3D volume rendering and measurement

[Joan Sim]

Dear all,
I would like to use WCIF ImageJ to perform 3D volume rendering and
calculation of the volume. May I know which plug-in or analysis module
should I use after obtaining Z-stack immunostained images from confocal
microscopy? Am I correct to say that I will have to import these images as
tiff files, and not other formats, for analysis purposes?

I would greatly appreciate any advices on this matter. Thank you!

Best regards,
Joan, PhD student
Singapore

[dksamuel]

I am sure you would have seen
http://webscreen.ophth.uiowa.edu/bij/vr.htm, regards Samuel

On Tue, Sep 15, 2009 at 11:11 AM, Joan Sim <[hidden email]> wrote:

> Dear all,
> I would like to use WCIF ImageJ to perform 3D volume rendering and
> calculation of the volume. May I know which plug-in or analysis module
> should I use after obtaining Z-stack immunostained images from confocal
> microscopy? Am I correct to say that I will have to import these images as
> tiff files, and not other formats, for analysis purposes?
>
> I would greatly appreciate any advices on this matter. Thank you!
>
> Best regards,
> Joan, PhD student
> Singapore
>

[Jean-Yves Tinevez-2]

On Sep 15, 2009, at 7:59 AM, Duleep Samuel wrote:

> I am sure you would have seen
> http://webscreen.ophth.uiowa.edu/bij/vr.htm, regards Samuel
>

Hi all,
You can also try the 3D viewer:

http://132.187.25.13/home/?category=Download&page=Viewer3D

who does it on the fly "a la" Imaris. It is packaged and pre-
configured in Fiji:

http://pacific.mpi-cbg.de/wiki/index.php/Main_Page

cheers
jy

> On Tue, Sep 15, 2009 at 11:11 AM, Joan Sim <[hidden email]>  
> wrote:
>> Dear all,
>> I would like to use WCIF ImageJ to perform 3D volume rendering and
>> calculation of the volume. May I know which plug-in or analysis  
>> module
>> should I use after obtaining Z-stack immunostained images from  
>> confocal
>> microscopy? Am I correct to say that I will have to import these  
>> images as
>> tiff files, and not other formats, for analysis purposes?
>>
>> I would greatly appreciate any advices on this matter. Thank you!
>>
>> Best regards,
>> Joan, PhD student
>> Singapore
>>

--
Jean-Yves Tinevez
PFID - Imagopole
Institut Pasteur
25-28, rue du Docteur Roux
75724 Paris cedex 15
France
tel: [phone]

[Colin Poczatek]

A non-imagej option if you don't mind learning new software are the
applications from the University of Utah:
http://www.sci.utah.edu/software.html

Specifically Seg3D, SCIRun, and ImageVis3D.  I've been very happy with them.

A plugin to save in the correct format:
http://flybrain.stanford.edu/nrrd

Collin

Jean-Yves Tinevez wrote:

> On Sep 15, 2009, at 7:59 AM, Duleep Samuel wrote:
>
>> I am sure you would have seen
>> http://webscreen.ophth.uiowa.edu/bij/vr.htm, regards Samuel
>>
>
> Hi all,
> You can also try the 3D viewer:
>
> http://132.187.25.13/home/?category=Download&page=Viewer3D
>
> who does it on the fly "a la" Imaris. It is packaged and
> pre-configured in Fiji:
>
> http://pacific.mpi-cbg.de/wiki/index.php/Main_Page
>
> cheers
> jy
>
>
>> On Tue, Sep 15, 2009 at 11:11 AM, Joan Sim <[hidden email]> wrote:
>>> Dear all,
>>> I would like to use WCIF ImageJ to perform 3D volume rendering and
>>> calculation of the volume. May I know which plug-in or analysis module
>>> should I use after obtaining Z-stack immunostained images from confocal
>>> microscopy? Am I correct to say that I will have to import these
>>> images as
>>> tiff files, and not other formats, for analysis purposes?
>>>
>>> I would greatly appreciate any advices on this matter. Thank you!
>>>
>>> Best regards,
>>> Joan, PhD student
>>> Singapore
>>>
>
> --
> Jean-Yves Tinevez
> PFID - Imagopole
> Institut Pasteur
> 25-28, rue du Docteur Roux
> 75724 Paris cedex 15
> France
> tel: [phone]

The information in this e-mail is intended only for the person to whom it is
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[Joan Sim]

Dear all,

Thank you very much for the useful advices provided. It is a good starting
point for me and I will be looking through them to see which is most
suitable for my applications.

Best wishes,
Joan

On Tue, Sep 15, 2009 at 8:42 PM, Colin Poczatek <
[hidden email]> wrote:

> A non-imagej option if you don't mind learning new software are the
> applications from the University of Utah:
> http://www.sci.utah.edu/software.html
>
> Specifically Seg3D, SCIRun, and ImageVis3D.  I've been very happy with
> them.
>
> A plugin to save in the correct format:
> http://flybrain.stanford.edu/nrrd
>
> Collin
>
> Jean-Yves Tinevez wrote:
> > On Sep 15, 2009, at 7:59 AM, Duleep Samuel wrote:
> >
> >> I am sure you would have seen
> >> http://webscreen.ophth.uiowa.edu/bij/vr.htm, regards Samuel
> >>
> >
> > Hi all,
> > You can also try the 3D viewer:
> >
> > http://132.187.25.13/home/?category=Download&page=Viewer3D
> >
> > who does it on the fly "a la" Imaris. It is packaged and
> > pre-configured in Fiji:
> >
> > http://pacific.mpi-cbg.de/wiki/index.php/Main_Page
> >
> > cheers
> > jy
> >
> >
> >> On Tue, Sep 15, 2009 at 11:11 AM, Joan Sim <[hidden email]> wrote:
> >>> Dear all,
> >>> I would like to use WCIF ImageJ to perform 3D volume rendering and
> >>> calculation of the volume. May I know which plug-in or analysis module
> >>> should I use after obtaining Z-stack immunostained images from confocal
> >>> microscopy? Am I correct to say that I will have to import these
> >>> images as
> >>> tiff files, and not other formats, for analysis purposes?
> >>>
> >>> I would greatly appreciate any advices on this matter. Thank you!
> >>>
> >>> Best regards,
> >>> Joan, PhD student
> >>> Singapore
> >>>
> >
> > --
> > Jean-Yves Tinevez
> > PFID - Imagopole
> > Institut Pasteur
> > 25-28, rue du Docteur Roux
> > 75724 Paris cedex 15
> > France
> > tel: [phone]
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>