Particle tracking with defaults

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Particle tracking with defaults

Philippe CARL
Dear all,

I would like to track some fluorescent beads displacements within pictures
like these examples:

http://punias.free.fr/ImageJ/Stack1.tif

or

http://punias.free.fr/ImageJ/Stack2.tif

But very unfortunately besides the beads signals, I have as well some
undetermined fluorescent sources within the pictures which are quite
disturbing the analysis.

Thus would somebody of you have an idea on how to clean out this unwanted
signal or on the contrary how to only isolate the beads positions within the
pictures?

I thank you very much in advance for your help and suggestions.

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 : +33(0)3 68 85 41 84


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Re: Particle tracking with defaults

Michael Schmid-3
Hi Philippe,

as the image is very noisy, I think that first you need de-noising.
I tried my 'Thresholded blur' [] with radius=3 and threshold of 1000.
Somewhat stronger denoising might be better.

Then, the ImageJ built-in 'Subtract Background' with 'sliding
paraboloid' and a small curvature radius between 0.1 and 1 removes most
of the blurred patches. it is not perfect, but better.

Another possibility is th Feature_Finder plugin [2]; select one of the
most prominent (brightest) beads with a small circular selection as a
template, and use 'point map' output.

Michael

[1]
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start

[2]
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:feature_finder:start
________________________________________________________________

On 2016-12-20 16:14, Philippe CARL wrote:

> Dear all,
>
> I would like to track some fluorescent beads displacements within pictures
> like these examples:
>
> http://punias.free.fr/ImageJ/Stack1.tif
>
> or
>
> http://punias.free.fr/ImageJ/Stack2.tif
>
> But very unfortunately besides the beads signals, I have as well some
> undetermined fluorescent sources within the pictures which are quite
> disturbing the analysis.
>
> Thus would somebody of you have an idea on how to clean out this unwanted
> signal or on the contrary how to only isolate the beads positions within the
> pictures?
>
> I thank you very much in advance for your help and suggestions.
>
> 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 : +33(0)3 68 85 41 84
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Particle tracking with defaults

jerie
In reply to this post by Philippe CARL
Hi Philippe,

I tried the following, if that is sufficient will depend on later analysis
---
selectWindow("Stack1.tif");
run("Non-local Means Denoising", "sigma=15 smoothing_factor=1 auto stack");
run("Subtract Background...", "rolling=0.1 sliding stack");
run("Bandpass Filter...", "filter_large=9 filter_small=0 suppress=None
tolerance=5 process");
setAutoThreshold("Otsu dark stack");
run("Analyze Particles...", "size=5-50 circularity=0.70-1.00 show=Masks
summarize stack");
---

Abraços, Jens

Dr. Jens Rietdorf, visiting scientist @ center for technological
development in health CDTS, Oswaldo Cruz Foundation Fiocruz, Rio de Janeiro
Brasil.

On Tue, Dec 20, 2016 at 1:14 PM, Philippe CARL <[hidden email]>
wrote:

> Dear all,
>
> I would like to track some fluorescent beads displacements within pictures
> like these examples:
>
> http://punias.free.fr/ImageJ/Stack1.tif
>
> or
>
> http://punias.free.fr/ImageJ/Stack2.tif
>
> But very unfortunately besides the beads signals, I have as well some
> undetermined fluorescent sources within the pictures which are quite
> disturbing the analysis.
>
> Thus would somebody of you have an idea on how to clean out this unwanted
> signal or on the contrary how to only isolate the beads positions within
> the
> pictures?
>
> I thank you very much in advance for your help and suggestions.
>
> 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 : +33(0)3 68 85 41 84
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Jens Rietdorf Visiting Scientist Fundação Oswaldo Cruz - Ministério da Saúde, Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Rio de Janeiro, Brasil.
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Re: Particle tracking with defaults

Philippe CARL
Dear Jens and Mickael,
I thank you very much for your answers and help on the denoising issue I submitted you.
Without any doubt it is way better to try to improve the quality of the acquired pictures rather than to try to clean them out afterwards.
Unfortunately the data I sent you come from a new mutant and since I'm getting already twice such noised data, I start to think that I will need to live with it.
Even if I'm still trying to improve the acquisition conditions on first hand.
Jens: your code if working quite nicely on the first slice of the "Stack1.tif" but for the second slice it is destroying a lot of beads positions.
And this comes already from the "Non-local Means Denoising" filter application.
So I tried to play around with its parameters without being able to find a good setting that would not be this destructive.
Mickael: your solution (i.e. the first option) is quite improving the pictures so I'm using it now in the analysis code.
I saw as well that you were the author of the two plugins you were referring!!!
So thanks a lot for both of you for your help.
I wish you all a merry Christmas and Happy New Year!!!
My best regards,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de jens rietdorf
Envoyé : mercredi 21 décembre 2016 22:51
À : [hidden email]
Objet : Re: Particle tracking with defaults

Hi Philippe,

I tried the following, if that is sufficient will depend on later analysis
---
selectWindow("Stack1.tif");
run("Non-local Means Denoising", "sigma=15 smoothing_factor=1 auto stack"); run("Subtract Background...", "rolling=0.1 sliding stack"); run("Bandpass Filter...", "filter_large=9 filter_small=0 suppress=None
tolerance=5 process");
setAutoThreshold("Otsu dark stack");
run("Analyze Particles...", "size=5-50 circularity=0.70-1.00 show=Masks summarize stack");
---

Abraços, Jens

Dr. Jens Rietdorf, visiting scientist @ center for technological development in health CDTS, Oswaldo Cruz Foundation Fiocruz, Rio de Janeiro Brasil.

On Tue, Dec 20, 2016 at 1:14 PM, Philippe CARL <[hidden email]>
wrote:

> Dear all,
>
> I would like to track some fluorescent beads displacements within
> pictures like these examples:
>
> http://punias.free.fr/ImageJ/Stack1.tif
>
> or
>
> http://punias.free.fr/ImageJ/Stack2.tif
>
> But very unfortunately besides the beads signals, I have as well some
> undetermined fluorescent sources within the pictures which are quite
> disturbing the analysis.
>
> Thus would somebody of you have an idea on how to clean out this
> unwanted signal or on the contrary how to only isolate the beads
> positions within the pictures?
>
> I thank you very much in advance for your help and suggestions.
>
> 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 : +33(0)3 68 85 41 84
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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