Re: Temporal high pass filter within ImageJ

Posted by CARL Philippe (LBP) on Dec 04, 2015; 10:27am
URL: http://imagej.273.s1.nabble.com/Temporal-high-pass-filter-within-ImageJ-tp5015115p5015131.html

Dear Jens,
I thank you very much for your answer which is completely answering to my issue and even going further.
Especially the image->adjust->bleaching_correction feature which details can be found under:
http://cmci.embl.de/downloads/bleach_corrector
And thanks a lot for Kota for the development of this plugin.
Kindest regards,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de jens rietdorf
Envoyé : jeudi 3 décembre 2015 16:37
À : [hidden email]
Objet : Re: Temporal high pass filter within ImageJ

Dear Carl,

there is a bleaching correction available in FijI from image...adjust...bleaching correction which offers you 3 ways to correct bleaching. There are also various implementations of walking averages, for example git <https://code.google.com/p/fiji-bi/source/browse/?r=6367a8665b43b551795de16432f9a1ba71ce00f0>
/  src-plugins
<https://code.google.com/p/fiji-bi/source/browse/src-plugins/?r=6367a8665b43b551795de16432f9a1ba71ce00f0>
/ Multi_Kymograph
<https://code.google.com/p/fiji-bi/source/browse/src-plugins/Multi_Kymograph/?r=6367a8665b43b551795de16432f9a1ba71ce00f0>
/ WalkingAverage_.java

Abraços,

Dr. Jens Rietdorf, visiting scientist @ center for technological development in health http://br.linkedin.com/pub/jens-rietdorf/6/4a3/189/

On Thu, Dec 3, 2015 at 7:52 AM, Philippe CARL <[hidden email]>
wrote:

> Dear all,
>
> I try to perform fluorescence spectroscopy experiences where I acquire
> several (typically 100) pictures for which I determine for each pixel
> the intensity SD to average ratio in order to extract the relative
> brightness distribution over the picture.
>
> Nevertheless during these temporal acquisitions, the fluorophores are
> subjected to photo bleaching which effect needs to be "cleaned away"
> from the calcultation.
>
> My idea for correcting this effect is to implement a moving average
> filter pixel by pixel over the time series pictures.
>
> Where I would determine the temporal average (over a certain number of
> pictures to be determined empirically) which I would then subtract
> from the given pixel value over the whole stack.
>
> But maybe somebody has a better idea and/or already a plugin/macro for
> performing such a correction.
>
> I thank you very much in advance for your help and hints.
>
> My best regards,
>
> Philippe
>
>
>
> Philippe CARL
>
> Laboratoire de Biophotonique et Pharmacologie
>
> UMR 7213 CNRS - Université de Strasbourg
>
> Faculté de Pharmacie
>
> 74 route du Rhin
>
> 67401 ILLKIRCH
>
> Tel : [phone]
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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