colocalization in Fiji analyze menu

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colocalization in Fiji analyze menu

Cammer, Michael-2
Is there a way to set the threshold for each channel manually for each of the methods (Colocalization Threshhold and Coloc 2)?


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567


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Re: colocalization in Fiji analyze menu

CARL Philippe (LBP)
Dear Michael,
Did you try the following plugin?:
http://questpharma.u-strasbg.fr/html/colocalization-finder.html
By moving around the ROI defining the analysis window isn't it what you are looking for?
My best regards,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

----- Mail original -----
De: "Cammer, Michael" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Dimanche 8 Septembre 2019 05:21:38
Objet: colocalization  in Fiji analyze menu

Is there a way to set the threshold for each channel manually for each of the methods (Colocalization Threshhold and Coloc 2)?


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567


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Re: colocalization in Fiji analyze menu

CARL Philippe (LBP)
Dear Michael,



Thank you for pointing me to this plugin.




You are welcome!




The scatterplot, ability to draw ROIs on it, and white pixels on the composite image are great.




Actually there are more available features than what you have found.

Indeed, in the case you make a double click on a ROI within the scatterplot, the ROI will be "fixed" within a given color, the corresponding pixels within the composite picture "fixed" as well with the same color and a new line generated within the Results window, giving you thus the possibility to define several ROI positions for analysis.

Also a ROI being already drawn within the scatterplot, by pressing on Ctrl and clicking somewhere within the composite window the ROI will be centered on the corresponding pixel position within the scatterplot.

So you have a back and forth linking between the scatterplot and the composite picture.




Also, the r= number is what we expect. This is going to be extremely useful for us for interactive use.




I guess this is mandatory, isn't it?

Nevertheless, nobody is free of making some calculation errors.




However, can it be driven from the macro language?




The code is recordable, why do you have some issues on this?

I made a "more advanced" version of the plugin that you can download under the following link:

[ http://punias.free.fr/ImageJ/Colocalization_Finder_with_ROI.jar | http://punias.free.fr/ImageJ/Colocalization_Finder_with_ROI.jar ]

where you can additionally define the position of the analysis ROI within the scatter plot (this feature was needed by a colleague) .




Out goal is to automate colocalization results from multiple images collected in the same way. We'd a macro to open a pair of images and report a few colocalization results at a few different preset thresholds and apply this automatically to many files in a directory. I have a routine that can do this with Pearsons, but would be great to do this with all the other statistics this plugin reports.




Can't the plugin as it is perform your needed job?

Is there something missing within the code?




My best regards,




Philipppe



De: "Cammer, Michael" <[hidden email]>
À: "philippe carl" <[hidden email]>
Cc: "Deng, Yan" <[hidden email]>
Envoyé: Lundi 9 Septembre 2019 02:24:46
Objet: Re: colocalization in Fiji analyze menu



Thank you for pointing me to this plugin.

The scatterplot, ability to draw ROIs on it, and white pixels on the composite image are great. Also, the r= number is what we expect. This is going to be extremely useful for us for interactive use.

However, can it be driven from the macro language?

Out goal is to automate colocalization results from multiple images collected in the same way. We'd a macro to open a pair of images and report a few colocalization results at a few different preset thresholds and apply this automatically to many files in a directory. I have a routine that can do this with Pearsons, but would be great to do this with all the other statistics this plugin reports.

Cheers-










Michael Cammer, Sr Research Scientist , DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY 10016

[ mailto:[hidden email] | [hidden email] ] [ http://nyulmc.org/micros | http://nyulmc.org/micros ] [ http://microscopynotes.com/ | http://microscopynotes.com/ ]

Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567









From: CARL Philippe (LBP) <[hidden email]>
Sent: Sunday, September 8, 2019 11:41:35 AM
To: [hidden email]
Subject: Re: colocalization in Fiji analyze menu
Dear Michael,
Did you try the following plugin?:
[ https://urldefense.proofpoint.com/v2/url?u=http-3A__questpharma.u-2Dstrasbg.fr_html_colocalization-2Dfinder.html&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=wk_WjgzPYEVGyw8MU4dNcHC8ywcVe8_ktb7Kt4LXJPA&e= | https://urldefense.proofpoint.com/v2/url?u=http-3A__questpharma.u-2Dstrasbg.fr_html_colocalization-2Dfinder.html&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=wk_WjgzPYEVGyw8MU4dNcHC8ywcVe8_ktb7Kt4LXJPA&e= ]
By moving around the ROI defining the analysis window isn't it what you are looking for?
My best regards,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

----- Mail original -----
De: "Cammer, Michael" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Dimanche 8 Septembre 2019 05:21:38
Objet: colocalization in Fiji analyze menu

Is there a way to set the threshold for each channel manually for each of the methods (Colocalization Threshhold and Coloc 2)?


