Straightening an image according to a line selection

Hi there.

I am working on transport of small particles through a tube and my whole analysis procedure is written in MatLab except for one little step: Somewhere in the middle I have to straighten the slightly wiggly tubes. Currently, in order to do this, I export my video from Matlab, open it in ImageJ, and manually select the tube by drawing a polyline along it. I then use a plugin which performs a spline fit to the poly line and then straightens the tube along the line. An example can be found here: "http://fiji.sc/Straighten..." . Now, I would love to be able to do this in MatLab and I know how to make and use a polyline selection but how could I do the actual straightening? Any help is greatly appreciated.

Thanks. Fabian

[fromLondon]

Sorry, I just realized that the link didn't work because the third dot was recognized as a full stop. The correct link is here

[Johannes Holm]

I have the exact same problem, and would very much like to avoid having to step out of matlab and use ImageJ to solve it.

I wouldn't want to implement the straightening algorithm myself based on the documentation. Instead as a work around this build of ImageJ called Miji might do the trick: http://fiji.sc/Miji

Answer 1

[rolf harkes]

I also required this function and looked it up in the ImageJ source code. A simple matlab implementation can be found here:

https://nl.mathworks.com/matlabcentral/fileexchange/72266-straighten