ROIs out of 3D objects counter?

[Anda Cornea]

Hello!



I am trying to count small bright objects included in larger less intense somewhat spherical objects.  Using the 3D Objects Counter in FIJI/Analyze I can get nice identification and counts of the larger 3D objects.  Now it would seem easy to make each of them a region of interest but I am at a loss on how to do it.  Below is an orthogonal cut through the top orange object to give an idea of how this looks.   Anyone can please help?



Thank you so very much!


Anda



Anda Cornea, Ph.D.
Director of the Imaging and Morphology Support Core
Oregon National Primate Research Center
OHSU
503-690-5293






[cid:[e-mail]85E60]      [cid:[e-mail]85E60]





[cid:[e-mail]85E60]

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[Thomas Boudier]

Hi Anda,

You can use the 3DRoiManager, which can display Rois of 3D objects in
selected slices. I can send you macros for automation if you are interested.

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

best,

Thomas


Le 20/09/2013 01:28, Anda Cornea a écrit :

> Hello!
>
>
>
> I am trying to count small bright objects included in larger less intense somewhat spherical objects.  Using the 3D Objects Counter in FIJI/Analyze I can get nice identification and counts of the larger 3D objects.  Now it would seem easy to make each of them a region of interest but I am at a loss on how to do it.  Below is an orthogonal cut through the top orange object to give an idea of how this looks.   Anyone can please help?
>
>
>
> Thank you so very much!
>
>
> Anda
>
>
>
> Anda Cornea, Ph.D.
> Director of the Imaging and Morphology Support Core
> Oregon National Primate Research Center
> OHSU
> 503-690-5293
>
>
>
>
>
>
> [cid:[e-mail]85E60]      [cid:[e-mail]85E60]
>
>
>
>
>
> [cid:[e-mail]85E60]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

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[Anda Cornea]

I think that this is exactly what I was looking for, thank you so much!  I'll give it a try and see if I need more automation.  It is so awesome that you would offer.

Best wishes,

Anda

Sent from my iPad

On Sep 20, 2013, at 12:41 AM, "Thomas Boudier" <[hidden email]> wrote:

> Hi Anda,
>
> You can use the 3DRoiManager, which can display Rois of 3D objects in
> selected slices. I can send you macros for automation if you are interested.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start
>
> best,
>
> Thomas
>
>
> Le 20/09/2013 01:28, Anda Cornea a écrit :
>> Hello!
>>
>>
>>
>> I am trying to count small bright objects included in larger less intense somewhat spherical objects.  Using the 3D Objects Counter in FIJI/Analyze I can get nice identification and counts of the larger 3D objects.  Now it would seem easy to make each of them a region of interest but I am at a loss on how to do it.  Below is an orthogonal cut through the top orange object to give an idea of how this looks.   Anyone can please help?
>>
>>
>>
>> Thank you so very much!
>>
>>
>> Anda
>>
>>
>>
>> Anda Cornea, Ph.D.
>> Director of the Imaging and Morphology Support Core
>> Oregon National Primate Research Center
>> OHSU
>> 503-690-5293
>>
>>
>>
>>
>>
>>
>> [cid:[e-mail]85E60]      [cid:[e-mail]85E60]
>>
>>
>>
>>
>>
>> [cid:[e-mail]85E60]
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
>   /**********************************************************/
>      Thomas Boudier, MCU Université Pierre et Marie Curie,
>      Modélisation Cellulaire et Imagerie Biologique (EE1),
>      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
>      Tel : [phone]   Fax : [phone]
> /*******************************************************/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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