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY 10016

[hidden email]<mailto:[hidden email]> [ https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=eWHTI--v7PfY9PiJUcnjY66Mg5iCqVYQhlUPRy4bdt0&e= |
https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=eWHTI--v7PfY9PiJUcnjY66Mg5iCqVYQhlUPRy4bdt0&e= ] [ https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=PK37J4p_HrNVEitMDMAgmKUcEoc3_k0-MJrMoKrRzjk&e= |
https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=PK37J4p_HrNVEitMDMAgmKUcEoc3_k0-MJrMoKrRzjk&e= ]

Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567


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Re: colocalization in Fiji analyze menu

CARL Philippe (LBP)
Dear Michael,
With the "native plugin" recording the instruction and launching it then through a macro indeed doesn't generate you the analysis result.
But with the extended version of the plugin that you can download under the following link:
[ http://punias.free.fr/ImageJ/Colocalization_Finder_with_ROI.jar | http://punias.free.fr/ImageJ/Colocalization_Finder_with_ROI.jar ]
The run of the (for example) following code (obtained through the recorder):
run("Colocalization Finder with ROI", "image_1=Brillance.tif image_2=Intensity.tif specify_minimum_ratio_(0-100%)=0 left_roi_position=167 upper_roi_position=20 roi_width=150 roi_height=150");
will generate the Composite picture as well as the ScatterPlot and the Results window using the ROI positions on the ScatterPlot defined through:
left_roi_position=167 upper_roi_position=20 roi_width=150 roi_height=150"
My best regards,




Philippe



De: "Michael Cammer" <[hidden email]>
À: "CARL Philippe (LBP)" <[hidden email]>
Cc: "Yan Deng" <[hidden email]>
Envoyé: Mardi 10 Septembre 2019 02:59:56
Objet: Re: colocalization in Fiji analyze menu



Thank you for sending the updated version. The one on the web page does not generate code in the Record window but the updated version does generate this:

run("Colocalization Finder...", "image_1=[MAX_D4_PYCR2_012 MAX34 enh.tif] image_2=[MAX_D4_PYCR2_012 MAX45 enh.tif] specify_minimum_ratio_(0-100%)=0");


Question: from a macro, after drawing the ROI, how do we tell the plugin to generate the results?

Thank you!!










Michael Cammer, Sr Research Scientist , DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY 10016

[ mailto:[hidden email] | [hidden email] ] [ http://nyulmc.org/micros | http://nyulmc.org/micros ] [ http://microscopynotes.com/ | http://microscopynotes.com/ ]

Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567









From: CARL Philippe (LBP) <[hidden email]>
Sent: Monday, September 9, 2019 5:38:13 AM
To: Cammer, Michael; imagej
Cc: Deng, Yan
Subject: Re: colocalization in Fiji analyze menu
Dear Michael,



Thank you for pointing me to this plugin.




You are welcome!




The scatterplot, ability to draw ROIs on it, and white pixels on the composite image are great.




Actually there are more available features than what you have found.

Indeed, in the case you make a double click on a ROI within the scatterplot, the ROI will be "fixed" within a given color, the corresponding pixels within the composite picture "fixed" as well with the same color and a new line generated within the Results window, giving you thus the possibility to define several ROI positions for analysis.

Also a ROI being already drawn within the scatterplot, by pressing on Ctrl and clicking somewhere within the composite window the ROI will be centered on the corresponding pixel position within the scatterplot.

So you have a back and forth linking between the scatterplot and the composite picture.




Also, the r= number is what we expect. This is going to be extremely useful for us for interactive use.




I guess this is mandatory, isn't it?

Nevertheless, nobody is free of making some calculation errors.




However, can it be driven from the macro language?




The code is recordable, why do you have some issues on this?

