I’m new with CellProfiler. I need some help with the module “Measure Neurons”. I have GFP expressing neurons with no nuclear staining. I want to quantify the total neurite growth over a period of time using time lapse imaging. I created a pipeline to study some pictures of neurons and get the neurite length from the images.
My pipeline is as follows:
EnhanceOrSuppressFeatures - (used to enhance the neurites)
ApplyThreshold - (used to enhance the cell body, such that low GFP expressing cells and the neurites are not detected)
IdentifyPrimaryObjects - (identifies the cell body)
ApplyThreshold - (to create a binary image)
Morph - (used the skel module to generate skeletonized image)
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Using this pipeline I’m able to generate skeletonized image of the neurons, My problem is that there is still some background in the images generated and not all detected neurites are attached to the cell soma and therefore not detected. How can I overcome this problem and also is it the right way to construct this pipeline. It would be great if you could please help me.
Thank you so much