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I have an image of a layer of carbon nanotubes taken with an electronic microscope and I would like to extract the "shape" of every nanotube.

I think that ImageJ could be very helpful since it has already led me to encouraging results, but I am sure that they could be improved.

Here is the image I start with :Several nanotubes

I have seen that there are many tools to detect for example cells, or to divide an image in two areas (with the trainable Weka segmentation tool for instance), but I did not find anything to "follow" a tube from the beginning to the end. Does such a tool exist ?

What would you advise me to do to clean the image ? So far, I have tried 'auto local threshold' (loss of information), 'Remove outliers', 'analyse particles' (to remove the too-little-to-be-tubes-particles), and some skeleton tools + OrientationJ to extract information.

Thank you very much for your help !

EDIT : the "Tubeness" plugin was very helpful Tubeness documentation

George Profenza
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Frowl
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  • Welcome to Stack Overflow! Please [edit] your question to show [what you have tried so far](http://whathaveyoutried.com). You should include a [mcve] of the code that you are having problems with, then we can try to help with the specific problem. You should also read [ask]. – Toby Speight Nov 23 '16 at 16:14

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