[3dem] Fibers segmentation

[Pranav Shah]

Furthur to Karthik's query is there an alternative to amira for segmenting
vesicles?


Thanking you,

Pranav


On Tue, Jul 16, 2013 at 8:53 PM, <rigort at biochem.mpg.de> wrote:

> 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<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<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<http://sculptor.biomachina.org/tut.interpretation.html> or the Situs
>> user guide at http://situs.biomachina.org/**fguide.html#voltrac<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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>>
>
>
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-- 
Pranav Shah
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