3D volume measurement

[Mauricio Aguirre Morales]

Dear Community

I am trying to quantify the volume of a hypha in a stack of images. The
3D model was made with a CLSM and I have done some treatment
(brightness-contrast, 3D filters, etc) and finally aquire a model that
could be transformed into 8 bit and being black and white with "white"
fungi and black background or just not fungi. When I use the option 3D
viewer in the description there is a volume displayed but I wonder how
this volume is acquired and furthermore I would really appreciate if
somebody can tell me a better, more accurate way to measure a volume or
even a manual selection way slide after slide or something similar.

--
Sincerely
Mauricio Aguirre Morales


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[Thomas Boudier]

Dear Mauricio,

If you only want the volume of your object, just look at the histogram,
the number of white pixels (or voxels in 3D) will give you the
uncalibrated volume, multiply this number by the calibrated volume of
one voxel. For more complex analysis like shape descriptors use 3D
Object Counter or 3D Manager.

Best,

Thomas


On 08/10/14 22:39, Mauricio Aguirre Morales wrote:

> Dear Community
>
> I am trying to quantify the volume of a hypha in a stack of images. The
> 3D model was made with a CLSM and I have done some treatment
> (brightness-contrast, 3D filters, etc) and finally aquire a model that
> could be transformed into 8 bit and being black and white with "white"
> fungi and black background or just not fungi. When I use the option 3D
> viewer in the description there is a volume displayed but I wonder how
> this volume is acquired and furthermore I would really appreciate if
> somebody can tell me a better, more accurate way to measure a volume or
> even a manual selection way slide after slide or something similar.
>

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

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[Mauricio Aguirre Morales]

Dear Thomas
Thank you very much for your answer. One of the problems I have also
encountered is the background noise and artifacts in my sample which I
cannot remove, otherwise I will end up without any signal at all. Thus I
am pushing more if possible for a manual selection, however so far I
have not yet found the way.

El 09/10/2014 03:26 a.m., Thomas Boudier escribió:

> Dear Mauricio,
>
> If you only want the volume of your object, just look at the
> histogram, the number of white pixels (or voxels in 3D) will give you
> the uncalibrated volume, multiply this number by the calibrated volume
> of one voxel. For more complex analysis like shape descriptors use 3D
> Object Counter or 3D Manager.
>
> Best,
>
> Thomas
>
>
> On 08/10/14 22:39, Mauricio Aguirre Morales wrote:
>> Dear Community
>>
>> I am trying to quantify the volume of a hypha in a stack of images. The
>> 3D model was made with a CLSM and I have done some treatment
>> (brightness-contrast, 3D filters, etc) and finally aquire a model that
>> could be transformed into 8 bit and being black and white with "white"
>> fungi and black background or just not fungi. When I use the option 3D
>> viewer in the description there is a volume displayed but I wonder how
>> this volume is acquired and furthermore I would really appreciate if
>> somebody can tell me a better, more accurate way to measure a volume or
>> even a manual selection way slide after slide or something similar.
>>
>

--
Sincerely
Mauricio Aguirre Morales

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

[Robert Dougherty]

Mauricio,
There is a manual plugin called Measure Stack on the OptiNav web site.
Bob

Sent from my iPhone

> On Oct 13, 2014, at 7:07 AM, Mauricio Aguirre Morales <[hidden email]> wrote:
>
> Dear Thomas
> Thank you very much for your answer. One of the problems I have also encountered is the background noise and artifacts in my sample which I cannot remove, otherwise I will end up without any signal at all. Thus I am pushing more if possible for a manual selection, however so far I have not yet found the way.
>
> El 09/10/2014 03:26 a.m., Thomas Boudier escribió:
>> Dear Mauricio,
>>
>> If you only want the volume of your object, just look at the histogram, the number of white pixels (or voxels in 3D) will give you the uncalibrated volume, multiply this number by the calibrated volume of one voxel. For more complex analysis like shape descriptors use 3D Object Counter or 3D Manager.
>>
>> Best,
>>
>> Thomas
>>
>>
>>> On 08/10/14 22:39, Mauricio Aguirre Morales wrote:
>>> Dear Community
>>>
>>> I am trying to quantify the volume of a hypha in a stack of images. The
>>> 3D model was made with a CLSM and I have done some treatment
>>> (brightness-contrast, 3D filters, etc) and finally aquire a model that
>>> could be transformed into 8 bit and being black and white with "white"
>>> fungi and black background or just not fungi. When I use the option 3D
>>> viewer in the description there is a volume displayed but I wonder how
>>> this volume is acquired and furthermore I would really appreciate if
>>> somebody can tell me a better, more accurate way to measure a volume or
>>> even a manual selection way slide after slide or something similar.
>
> --
> Sincerely
> Mauricio Aguirre Morales
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Mauricio Aguirre Morales]

Thank you very much Bob, I see is your own plug in ;) at first glance it
looks exactly like what I need!!!
El 13/10/2014 04:50 p.m., Robert Dougherty escribió:
> Measure Stack on the OptiNav

--
Sincerely
Mauricio Aguirre Morales

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[Stoyan Pavlov]

1) SUM ( Cross-sectional area)X(section thickness +distance between
sections)

OR
2) Average Cross-sectional areaX(section thickness +distance between
sections)X Number of measured sections
На 08.10.2014 17:48 "Mauricio Aguirre Morales" <[hidden email]>
написа:

> Dear Community
>
> I am trying to quantify the volume of a hypha in a stack of images. The 3D
> model was made with a CLSM and I have done some treatment
> (brightness-contrast, 3D filters, etc) and finally aquire a model that
> could be transformed into 8 bit and being black and white with "white"
> fungi and black background or just not fungi. When I use the option 3D
> viewer in the description there is a volume displayed but I wonder how this
> volume is acquired and furthermore I would really appreciate if somebody
> can tell me a better, more accurate way to measure a volume or even a
> manual selection way slide after slide or something similar.
>
> --
> Sincerely
> Mauricio Aguirre Morales
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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