Mean Free Path and Waterfall or P-Algorithm Segmentation

[wustlmed]

I'm trying to analyze cytoskeletal filaments and get some quantitative parameters in terms of density, branching, etc. I'm familiar with existing techniques like watershed segmentation but even with pre-processing I'm still having problems with oversegmentation. I've read some research about refinements of the watershed method, such as Hierarchical segmentation, waterfall, and p-algorithm segmentation but it seems that even though these techniques were published some years ago there are no plugins available in FIJI to do this so firstly is anyone aware of these methods being implemented in FIJI or other similar packages?

Secondly, I was wondering if anyone is familiar with a plugin for calculating the "mean free path" in an image. For instance, imagine a binary image of a spider web, is there a way to randomly place hundreds of seed points in the image and then calculate a mean free path that they travel before they run into a white pixel?  

[Ignacio Arganda-Carreras-2]

Hello miwo,

A few months ago I implemented the Hierarchical segmentation algorithm in
MorpholibJ. It's on an experimental branch:
https://github.com/ijpb/MorphoLibJ/tree/waterfalls

I didn't find it improved much my results so I didn't keep developing.
You're very welcome to contribute to the project if you are interested.

Best,

ignacio

On Sat, Apr 4, 2015 at 1:00 AM, wustlmed <[hidden email]> wrote:

> I'm trying to analyze cytoskeletal filaments and get some quantitative
> parameters in terms of density, branching, etc. I'm familiar with existing
> techniques like watershed segmentation but even with pre-processing I'm
> still having problems with oversegmentation. I've read some research about
> refinements of the watershed method, such as Hierarchical segmentation,
> waterfall, and p-algorithm segmentation but it seems that even though these
> techniques were published some years ago there are no plugins available in
> FIJI to do this so firstly is anyone aware of these methods being
> implemented in FIJI or other similar packages?
>
> Secondly, I was wondering if anyone is familiar with a plugin for
> calculating the "mean free path" in an image. For instance, imagine a
> binary
> image of a spider web, is there a way to randomly place hundreds of seed
> points in the image and then calculate a mean free path that they travel
> before they run into a white pixel?
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Mean-Free-Path-and-Waterfall-or-P-Algorithm-Segmentation-tp5012341.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

Tel : [phone] - fax : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html