3D segmentation in ImageJ

[Kaustav Nandy]

Hello List Users,

I am new to ImageJ and would like to get some information about the
software. I am planning to do some 3D segmentation using ImageJ. I
looked into the plugins page, but couldn't find anything that would help
me in doing the job. I have z-stacks of mouse embryos and would like to
do the segmentation of individual nuclei. It would be very helpful for
me if someone can provide me some information about any tools that
available in ImageJ to do the segmentation in 3D.

Thanks in advance.

--

Thanks and Regards,
 

Kaustav Nandy (Contractor)
Scientist 1,
Image Analysis Lab - Advanced Technology Program, Bldg. 538/125,
SAIC-Frederick, Inc./NCI at Frederick
P.O. Box B, Frederick, MD 21702
[phone] (v)
[phone] (f)
[hidden email], [hidden email]


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[Thomas Boudier]

Hi,

For 3D segmentation I can advise you the plugin objectCounter :

http://rsb.info.nih.gov/ij/plugins/track/objects.html

I also have some plugins to process 3D binary images :
http://imagejdocu.tudor.lu/Members/tboudier/plonearticle.2007-01-08.6704298355/

Thomas


Kaustav Nandy a écrit :

> Hello List Users,
>
> I am new to ImageJ and would like to get some information about the
> software. I am planning to do some 3D segmentation using ImageJ. I
> looked into the plugins page, but couldn't find anything that would help
> me in doing the job. I have z-stacks of mouse embryos and would like to
> do the segmentation of individual nuclei. It would be very helpful for
> me if someone can provide me some information about any tools that
> available in ImageJ to do the segmentation in 3D.
>
> Thanks in advance.
>

--
/*****************************************************/
     Thomas Boudier, MCU Université Paris 6,
     UMR 7101 / IFR 83. Bat A 328, Jussieu.
     Tel : [phone]  Fax : [phone]
/****************************************************/

[Joel Sheffield]

You might also be able to use Michael Abramoff's VolumeJ plugin.  It
includes threshold settings for volume rendering.

Joel


Date sent:       Tue, 11 Mar 2008 16:33:56 +0100
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Thomas Boudier <[hidden email]>
Organization:   UPMC
Subject:         Re: 3D segmentation in ImageJ
To:             [hidden email]

> Hi,
>
> For 3D segmentation I can advise you the plugin objectCounter :
>
> http://rsb.info.nih.gov/ij/plugins/track/objects.html
>
> I also have some plugins to process 3D binary images :
> http://imagejdocu.tudor.lu/Members/tboudier/plonearticle.2007-01-08.6704298355/
>
> Thomas
>
>
> Kaustav Nandy a écrit :
> > Hello List Users,
> >
> > I am new to ImageJ and would like to get some information about the
> > software. I am planning to do some 3D segmentation using ImageJ. I
> > looked into the plugins page, but couldn't find anything that would help
> > me in doing the job. I have z-stacks of mouse embryos and would like to
> > do the segmentation of individual nuclei. It would be very helpful for
> > me if someone can provide me some information about any tools that
> > available in ImageJ to do the segmentation in 3D.
> >
> > Thanks in advance.
> >
>
> --
> /*****************************************************/
>      Thomas Boudier, MCU Université Paris 6,
>      UMR 7101 / IFR 83. Bat A 328, Jussieu.
>      Tel : [phone]  Fax : [phone]
> /****************************************************/

--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]
[phone], fax [phone]
http://astro.temple.edu/~jbs