Posted by
Fabrice Cordelières on
Jun 20, 2007; 9:55pm
URL: http://imagej.273.s1.nabble.com/JACoP-problem-tp3699044p3699048.html
Hi Michael,
In the original calculation of Pearson's coefficient, a threshold value is
not supposed to be set. This is surely due to the fact that its first use
was on confocal images where the offset value is supposed to have been well
set to get rid of background pixels. As JACoP applies the original formula,
it doesn't take into account any threshold value. However, as you suggested,
you may subtract background on both images before launching JACoP.
Cheers,
Fab
Fabrice Cordelières, PhD
Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
Bâtiment 112 - Centre universitaire
91405 Orsay Cedex
FRANCE
Tél. : +33 1 69 86 31 30
Fax. : +33 1 69 86 17 03
-----Message d'origine-----
De : ImageJ Interest Group [mailto:
[hidden email]] De la part de
Michael Cammer
Envoyé : mercredi 20 juin 2007 19:02
À :
[hidden email]
Objet : Re: JACoP problem
I just realized that the Pearson's may not use the threshold. Should
we be subtracting the background to zero before running this to avoid
getting correlation from bg pixels?
Thanks.
At 12:32 PM 06/20/07, you wrote:
>Thanks.
>
>I did this which got rid of the error message, but the software
>appears to disregard a manual change in the threshold settings.
>
>-Michael
>
>At 12:05 PM 06/20/07, you wrote:
>>This is a command recorder error. You can avoid it by closing the
>>Recorder window. The recorder is displaying this error because the
>>first dialog displayed by the JACoP plugin has two labels that start
>>with the word "Image". To fix the problem, change the labels to
>>"Image_A" and "Image_B" and recompile.
>>
>>-wayne
>>
>>On Jun 20, 2007, at 10:53 AM, Michael Cammer wrote:
>>
>>>We are having problems with the JACoP plugin and would appreciate help.
>>>
>>>The plugin worked for a while and then began giving the following
>>>error:
>>>
>>>Duplicate keyword:
>>>Command: "JACoP"
>>>Keyword: "image"
>>>Value: green
>>>Add an underscore to the corresponding label
>>>in the dialog to make the first word unique.
>>>
>>>It then continues to run but always prints out the same r= value for
>>>any given pair of images regardless of how we set the threshold.
>>>
>>>We're using 1.38u with Java 1.5.0_09.
>>>
>>>Thanks.
>>>_______________________________________________________________________
>>>_____
>>>Michael Cammer Analytical Imaging Facility Albert Einstein Coll.
>>>of Med.
>>>URL:
http://www.aecom.yu.edu/aif/>
>___________________________________________________________________________
_
>Michael Cammer Analytical Imaging Facility Albert Einstein Coll. of
Med.
>URL:
http://www.aecom.yu.edu/aif/____________________________________________________________________________
Michael Cammer Analytical Imaging Facility Albert Einstein Coll. of Med.
URL:
http://www.aecom.yu.edu/aif/