I am trying to measure NileRed in C. elegans. I have been working on the pipeline to do it, but I do have one big problem. My images have shade on the edges of the wells and my pipeline recognizes it as an object.
I was trying to change number of pixels by which to expand or shrink, in Expand orShrinkObjects up to 1000 and I still have the edges outlined as objects.
Also, I was trying to untangle worms just as in OilRedO pipeline but it doesn’t seem to work for me.
I am new to making pipeline in Cell Profiler so I think I may be missing something obvious.
I would be grateful for the advice how to remove the shades on edges of wells or for the pipeline not to recognize it, so they won’t be recognized as an worm object and how to untangle worms, so I can get measurement from each worm and not an average of all objects.
I am adding a link to pipeline, images and the output from CellProfiler