intensity correction of z stacks (linear, nonlinear)

Posted by Guenter Giese on May 15, 2006; 8:03am
URL: http://imagej.273.s1.nabble.com/intensity-correction-of-z-stacks-linear-nonlinear-tp3702778.html

Hi all,

It is common in confocal microscopy that, despite of careful selection of
embedding media, objectives etc., signal intensity drops with increasing
focus depth (e.g in thick tissue samples).

Is there any built-in function or a plugin available for intensity
correction of z stacks (linear, nonlinear)?

linear: scaling of intensities using a linear gradient of the scaling factor
along the z axis
nonlinear: scaling, e.g. with a gamma function along the z axis

Does such a function include conversion from integer to float and back to
integer intensity values?

Scaling by maximizing contrast of individual image planes is not what I am
looking for.

Guenter


------------------------------------------
Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung Jahnstr. 29
D-69120 Heidelberg, Germany
Phone [phone] (Fax: -325)
e-mail: [hidden email]
http://lightmicro.mpimf-heidelberg.mpg.de