CellProfiler 3.1.8 3D-detection, remove objects touching border

Hi,

When detecting cells in 3D using watershed I can not find a way to avoid objects touching image border. I have tried to use filter objects (Image and border) but then all objects are removed. Any tips?

Best
Frank

Hi @Frank3,

I tried with the example 3D pipeline, it works fine. May be it would be great if you could share your pipeline with your sample images. Nevertheless, Check your binary mask values from your segmentation/thresholding step. Check if it 0(Pixels that are not interest) and 1(Pixels of interest) that you would be using for filter objects.

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

Join us at the High Content Analysis Symposium Oct 21-22, London
Society for Laboratory Automation and Screening

SLAS 2019 Advanced 3D Human Models and High-Content Analysis Symposium

Read more on our site.

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

Hi Lakshmi,

Thank you for your reply!

Pipeline + image set

Hi again, checked threshold, it is 0 and 1, but came to think about the objects also beeing in first and last slice of z-stack. Is that the problem perhaps, that first and last slice also is considered image border?

@Frank3,

@bcimini

Ok. I don’t think the objects in the first and the last slice of Z-stack will be a problem. It considers the object that touches the borders in the frame. But not sure though!
Please look at the screenshot,

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

Join us at the High Content Analysis Symposium Oct 21-22, London
Society for Laboratory Automation and Screening

SLAS 2019 Advanced 3D Human Models and High-Content Analysis Symposium

Read more on our site.

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

Thanks! I have been trying a bit at home laptop, seems my problems are solved if I add empty slide first and last, but had to readjust threshold, so could also be that.

In case first links did not work:

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