Re: Measuring Volume

Posted by Justin McGrath on Dec 06, 2007; 8:12pm
URL: http://imagej.273.s1.nabble.com/Measuring-Volume-tp3697814p3697816.html

Does the autothreshold not work because it doesn't include 255?  If
that's the problem, you can use
setAutoThreshold();
getThreshold(lower,upper);
setThreshold(lower,255);

Which would get the bottom cutoff automatically then set the upper to
255.  If the bottom cutoff isn't good, then you might try some of the
threshold plugins listed on the ImageJ website, or you can come up
with your own criterion and make a macro or plugin for it.  I wrote a
macro once that cut off the leftmost peak of the histogram, which in
my images was always unwanted.  I could find it if sounds useful to
you.  However, it's kind of shoddy coding.

Justin

On Dec 6, 2007 9:47 AM, Aaron Johnson <[hidden email]> wrote:

> Hello, I'm interested in finding a way to do a volume measurement of an 8-
> bit grayscale stack (usually between 15-20 images) coming from a confocal
> microscope.  The structure I'm measuring (ACh receptor) is fairly
> contiguous and could be characterized as blob-shaped.  My main questions
> are:
>
> 1) What are your recommendations regarding thresholding?  I always want to
> capture the max (255), and am more concerned about finding an automated
> way of finding the minimum.  The "auto-threshold" doesn't work for me.
>
> 2) What do you recommend for the volume measurement?  I've tried voxel
> counter with some success, but I'm wondering if there are other easy ways
> to do this, if for no other reason than to confirm my measurements with
> voxel counter.
>
> Thanks!
> Aaron
>