[3dem] Fibers segmentation

[rigort at biochem.mpg.de]

Hello Karthik,

In addition to Willy recommendation you might also try our actin  
segmentation software for this. The cylindrical template can be  
adjusted to match different filament diameters and the tracing  
algorithm can trace curved filaments by influencing the parameter  
'cocircularity'...

Have a look at the tutorial pdf on the software webpage:

==> http://www.zib.de/en/visual/software/cryoem.html


A good resource and overview on what's available in the community in
terms of visualization packages etc. is found here:

==> http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy


best regards,

Alex






Zitat von wriggers <wriggers at biomachina.org>:

> Hello Karthik,
>
> You can try our voltrac segmentation tool which is available in   
> Situs (command
> line tool) or in Sculptor (GUI). It uses a genetic algorithm to place seed
> templates and then performs a bidirectional search to trace the   
> fibers. Voltrac
> was developed for curved densities such as in alpha helix detection (high res
> EM) or the segmentation of actin filaments in tomograms. You can adjust the
> diameter of the template (and many other parameters) as needed. See   
> the Sculptor
> tutorial at: http://sculptor.biomachina.org/tut.interpretation.html   
> or the Situs
> user guide at http://situs.biomachina.org/fguide.html#voltrac.
>
> Best wishes,
> Willy
>
>
> Willy Wriggers, Ph.D.
> http://biomachina.org
>
>
> On 7/15/2013 1:04 PM, Gnanasekaran, K. wrote:
>>
>> Hello,
>>
>> I have been having some difficulties in segmenting fibers in polymer matrix
>> from a STEM tomography dataset. The problem is the fibers are of different
>> length, different diameter and curly (Not straight). I am looking for some
>> software which can track along the length of the fiber for a given diameter.
>> Can you suggest any software which I can try for these datasets?
>>
>>
>>
>> Regards
>>
>> Karthik
>>
>>
>>
>>
>>
>> Karthikeyan Gnanasekaran, PhD Candidate
>>
>> Dept. of Chemical Engg. and Chemistry
>>
>> Lab. of Materials and Interface Chemistry
>>
>> Eindhoven University of Technology
>>
>> P.O. Box 513, 5600MB Eindhoven
>>
>> Email: k.gnanasekaran at tue.nl
>>
>> Ph: +31 40 247 8073
>>
>>
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