Volume Viewer and 3D Surface Plugins

[Rachel Golden]

I recently acquired the ImageJ software and I'm working with the
Interactive 3D surface plot and the Volume Viewer plugins.  Using these
plugins, I am trying to find the volume of a small region of lesioned
coral in order to quantify the rate of polyp regeneration.  I need to
assign exact values and units to the 3D graph.  Can you send me more
information about these (and other related/helpful) plugins?
Thanks!
Rachel Golden
Undergraduate Researcher, Boston University
5 Cummington Street
Boston, MA 02215

[David Hovis]

It isn't clear to me how you plan on obtaining the data.  The  
Interactive 3D surface plot and Volume Viewer plugins are for display,  
not quantization.  You have to have 3D data to put into them in the  
first place (from a confocal microscope or something).

Without knowing what your imaging technique is, we can't help you.

--David


On Jul 1, 2008, at 2:02 PM, Rachel Golden wrote:

> I recently acquired the ImageJ software and I'm working with the  
> Interactive 3D surface plot and the Volume Viewer plugins.  Using  
> these plugins, I am trying to find the volume of a small region of  
> lesioned coral in order to quantify the rate of polyp regeneration.  
> I need to assign exact values and units to the 3D graph.  Can you  
> send me more information about these (and other related/helpful)  
> plugins?
> Thanks!
> Rachel Golden
> Undergraduate Researcher, Boston University
> 5 Cummington Street
> Boston, MA 02215

[Rachel Golden]

David,

We are using a dissecting scope with a 63mm Nikon digital camera.  We
do not have 3D data (the depth measurements) which is what we need.  Is
there another plugin or software program that we can use to analyze the
depth/volume of the coral?

If this is not possible, then we can use 2D measurements and find the
surface area for example.  Which plugin/analysis should we use to
measure the surface area of an ellipse?

Thanks,
Rachel Golden
Undergraduate Researcher, Boston University
5 Cummington Street
Boston, MA 02215

Quoting David Hovis <[hidden email]>:

> It isn't clear to me how you plan on obtaining the data.  The
> Interactive 3D surface plot and Volume Viewer plugins are for display,
> not quantization.  You have to have 3D data to put into them in the
> first place (from a confocal microscope or something).
>
> Without knowing what your imaging technique is, we can't help you.
>
> --David
>
>
> On Jul 1, 2008, at 2:02 PM, Rachel Golden wrote:
>
>> I recently acquired the ImageJ software and I'm working with the  
>> Interactive 3D surface plot and the Volume Viewer plugins.  Using  
>> these plugins, I am trying to find the volume of a small region of  
>> lesioned coral in order to quantify the rate of polyp regeneration.  
>>  I need to assign exact values and units to the 3D graph.  Can you  
>> send me more information about these (and other related/helpful)  
>> plugins?
>> Thanks!
>> Rachel Golden
>> Undergraduate Researcher, Boston University
>> 5 Cummington Street
>> Boston, MA 02215
>
>

[Joel Sheffield]

Rachel,

Can you calibrate the focus on your microscope so that you can
actually make some measurements?  That is, take an object of known
thickness --say a microscope slide, draw a line on the top and the
bottom, and then see how much of a turn of the focus knob is
necessary for that distance.  If you want to be much fancier, you can
take pictures at each depth and see if it is possible to make 3d
images.  But, first things first.  Can you use the microscope to
measure depth?

Joel


Date sent:       Tue, 1 Jul 2008 15:38:34 -0400
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Rachel Golden <[hidden email]>
Subject:         Re: Volume Viewer and 3D Surface Plugins
To:             [hidden email]

> David,
>
> We are using a dissecting scope with a 63mm Nikon digital camera.  We
> do not have 3D data (the depth measurements) which is what we need.  Is
> there another plugin or software program that we can use to analyze the
> depth/volume of the coral?
>
> If this is not possible, then we can use 2D measurements and find the
> surface area for example.  Which plugin/analysis should we use to
> measure the surface area of an ellipse?
>
> Thanks,
> Rachel Golden
> Undergraduate Researcher, Boston University
> 5 Cummington Street
> Boston, MA 02215
>
> Quoting David Hovis <[hidden email]>:
>
> > It isn't clear to me how you plan on obtaining the data.  The
> > Interactive 3D surface plot and Volume Viewer plugins are for display,
> > not quantization.  You have to have 3D data to put into them in the
> > first place (from a confocal microscope or something).
> >
> > Without knowing what your imaging technique is, we can't help you.
> >
> > --David
> >
> >
> > On Jul 1, 2008, at 2:02 PM, Rachel Golden wrote:
> >
> >> I recently acquired the ImageJ software and I'm working with the  
> >> Interactive 3D surface plot and the Volume Viewer plugins.  Using  
> >> these plugins, I am trying to find the volume of a small region of  
> >> lesioned coral in order to quantify the rate of polyp regeneration.  
> >>  I need to assign exact values and units to the 3D graph.  Can you  
> >> send me more information about these (and other related/helpful)  
> >> plugins?
> >> Thanks!
> >> Rachel Golden
> >> Undergraduate Researcher, Boston University
> >> 5 Cummington Street
> >> Boston, MA 02215
> >
> >

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs