Re: Segmentation and volume measurements

Posted by Ignacio Arganda-Carreras-2 on Apr 13, 2015; 8:55am
URL: http://imagej.273.s1.nabble.com/Segmentation-and-volume-measurements-tp5012339p5012448.html

Hello Eric,

If you have a label image, you can also use all the measurement tools in
MorphoLibJ:

https://github.com/ijpb/MorphoLibJ

Cheers!

ignacio

On Wed, Apr 8, 2015 at 11:07 PM, Eric Denarier <
[hidden email]> wrote:

>  I will use it too !!! Thanks
>
> Eric Denarier
> Grenoble Institut des Neurosciences
> Inserm U836
> Chemin Fortuné Ferrini
> 38700 La Tronche
> France
>
>
> Tél :[phone]
> Fax :[phone]
>
> http://neurosciences.ujf-grenoble.fr/
>
> Le 08/04/2015 17:02, Diana, Paolo *HS a écrit :
>
>> Thank you Eric for your suggestions!
>>
>> I am now trying with the Segmentation Editor http://wiki.imagej.net/
>> Segmentation_Editor to segment the original DICOM image and create an
>> 8-bit TIFF segmented image, which I then import in the 3DRoiManager for
>> measuring the volumes of the segmented regions
>> http://imagejdocu.tudor.lu/doku.php?id=tutorial:working:
>> tutorial_for_3d_roi_manager
>>
>> Thank you,
>>
>> Paolo
>>
>> ________________________________________
>> From: ImageJ Interest Group [[hidden email]] On Behalf Of Eric
>> Denarier [[hidden email]]
>> Sent: Tuesday, April 07, 2015 3:15 AM
>> To: [hidden email]
>> Subject: Re: Segmentation and volume measurements
>>
>> Hi Diana,
>> In Fiji you can use the Voxel counter : On your segmented image (saved
>> as a 8 bit color) you select with the thresholder the structure to be
>> measured and use Plugin\Voxel counter. If your dimensions are set it
>> gives you the number of counted pixel per image and the total volume in
>> voxel and in the units you defined.
>> Tha twhat we did you MRI image of mouse
>> Hope it Help !!
>>
>> Eric Denarier
>> Grenoble Institut des Neurosciences
>> Inserm U836
>> Chemin Fortuné Ferrini
>> 38700 La Tronche
>> France
>>
>>
>> Tél :[phone]
>> Fax :[phone]
>>
>> http://neurosciences.ujf-grenoble.fr/
>>
>> Le 03/04/2015 23:39, Diana, Paolo *HS a écrit :
>>
>>> Hello,
>>>
>>> I am a neuroscience researcher and I am trying to analyze brain MRI
>>> images and measure the volume of different brain structures. I have been
>>> using the Segmentation Editor as part of Fiji to isolate the different
>>> structures but I do not know how to continue from there. May I ask you if
>>> anyone could please suggest me an easy technique to measure the volume of
>>> the different ROI/labels?
>>>
>>> Thank you very much for any help.
>>>
>>> Best regards,
>>>
>>> Paolo
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
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>
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--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
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78026 Versailles Cedex France

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