, and the pipeline that you used to generate your current image. That seems to be the most useful for the CellProfiler folks to provide help.

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Hi sspag1,

Yes. As mentioned please provide raw image along with the pipeline that you are trying with, so that we could help you better. Nevertheless, it looks you are under segmented. This could be even solved just by playing with your threshold cutoff. For this too, we might need to have a look at raw image.

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

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Apologies, heres the pipeline and image. Iā€™m not too sure that I understand the thresholding. Any advice will be greatly appreciated

MSC5x5Complexx10zoom.cpproj (182.2 KB)

Hi @sspag1,

The problem was you were using a smoothening filter for nuclei image which is not necessary. In the process of median filter you are losing the signal as well in this example. Actually for primary object, you can just use the DAPI image directly since there is not much of background & also I had altered the size filter you had used. In addition, secondary objects parameters I had altered a bit. PFA pipeline with changes & screenshot.
MSC5x5Complexx10zoom_new.cpproj (689.0 KB)

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

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

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Cheers for the help lakshmi

Much appreciated

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