I am using ImageJ/FIJI for my image analysis. I have a cross-sectional fluorescent image of a cell monolayer and would like to use these images to estimate the monolayer/cell height. The strategy I am hoping to use is fit a smooth curve to the upper and lower portion of the image, and then eventually subtract the z values of the two curves to calculate height at every point. I attached some sample images explaining what I’m hoping to do with manually drawn curves. Not all the cells are fluorescent which results in some dark gaps.
Does anyone know of a plugin which could automate fitting a smooth curve to the binary image? Or maybe there is a better strategy to calculate cell height? I can also import the images into Matlab if there are builtin functions which would be easier to use.