cell projections cuantification?

[Guadalupe]

Good afternoon,

I am trying to count cell projections (like filopodia extensions) and I was wondering if anyone is aware of an automated way to do it with ImageJ? I would need to know number and length of all the extensions from the cells.

Thank you very much

Guadalupe

[carlo bianco]

maybe you can try with plugins developed for neurons, like neuronj
or you can, after a tresholding, measure perimeter of the extracted objects.
But I think that plugins developed for neurons are the main,
best wishes for your research
carlo-bologna university





Il Domenica 9 Febbraio 2014 22:44, Guadalupe <[hidden email]> ha scritto:
 
Good afternoon,

I am trying to count cell projections (like filopodia extensions) and I was
wondering if anyone is aware of an automated way to do it with ImageJ? I
would need to know number and length of all the extensions from the cells.

Thank you very much

Guadalupe



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[6:1135]

hi,
could you share some images to make me an idea, I wrote a macro to
analyze mitochondria (number, length) using different plugins (tubeness,
squeletonize..) wich could do the trick

regards

Gilles COURTAND
Institut de Neurosciences Cognitives et Intégratives d'Aquitaine
UMR 5287 CNRS-Université de Bordeaux
Bat B2
Avenue des facultés 33405 Talence France
tel: [phone]
fax: [phone]
http://www.incia.u-bordeaux1.fr/

Le 09/02/2014 22:42, Guadalupe a écrit :

> Good afternoon,
>
> I am trying to count cell projections (like filopodia extensions) and I was
> wondering if anyone is aware of an automated way to do it with ImageJ? I
> would need to know number and length of all the extensions from the cells.
>
> Thank you very much
>
> Guadalupe
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/cell-projections-cuantification-tp5006468.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Adam Hughes]

If there's not a tool specific to this task, it seems like trainable
segmentation might be the first step; at least to separate the extensions
from the core cell.

http://www.youtube.com/watch?v=8yfBHiGufFE


On Mon, Feb 10, 2014 at 3:46 AM, Courtand Gilles <
[hidden email]> wrote:

> hi,
> could you share some images to make me an idea, I wrote a macro to analyze
> mitochondria (number, length) using different plugins (tubeness,
> squeletonize..) wich could do the trick
>
> regards
>
> Gilles COURTAND
> Institut de Neurosciences Cognitives et Intégratives d'Aquitaine
> UMR 5287 CNRS-Université de Bordeaux
> Bat B2
> Avenue des facultés 33405 Talence France
> tel: [phone]
> fax: [phone]
> http://www.incia.u-bordeaux1.fr/
>
> Le 09/02/2014 22:42, Guadalupe a écrit :
>
>  Good afternoon,
>>
>> I am trying to count cell projections (like filopodia extensions) and I
>> was
>> wondering if anyone is aware of an automated way to do it with ImageJ? I
>> would need to know number and length of all the extensions from the cells.
>>
>> Thank you very much
>>
>> Guadalupe
>>
>>
>>
>> --
>> View this message in context: http://imagej.1557.x6.nabble.
>> com/cell-projections-cuantification-tp5006468.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Zian_Fanti]

You can try NeuronJ or if you have an image sequence maybe a better solution is NeuronGrowth  that you can find in http://www.ifc.unam.mx/ffm/index.html and for more information
http://onlinelibrary.wiley.com/doi/10.1002/dneu.20866/abstract;jsessionid=E9EAA1196732832D8729BDF8EF4FF1CA.f01t04

[ZazaTSRI]

Hi All, I have a problem similar to Guadalupe`s one, and I have never used ImageJ before..so I`m quite lost.. I have Scanning Electron Microscopy images of cells and a "tubular" matrix; I would like to be able to quantify the number, diameter of all the fibers in the image, and as well measuring the contact points between the fibers and the cells..I have tried NeuronJ and other neuronJ-like plug-ins..but with not that much luck..As far as I understood with NeuronJ I will have to manually find all the path of the fibers, where I was looking for something more automatic.. Any help will be much appreciated!