ImgLib2 and RGB Stack Images / Extending TrackMate

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ImgLib2 and RGB Stack Images / Extending TrackMate

Thorsten Wagner
Dear list,

I currently want to extend TrackMate with a spot feature for RGB Stacks.
I want to calculate the hue of the center for each spot to filter the
particle by color before connecting the dots to tracks.

However, TrackMate uses ImgLib2 and I wondering how to work with RGB
Stack images. I cant find any examples how to do that.

Any help is highly appreciated!

Cheers,
Thorsten



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Re: ImgLib2 and RGB Stack Images / Extending TrackMate

Jean-Yves Tinevez-2
Hi Thorsten,

I think the way is to wrap your image into a ARGBType ImgLib2 images.
But you would have to change TrackMate because right now the GUI refuses to start with a RGB image.

Best
jy


--
Jean-Yves Tinevez
PFID - Imagopole
Institut Pasteur
25-28, rue du Docteur Roux
75724 Paris cedex 15
France
mob: +33 7 88 17 97 69
tel: +33 1 45 68 82 18
fax: +33 1 44 38 92 54

De : [hidden email]
Envoyé : ‎lundi‎ ‎9‎ ‎mars‎ ‎2015 ‎20‎:‎47
À : [hidden email]

Dear list,

I currently want to extend TrackMate with a spot feature for RGB Stacks.
I want to calculate the hue of the center for each spot to filter the
particle by color before connecting the dots to tracks.

However, TrackMate uses ImgLib2 and I wondering how to work with RGB
Stack images. I cant find any examples how to do that.

Any help is highly appreciated!

Cheers,
Thorsten



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[hidden email]
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Re: ImgLib2 and RGB Stack Images / Extending TrackMate

Thorsten Wagner
Dear Jean-Yves,

thank you for your answer. I will have look into the ARGBType of the
ImgLib2. You are right, TrackMate refuses to start with RGB images but
it does not to refuse to start with RGB-Stack images. So my thought was,
that I can simply work with RGB-Stack images instead of RGB images?

Cheers,
Thorsten

Am Montag, den 09.03.2015, 19:55 +0000 schrieb [hidden email]:

> Hi Thorsten,
>
>
> I think the way is to wrap your image into a ARGBType ImgLib2 images.
> But you would have to change TrackMate because right now the GUI
> refuses to start with a RGB image.
>
>
> Best
> jy
>
>
>
>
> --
> Jean-Yves Tinevez
> PFID - Imagopole
> Institut Pasteur
> 25-28, rue du Docteur Roux
> 75724 Paris cedex 15
> France
> mob: +33 7 88 17 97 69
> tel: +33 1 45 68 82 18
> fax: +33 1 44 38 92 54
>
>
> De : Thorsten Wagner
> Envoyé : ‎lundi‎ ‎9‎ ‎mars‎ ‎2015 ‎20‎:‎47
> À : [hidden email]
>
>
> Dear list,
>
> I currently want to extend TrackMate with a spot feature for RGB
> Stacks.
> I want to calculate the hue of the center for each spot to filter the
> particle by color before connecting the dots to tracks.
>
> However, TrackMate uses ImgLib2 and I wondering how to work with RGB
> Stack images. I cant find any examples how to do that.
>
> Any help is highly appreciated!
>
> Cheers,
> Thorsten
>
>
>
> _______________________________________________
> ImageJ-devel mailing list
> [hidden email]
> http://imagej.net/mailman/listinfo/imagej-devel
>


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Re: ImgLib2 and RGB Stack Images / Extending TrackMate

Jean-Yves Tinevez-2
Ah! But yes absolutely.
Then what you need is the multi channel analyzer module that Benoit Lombardo did in the MPI-CBG.
It will measure spot features in all the channels you provide it with.
You will find it here:

best
jy
--
Jean-Yves Tinevez
PFID - Imagopole
Institut Pasteur
25-28, rue du Docteur Roux
75724 Paris cedex 15
France
mob: +33 7 88 17 97 69
tel: +33 1 45 68 82 18
fax: +33 1 44 38 92 54

De : [hidden email]
Envoyé : ‎lundi‎ ‎9‎ ‎mars‎ ‎2015 ‎21‎:‎25
À : [hidden email]
Cc : [hidden email]

Dear Jean-Yves,

thank you for your answer. I will have look into the ARGBType of the
ImgLib2. You are right, TrackMate refuses to start with RGB images but
it does not to refuse to start with RGB-Stack images. So my thought was,
that I can simply work with RGB-Stack images instead of RGB images?

Cheers,
Thorsten

Am Montag, den 09.03.2015, 19:55 +0000 schrieb [hidden email]:

> Hi Thorsten,
>
>
> I think the way is to wrap your image into a ARGBType ImgLib2 images.
> But you would have to change TrackMate because right now the GUI
> refuses to start with a RGB image.
>
>
> Best
> jy
>
>
>
>
> --
> Jean-Yves Tinevez
> PFID - Imagopole
> Institut Pasteur
> 25-28, rue du Docteur Roux
> 75724 Paris cedex 15
> France
> mob: +33 7 88 17 97 69
> tel: +33 1 45 68 82 18
> fax: +33 1 44 38 92 54
>
>
> De : Thorsten Wagner
> Envoyé : ‎lundi‎ ‎9‎ ‎mars‎ ‎2015 ‎20‎:‎47
> À : [hidden email]
>
>
> Dear list,
>
> I currently want to extend TrackMate with a spot feature for RGB
> Stacks.
> I want to calculate the hue of the center for each spot to filter the
> particle by color before connecting the dots to tracks.
>
> However, TrackMate uses ImgLib2 and I wondering how to work with RGB
> Stack images. I cant find any examples how to do that.
>
> Any help is highly appreciated!
>
> Cheers,
> Thorsten
>
>
>
> _______________________________________________
> ImageJ-devel mailing list
> [hidden email]
> http://imagej.net/mailman/listinfo/imagej-devel
>


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