Quantification of Z-series in confocal microscopy

[kristiepy]

Hi there, I have performed immunofluorescence for the a protein in the brain tissue sections from two stages (i.e. one brain tissue section is 3 day younger than the other one). I am trying to compare the signal intensity from the two samples. I have taken Z-series for that sample and I am wondering whether there is any plugin to quantify the mean grey-scale value per unit volume in Image J? Your help is very much appreciated. Kristie

[dpoburko]

Hi Kristie,

   I'm going to suggest that the simplest approach to quantify average
intensity per unit volume is to generate an average intensity pimage of
a given number of slices (see Image > Stacks > Z Project...> set
dropdown box to average). Then you can simply define an X-Y region of
interest and measure the mean intensity in that ROI, which is already an
average of Z slices.
   Now if you need to define a 3D roi, then it will get a little more
complicated.

Best,
Damon


On 4/7/2010 5:09 PM, kristiepy wrote:

> Hi there,
>
> I have performed immunofluorescence for the a protein in the brain tissue
> sections from two stages (i.e. one brain tissue section is 3 day younger
> than the other one). I am trying to compare the signal intensity from the
> two samples. I have taken Z-series for that sample and I am wondering
> whether there is any plugin to quantify the mean grey-scale value per unit
> volume in Image J?
>
> Your help is very much appreciated.
>
> Kristie
>    

[kristiepy]

Hi Damon, Thanks for the reply. The protein is very localised to the nucleus and thus, it would be very helpful if I can define a 3D ROI. Would you have any idea to do this? cheers Kristie