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I'm trying to analyze some filaments in FIJI, getting parameters like number of intersections, basin size, filament length, etc. I know one can do watershed segmentation and with several built in features in FIJI analyze the resulting watershed map for some of the above mentioned parameters, but the problem is that image is a skeletonized version of the original. For thin filaments this makes sense but unfortunately I'm using confocal images with of filaments that have quite a large volume/cross-sectional area. I was wondering then if anyone knows of plugins that might be used for analyzing this kind of data. 3d would be great but 2d works as well. I know of some plugins like the simple neurite tracer that are available but it seems that works best for "eroded" or thin filaments as well. Much like watershed it generates a 1 pixel wide skeleton of the filament that was identified. The closest thing I've come across is the Imaris software FilamentTracer which I would like to avoid using given past experience with Imaris.
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