Volume measurements: subnuclear structures to total nuclear volume

[Hariharan Iyer]

Hi,
I am interested in calculating the ratio of volume occupied by specific
subnuclear structures (identified by immunostaining) with respect to the
total nuclear volume. I would appreciate hearing what plugins could be
used for this analysis (if it is possible in ImageJ).

Thanks and wishes,
Hari

[Michael Cammer]

What imaging method are you using?


> Hi,
> I am interested in calculating the ratio of volume occupied by specific
> subnuclear structures (identified by immunostaining) with respect to the
> total nuclear volume. I would appreciate hearing what plugins could be
> used for this analysis (if it is possible in ImageJ).
>
> Thanks and wishes,
> Hari
>


_________________________________________
Michael Cammer   http://www.aecom.yu.edu/aif/

[Hariharan Iyer]

I am sorry that I didn't specify the details.
I am using a Zeiss LSM 510 confocal to image the whole nuclear volume.
I detect the sub-nuclear structures using Cy3 conjugated antibody and use
a DNA dye like (Hoechst or TOPRO-3)for DNA counterstaining.
The images are deconvolved before making the measurements.

I would appreciate any help/suggestions.

Thanks and wishes,
Hari

[Joel Sheffield]

Hari

It seems to me that you are assuming that DNA volume is the same as
total nuclear volume.  This is probably not the case, since there are
all sorts of heterogeneities in the DNA distribution.  I wonder if
you would do better to use a second antibody, directed to nuclear
lamins, that would outline the submembrane area.  You could then
determine the volume enclosed by the lamin stain, and compare it to
the Cy3 stain.

Joel


Date sent:       Thu, 14 Jun 2007 11:36:34 -0400
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Hari Iyer <[hidden email]>
Subject:         Re: Volume measurements: subnuclear structures to
total nuclear volume
To:             [hidden email]

> I am sorry that I didn't specify the details.
> I am using a Zeiss LSM 510 confocal to image the whole nuclear volume.
> I detect the sub-nuclear structures using Cy3 conjugated antibody and use
> a DNA dye like (Hoechst or TOPRO-3)for DNA counterstaining.
> The images are deconvolved before making the measurements.
>
> I would appreciate any help/suggestions.
>
> Thanks and wishes,
> Hari

--
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