Fiber Orientation

[Sam Wu]

Hi all,

I am new to imagej and I am now working on the fiber orientation on SEM images. I have come SEM images of collagens fibers and I have to work out the fiber orientation function of it. Is there any methods to work that out?

Thank you for your suggestions.

Sam

[Michael Weber-4]

Hey Sam,

I never used it, but maybe the "directionality" plugin helps?

http://pacific.mpi-cbg.de/wiki/index.php/Directionality

Michael

> Hi all,
>
> I am new to imagej and I am now working on the fiber orientation on SEM
> images. I have come SEM images of collagens fibers and I have to work out
> the fiber orientation function of it. Is there any methods to work that
> out?
>
> Thank you for your suggestions.
>
> Sam
> --
> View this message in context:
> http://n2.nabble.com/Fiber-Orientation-tp4719113p4719113.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[Jean-Yves Tinevez-2]

On Mar 11, 2010, at 11:28 PM, Sam Wu wrote:

> Hi all,
>
> I am new to imagej and I am now working on the fiber orientation on  
> SEM
> images. I have come SEM images of collagens fibers and I have to  
> work out
> the fiber orientation function of it. Is there any methods to work  
> that out?
>
> Thank you for your suggestions.

Dear Sam,

We just put together a plugin that does that for very close purpose.
Have a look here:
http://pacific.mpi-cbg.de/wiki/index.php/Directionality

If this is what you need, it's in Fiji since 5 min.

Best
jy

[Sam Wu]

Hi JY,

Thanks so much but I just cannot find the download link of this plugin.

Sam

[Daniel Sage]

Hello,

You can have a look at the plugin OrientationJ (Distribution) that we have used for directional analysis of collagen fibers on a maximum intensity projection of 3D fluorescences images. OrientationJ computes the local orientation and the local coherency (anisotropy factor) of an image: <http://bigwww.epfl.ch/demo/orientation/>
The 3D version is coming soon...

A monogenic analysis is also an option. It gives access to the local direction, the instant frequency and the coherency at different dyadic scales: <http://bigwww.epfl.ch/demo/monogenic/>

--
Daniel Sage

On 11 mars 2010, at 23:28, Sam Wu wrote:

> Hi all,
>
> I am new to imagej and I am now working on the fiber orientation on SEM
> images. I have come SEM images of collagens fibers and I have to work out
> the fiber orientation function of it. Is there any methods to work that out?
>
> Thank you for your suggestions.
>
> Sam
> --
> View this message in context: http://n2.nabble.com/Fiber-Orientation-tp4719113p4719113.html
> Sent from the ImageJ mailing list archive at Nabble.com.

 

[Michael Doube]

> The 3D version is coming soon...

Daniel,

Please let us all know when that is ready!

Michael

[Jean-Yves Tinevez-2]

On Mar 14, 2010, at 8:36 PM, Sam Wu wrote:

> Hi JY,
>
> Thanks so much but I just cannot find the download link of this  
> plugin.

Hi Sam,

Right now, I just made it for Fiji (because of a lib dependency,  
jFreeChart, do people think I should do a non-Fiji plugin as well?).
So you have first to download fiji, here:

http://pacific.mpi-cbg.de/wiki/index.php/Main_Page

Install it, run it, and update it using the Help > Update Fiji menu  
item.
You have to go to Advanced mode and the Directionality plugin is going  
to be in the Non-installed category.
Just select Install it in the context menu, click Apply changes and  
when it's done, restart Fiji.

The directionality plugin will then be in the Analyze menu.

Also, for what you need, Daniel Sage pointed us on another mailing-
list this morning towards OrientationJ which might also do what you  
want:

http://bigwww.epfl.ch/demo/orientation/

Best!
jy

[edusleep]

Hi,

I am not sure if this will fit here but it is the closest thread I found. I am interested at the degree of alignment or elongation that cells show inside different biomaterials. I tested the Directionality plugin in a couple of images and while I can see that in the images where the alignment/elongation of the cells is more prominent the distribution of directions becomes sharper (narrower gaussian fit), I don't know how test whether there are significant differences between different sets of images.

Does anyone know if you can get statistical significance with the Directionality plugin or if there is another way to work it around?

Thanks,
Eduard