Identifying cells with lines through them

Hello,
I am interested in identifying cells that have lines through them (our experiment involves irradiation in this pattern).
I have looked at a related pipeline of counting GFP+ cells however I am not able to adapt it to this purpose since
I am not sure how to find lines in Cell profiler.
I have attached the image with two channels–the first channel is DAPI (nuclei) and the second channel detects line
formation of a certain GFP-fused protein.
Thank you
Lee

DAPI

GFP_line

Hi,

I don’t think you need to be concerned about finding ‘lines’ per se, since the Identify modules in CellProfiler will do a decent job as-is on long skinny objects like these. I think the more important thing to do is to:
(1) Identify the nuclei and lines in separate IdentifyPrimaryObjects modules (I didn’t tweak them too much)
(2) ‘Relate’ them as Parent-Child using RelateObjects.
(3) Export and look in the parent output table from RelateObjects (‘Nuclei.csv’ here) for the count of child line objects (“Children_LineObj_Count” column). If the count is >= 1, then there is a line in that nucleus.

See the attached pipeline for an example.
Cheers,
David
DLpipe.cppipe (9.13 KB)

Hi David
Thanks very much for the the pipeline. It works perfectly.
I can’t figure out how to create a handle to the resulting image after RelateObjects.
Can you give me a hint?
Lee

Hi Lee,

Note that all RelateObjects does is (not surprisingly) create relationships between objects. It doesn’t save any images for downstream processing. So the answer you’d rather hear ( :smile: ) depends on what you want to do with the RelateObjects output, i.e. I’m not quite sure how to interpret ‘create a handle to the resulting image’. If you mean to save the figure window, unfortunately CP can’t do that explicitly (yet). If you want to downstream process, say, only those nuclei that have child ‘line’ objects, then you can use
(1) FilterObjects, filtering on the parent measurement of _Count.
(2) After that you need to convert the filtered objects to an image to save, so we use the ConvertObjectsToImage module.
(3) Then SaveImages.

See the attached file DLproj_FilterObjects.cppipe for an example. Does that help?

Thanks,
David
DLproj_FilterObjects.cppipe (11.4 KB)