Temporal high pass filter within ImageJ

[CARL Philippe (LBP)]

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]

 


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[jerie]

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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[CARL Philippe (LBP)]

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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