C. elegans RFP GFP analysis

Hello, I have just started trying to use this software but I can’t even design the pipeline.

I developed a strain of C. elegans, that express both RFP and GFP.

I am taking 3 pictures at the time: without filters, GFP filter, and RFP filter.

What I want to do is delimitate the shape of the worm in the image without filters, and recognize the shape of the worms, and then with that shape use it in the GFP and RFP pictures to measure the fluorescence and (if possible) straighten them up.

I try to start using the program but I can’t even develop the pipeline (don’t know how to star or what configuration I must apply).

Did you try to use the pipelines and example image data that i referenced here? Measuring GFP and RFP in C elegans. Oftentimes, trying the pipeline first on the data provided and seeing how it performs is a good first step before applying it to your own data.
-Mark