TrakEM2 in 4D? (and surface contact)

[Gaelle Recher]

Dear all,

Do you know if TrackEM2 is compatible with 4D images (3D+time)?
So far I open each stack/time point in a separate layout, but I would be happy to process at least 3 or 4 successive time points and to re-use the same cells ID.

Moreover I saw in an old discussion that someone was trying to measure the surface contact between cells, and there was no direct measurement of this. Do you know if this feature will be developed in the future? What would be the more straightforward way to estimate this efficiently at the moment?

Thank you very much for your help,
All the best,

Gaëlle
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[Thomas Boudier-3]

Bonjour Gaelle,

In 3DRoiManager, you can analyse co-localisation between objects
including edge-contacts.

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

Best,

Thomas



On 26/05/15 17:50, Gaelle Recher wrote:

> Dear all,
>
> Do you know if TrackEM2 is compatible with 4D images (3D+time)?
> So far I open each stack/time point in a separate layout, but I would be happy to process at least 3 or 4 successive time points and to re-use the same cells ID.
>
> Moreover I saw in an old discussion that someone was trying to measure the surface contact between cells, and there was no direct measurement of this. Do you know if this feature will be developed in the future? What would be the more straightforward way to estimate this efficiently at the moment?
>
> Thank you very much for your help,
> All the best,
>
> Gaëlle
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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

[Gaelle Recher]

Thank you very much, Thomas, indeed that will be useful.

If I may ask again a question : how to import my 3D ROI from (TrakEM / 3D viewer objects) into the 3D ROI Manager?

Thanks a lot!
Best,

Gaëlle

> Le 28 mai 2015 à 09:01, Thomas Boudier <[hidden email]> a écrit :
>
> Bonjour Gaelle,
>
> In 3DRoiManager, you can analyse co-localisation between objects including edge-contacts.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start
>
> Best,
>
> Thomas
>
>
>
> On 26/05/15 17:50, Gaelle Recher wrote:
>> Dear all,
>>
>> Do you know if TrackEM2 is compatible with 4D images (3D+time)?
>> So far I open each stack/time point in a separate layout, but I would be happy to process at least 3 or 4 successive time points and to re-use the same cells ID.
>>
>> Moreover I saw in an old discussion that someone was trying to measure the surface contact between cells, and there was no direct measurement of this. Do you know if this feature will be developed in the future? What would be the more straightforward way to estimate this efficiently at the moment?
>>
>> Thank you very much for your help,
>> All the best,
>>
>> Gaëlle
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
>  /***************************************************************/
>     Thomas Boudier, Associate Professor, UPMC,
>     Université Pierre et Marie Curie, Paris, France.
>     BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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