Re: Raw versus calibrated integrated density

Posted by Norbert Vischer-2 on Oct 18, 2010; 2:12pm
URL: http://imagej.273.s1.nabble.com/Raw-versus-calibrated-integrated-density-tp3686613p3686623.html

On 18. Oct. 2010, at 15:03 , IJperson wrote:

> Hi everyone.
>
> This could well be a misunderstanding on my part, but why are the raw and
> calibrated integrated densities different?  I understand the per micron or
> per pixel means being different, but isn't the total intensity unit-free?
>
> Here is a quick calculation, where as I calculate it, the total integrated
> intensity should be the same. Where have I gone wrong? Is it my
> understanding of what 'density' means?

Integrated density in ImageJ relates indeed to scaled area units. However if one really was interested in the number of photons per micron, he needed to know a lot of other factors as well. Personally I think it would have been better not to include the image scale - in practice it may lead to misunderstandings, which often happened in our lab. Users often set the scale to their images only if spatial measurements are needed; sometimes images are silently scaled (or inadvertedly re-scaled) because the "Global" flag in the scale dialog is switched on. I always remove the scale in such cases and divide the result by 1000, so I am independent of scaling, and I get smaller numbers.

Norbert