Measuring features from bright field image CellProfiler

Hi,
I’m trying to setup a pipeline in Cell Profiler to analyse the attached bright field images that I would like to compare in terms of output features such as perimeter/diameter, shape, granularity, radial distribution, sphericity to assess cell heterogeneity in the culture.
Does anyone have any idea how I could achieve this in Cell Profiler or has any related pipeline that could be imported? Help will be much appreciated.

Thanks a lot!
Sandra


Hi @SPetrusReurer,

In CellProfiler you could use BF images & could be enhance or supressed based on the problem. This is achievable using EnhanceSupressfeatures using DIC option. Just tried one of your image, it works fine even without EnhanceSuppress. I using similar approach what has been used in this example.This is how my workflow was,

  1. colortoGray
  2. ImageMath - to invert the image
  3. IdentifyPrimary object
    And got this,

    This could be good start I think.

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

Hi @lakshmi,

Many thanks for your reply and for the pipeline advice!
Will give it a try with the rest of the images and see how it looks :slight_smile:
Best wishes,

Sandra

Hi @SPetrusReurer,

Welcome!! In case you need any assistance let me know.

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

Hi @lakshmi,

One more question: what are the parameters/settings you used to get to identify primary objects? Having troubles to replicate your output (see attached image) :wink:

Many thanks again!
Best,

Sandra

One more thing I forgot to ask: how can I save the identified object image with the new version of CellProfiler 3.1.9? The option I used to use to save objects in the SaveImages module seems not to be the new version anymore under “Select the type of images to save”.
Any suggestion will be greatly appreciated :slight_smile:
Thanks a lot!

Sandra

Hi @SPetrusReurer,

Here is the screenshot of the Primary object module settings that I used for your images. PFA pipeline.
I have added EnhanceSuppress feature module but didn’t use. You can try may be!!!

segmentation_BF.cpproj (647.6 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

Hi @SPetrusReurer,

My understanding is that you want to save the identified objects as a mask or image. You might have to use the “ConvertObjectToImage” module which allows you to convert your objects as binary or gray scale images which could be saved using "SaveImages"module.
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

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

Awesome @lakshmi! Both answers are very helpful :slightly_smiling_face:

Super thanks and best wishes,

Sandra

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