How do I select a region for CellProfiler to count in

test_1 (1).cpproj (643.5 KB)
counted.pdf (69.0 KB) Cell image.pdf (168.8 KB)

Hi everyone,
I am very new to cellprofiler so I am having trouble in figuring some stuff out. I would like to count CTB in a specific region as shown in cell image. My current pipeline is counting the entire region. How would I proceed with this? Also, some of my cells are not being picked up and I have tried everything to be able to pick those up. However once I do a change, it ends up messing something or another.
Anything will be appreciated! Thank you so much!!

Hi @Namratha_Tarigopula,

To identify in a specific region of the image, the region should be defined using a binary mask. The mask can be either created outside the pipeline using other software for example Fiji/ImageJ or in the pipeline itself (may be using IdentifyObjectsManually or by segmenting the region).
In your counted pdf, it looks that your nuclei is over segmented. I think you can changing the size cutoff or declumping filter. Though you cell segmentation question is not clear (I mean the cells in your image) may be before segmentation try applying some filter.
May this tutorial might help you.

Regards,
Lakshmi
www.wakoautomation.com

Hmm, I am having trouble with making a binary mask. How would I use a ROI already selected in Fiji and have cellprofiler identify that itself? This is the current pipeline but I am unable to it select for the ROI as selected in Fiji. Thanks so much! Pipeline.cpproj (428.8 KB)

Hi @Namratha_Tarigopula,

In case you want to use the same ROI from Fiji, then you might have to create the binary image with ROI in Fiji itself. Check here reference. Then you can use the resulted tiff image in Cellprofiler or any other software too.
In CellProfiler, you can create ROI manually using “IdentifyObjectManually” module as you have in your current pipeline. Then use “ConvertObjectToImage” module to convert the objects from previous module to binary image. Later you can save this using the “SaveImages” Module.
Hope this helps.

Regards,
Lakshmi
www.wakoautomation.com