Login  Register

Re: Automatic Measuring of Height and Diameter of regular Fibre-Structures

Posted by Fabian on Sep 29, 2010; 12:03pm
URL: http://imagej.273.s1.nabble.com/Automatic-Measuring-of-Height-and-Diameter-of-regular-Fibre-Structures-tp3686768p3686770.html

Hello everyone.

At first thanks for the constructive answers. The "Versatile Wand" seems to be what I need, as the regular "wand tracing tool" always marked the whole fibre-line from the top of the picture to the bottom.
I am not so sure about the "plot profile". It does the trick, but needs considerable effort to extract the actual diameters afterwards, not to forget, that you have to give lines for the program to follow.

I will try to make a macro which will do the following, but I might need help with one or two of the steps.

ROADMAP of the steps:
1) "Threshold" to get rid of the background and create sharp contrasts for the wand tool.
2) Automated "Versatile Wand" to separate any overlapping fibres.
3) Outline and labeling of the separated fibres. The way to go would be something like the "analyse particles" and "outline" method. It gives very good results, if the area threshold and circularity is set properly.
4) Fit an rectangle to the outlined fibres, which works indepentend of orientation of the fibres (unlike "bounding rectangle). I know "fit ellipses" exists, but it overestimates the longer site and underestimates the shorter one.
5) Gather long and short side of the fit
6)

I will keep you updated on how it goes and would appreciate any suggestions or comments or better roadmaps.
Yours,

Fabian