WG: intensity correction of z stacks (linear, nonlinear)

[Joachim Wesner]

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 -----
|---------+---------------------------->
|         |           Joachim Wesner   |
|         |                            |
|         |           15.05.2006 11:59 |
|---------+---------------------------->
  >------------------------------------------------------------------------------------------------------------------------------|
  |                                                                                                                              |
  |       An:      [hidden email]                                                                         |
  |       Kopie:                                                                                                                 |
  |       Thema:   Antwort: intensity correction of z stacks (linear, nonlinear)(Document link: Joachim Wesner)                  |
  >------------------------------------------------------------------------------------------------------------------------------|



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 [phone] (Fax: -325)
e-mail: [hidden email]
http://lightmicro.mpimf-heidelberg.mpg.de




______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________