Posted by
Joachim Wesner on
May 15, 2006; 11:38am
URL: http://imagej.273.s1.nabble.com/WG-intensity-correction-of-z-stacks-linear-nonlinear-tp3702776.html
Oops, sorry, this was meant to go to the list, not (only) to the original
poster!
----- Weitergeleitet von Joachim Wesner/DEWET/LMSCentral/Leica am
15.05.2006 12:36 -----
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| | Joachim Wesner |
| | |
| | 15.05.2006 11:59 |
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| An:
[hidden email] |
| Kopie: |
| Thema: Antwort: intensity correction of z stacks (linear, nonlinear)(Document link: Joachim Wesner) |
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Hi,
it seems such a plugin/capability does not yet exist, but it could be be
implemented easily (albeit slow) in a macro. If I understand correctly, you
only want to apply ONE scaling factor for each
image of the stack that varies with z-depth/image#!?
However, I would say a linear gradient is definitely not the way to go, a
power law with a gamma may be, but what about exponential (as in an
absorption model)??
On the other hand, a more elaborate correction would require a bit of
knowledge of the objective, sample and microscope (pinhole etc.) data
JW
|---------+--------------------------------------->
| | Guenter Giese |
| | <Guenter.Giese@mpimf-heidelb|
| | erg.mpg.de> |
| | Gesendet von: ImageJ |
| | Interest Group |
| | <
[hidden email]> |
| | |
| | |
| | 15.05.2006 09:03 |
| | Bitte antworten an |
| | Guenter.Giese |
|---------+--------------------------------------->
>-------------------------------------------------------------------------------------------------------------------------------|
| |
| An:
[hidden email] |
| Kopie: (Blindkopie: Joachim Wesner/DEWET/LMSCentral/Leica) |
| Thema: intensity correction of z stacks (linear, nonlinear) |
>-------------------------------------------------------------------------------------------------------------------------------|
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 (+49) 6221-486-360 (Fax: -325)
e-mail:
[hidden email]
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