I was wondering if there is a way to filter out foci within a parent object if they are below a certain number. There was an old thread from 2008 about it but the module in question described does not exist in that form any more. I have tried to use the FilterObjects module with Limits and Object_Number as measurement. Unfortunately it did not seem to work and it subtracted foci seemingly randomly.
Thank you very much for the help in advance!
I think one way to achieve this would be to first use RelateObjects to associate foci with parent objects, then use FilterObjects on the parent objects with Limits set by Count_Children to remove any objects which didn’t have enough foci. If you’re then only interested in the foci rather than the parents, you may want to remove any of the foci from the filtered parent objects using the masking modules.
Thank you! I have tried to do it, but after relating the parent and child objects I only have Object_Number in Limits. If I set the FilterObjects on the parent then I guess it will just count my parent object instead of the child. I’m not sure which part I am doing wrong.
You’ll need to filter the parents rather than the children, since the count of foci (children) will only be present for the parent object.
If you can upload a pipeline file we might be able to take a look at it.
I have attached the project file (my question is related to a part of a longer pipeline, but the part in question is modules 22- 23).
Test_analysis_with LMNA_20200409.cpproj (1.8 MB)
I’m attaching an edited version of the pipeline with the filter set up as I mentioned. I can’t properly test this without the source images but this should filter the cells down to those with the correct number of foci.
If there is no further analysis to be performed you should be able to pull out the correct cells and foci in the output spreadsheets.
I should also mention that “Object_Number” refers to the absolute identifying number of an object in the image, not it’s measurements. The original filter was therefore just removing the first 3 objects that were found in the image.
I went through your edit to understand my mistake and it seems that in my original pipeline for some reason I did not have a Children category to choose which made the confusion. But just closing and reopening it fixed that glitch. Thank you very much for the initial advice and also for helping out and checking the pipeline for me! It works now.