I made a "more advanced" version of the plugin that you can download under the following link:

[ https://urldefense.proofpoint.com/v2/url?u=http-3A__punias.free.fr_ImageJ_Colocalization-5FFinder-5Fwith-5FROI.jar&d=DwMFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=x5tYsX4gyFaHBoWO1BVenGMPZjUZJszOVnwTWRlUfMo&s=8qpkpVvvVA9wHOFw8V-yL-yyrO4efSFPhogKkTjSO94&e= | http://punias.free.fr/ImageJ/Colocalization_Finder_with_ROI.jar ]

where you can additionally define the position of the analysis ROI within the scatter plot (this feature was needed by a colleague) .




Out goal is to automate colocalization results from multiple images collected in the same way. We'd a macro to open a pair of images and report a few colocalization results at a few different preset thresholds and apply this automatically to many files in a directory. I have a routine that can do this with Pearsons, but would be great to do this with all the other statistics this plugin reports.




Can't the plugin as it is perform your needed job?

Is there something missing within the code?




My best regards,




Philipppe



De: "Cammer, Michael" <[hidden email]>
À: "philippe carl" <[hidden email]>
Cc: "Deng, Yan" <[hidden email]>
Envoyé: Lundi 9 Septembre 2019 02:24:46
Objet: Re: colocalization in Fiji analyze menu



Thank you for pointing me to this plugin.

The scatterplot, ability to draw ROIs on it, and white pixels on the composite image are great. Also, the r= number is what we expect. This is going to be extremely useful for us for interactive use.

However, can it be driven from the macro language?

Out goal is to automate colocalization results from multiple images collected in the same way. We'd a macro to open a pair of images and report a few colocalization results at a few different preset thresholds and apply this automatically to many files in a directory. I have a routine that can do this with Pearsons, but would be great to do this with all the other statistics this plugin reports.

Cheers-










Michael Cammer, Sr Research Scientist , DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY 10016

[ mailto:[hidden email] | [hidden email] ] [ https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwMFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=x5tYsX4gyFaHBoWO1BVenGMPZjUZJszOVnwTWRlUfMo&s=Z8MBbwX-NhYTBKsHSgBbaSHIt01TDbhsyD_6dchHWv4&e= | http://nyulmc.org/micros ] [ https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwMFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=x5tYsX4gyFaHBoWO1BVenGMPZjUZJszOVnwTWRlUfMo&s=lg--wsly-CPt1p5MtUX7NOqI9BQc-z5HSs9kLvbp50c&e= | http://microscopynotes.com/ ]

Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567









From: CARL Philippe (LBP) <[hidden email]>
Sent: Sunday, September 8, 2019 11:41:35 AM
To: [hidden email]
Subject: Re: colocalization in Fiji analyze menu
Dear Michael,
Did you try the following plugin?:
[ https://urldefense.proofpoint.com/v2/url?u=http-3A__questpharma.u-2Dstrasbg.fr_html_colocalization-2Dfinder.html&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=wk_WjgzPYEVGyw8MU4dNcHC8ywcVe8_ktb7Kt4LXJPA&e= | https://urldefense.proofpoint.com/v2/url?u=http-3A__questpharma.u-2Dstrasbg.fr_html_colocalization-2Dfinder.html&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=wk_WjgzPYEVGyw8MU4dNcHC8ywcVe8_ktb7Kt4LXJPA&e= ]
By moving around the ROI defining the analysis window isn't it what you are looking for?
My best regards,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

----- Mail original -----
De: "Cammer, Michael" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Dimanche 8 Septembre 2019 05:21:38
Objet: colocalization in Fiji analyze menu

Is there a way to set the threshold for each channel manually for each of the methods (Colocalization Threshhold and Coloc 2)?


Thank you.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY 10016

[hidden email]<mailto:[hidden email]> [ https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=eWHTI--v7PfY9PiJUcnjY66Mg5iCqVYQhlUPRy4bdt0&e= |
https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=eWHTI--v7PfY9PiJUcnjY66Mg5iCqVYQhlUPRy4bdt0&e= ] [ https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=PK37J4p_HrNVEitMDMAgmKUcEoc3_k0-MJrMoKrRzjk&e= |
https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=bp8Bd2HAerrt5NP0vX78INduwGv7x26eFB15mJLZ3bo&s=PK37J4p_HrNVEitMDMAgmKUcEoc3_k0-MJrMoKrRzjk&e= ]

Voice direct only, no text or messages: 1-914-309-3270 and 1-646-501-0567


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