I want to measure microtubule bundlings, but I have no clue how to cope with this. Do you know some plugins or methods? Thank you very much for your input!
If you work with fluorescently labelled microtubules in vitro you can measure mean brightness along the microtubules/bundles per unit length. Collect enough statistics and build a histogram. Make a control under similar conditions but with very diluted microtubules and without any bundling agents to measure what brightness corresponds to single microtubule. After determining the brightness of single microtubule you can analyze the brightness histogram from your experiment to see how strong is microtubule bundling.
Actually, I work with fluorescence labelled microtubules in vivo. I have had the method which you said in my mind. But, In your case, I think at some point, the brightness will be sature and not proportional to the number of microtubules.
You can always adjust the exposure time of your camera or the illumination brightness to make sure the signals you are measuring are in the linear range.