Coloc2 Output--histogram image?

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Coloc2 Output--histogram image?

Jacob Keller-2
Dear Developers of Coloc2,

It would seem to me really helpful to have the all of the resultant images
(esp the 2D histogram) output as images separately. Then one could use
whatever LUTs and change contrast levels etc. Is this possible as is, and
if not, wouldn't it be pretty easy to do? Are the images written somewhere?
As it is, it's a bit tricky to make them into publishable images.

All the best,

Jacob Keller

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Re: Coloc2 Output--histogram image?

Philippe CARL
Dear Jacob,
Please dowload and try the plugin found under this link:
http://punias.free.fr/ImageJ/Colocalization_Finder.jar
which is an improvement of the plugin originally developped by Jerôme Mutterer found under this link:
https://imagej.nih.gov/ij/plugins/colocalization-finder.html
This plugin ables the use of whatever LUT for the ScatterPlot picture (as you requested) as well as works for whatever type (even 32bits) of source pictures.
A single click on the ScatterPlot picture will calculate the values corresponding to the given selected ROI as a double click will save the ROI position on the ScatterPlot.
As if you press the Ctrl key and move the mouse over the Composite picture, the ROI within the ScatterPlot picture will center its position on the corresponding seleted pixel in the ScatterPlot picture.
At last, it is possible to generate the x or y histogram of the ScatterPlot picture with a Gaussian fit of it in order to extract the histogram maximum position by using the numeric pad 4/6 or 2/8 keys.
Feel free to contact me if you have some questions about the plugin or some requests for improving it.
My best regards,
Philippe

Le Vendredi 13 Avril 2018 23:52 CEST, Jacob Keller <[hidden email]> a écrit:

> Dear Developers of Coloc2,
>
> It would seem to me really helpful to have the all of the resultant images
> (esp the 2D histogram) output as images separately. Then one could use
> whatever LUTs and change contrast levels etc. Is this possible as is, and
> if not, wouldn't it be pretty easy to do? Are the images written somewhere?
> As it is, it's a bit tricky to make them into publishable images.
>
> All the best,
>
> Jacob Keller
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html





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Re: Coloc2 Output--histogram image?

Jacob Keller-2
Awesome--this is just what I needed! I actually also took the log of the 2D
plot to see things a bit better, which worked excellently. All the best,
and thanks for pointing me to this,

Jacob Keller

On Sun, Apr 15, 2018 at 4:46 PM, CARL Philippe (LBP) <
[hidden email]> wrote:

> Dear Jacob,
> Please dowload and try the plugin found under this link:
> http://punias.free.fr/ImageJ/Colocalization_Finder.jar
> which is an improvement of the plugin originally developped by Jerôme
> Mutterer found under this link:
> https://imagej.nih.gov/ij/plugins/colocalization-finder.html
> This plugin ables the use of whatever LUT for the ScatterPlot picture (as
> you requested) as well as works for whatever type (even 32bits) of source
> pictures.
> A single click on the ScatterPlot picture will calculate the values
> corresponding to the given selected ROI as a double click will save the ROI
> position on the ScatterPlot.
> As if you press the Ctrl key and move the mouse over the Composite
> picture, the ROI within the ScatterPlot picture will center its position on
> the corresponding seleted pixel in the ScatterPlot picture.
> At last, it is possible to generate the x or y histogram of the
> ScatterPlot picture with a Gaussian fit of it in order to extract the
> histogram maximum position by using the numeric pad 4/6 or 2/8 keys.
> Feel free to contact me if you have some questions about the plugin or
> some requests for improving it.
> My best regards,
> Philippe
>
> Le Vendredi 13 Avril 2018 23:52 CEST, Jacob Keller <[hidden email]>
> a écrit:
>
> > Dear Developers of Coloc2,
> >
> > It would seem to me really helpful to have the all of the resultant
> images
> > (esp the 2D histogram) output as images separately. Then one could use
> > whatever LUTs and change contrast levels etc. Is this possible as is, and
> > if not, wouldn't it be pretty easy to do? Are the images written
> somewhere?
> > As it is, it's a bit tricky to make them into publishable images.
> >
> > All the best,
> >
> > Jacob Keller
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Coloc2 Output--histogram image?

Ellen Arena-2
Hey Jacob - sorry the delay in reply regarding Coloc 2.  But we recently made updates to the plugin that allows users to access individual measurements/plots  http://forum.imagej.net/t/release-of-coloc-2-version-3-0-0/5099 <http://forum.imagej.net/t/release-of-coloc-2-version-3-0-0/5099>) - so you should be able to generate the data you need.  Here is a forum post that shows a user how to do just that via a Groovy script:  http://forum.imagej.net/t/problem-with-li-plot-using-coloc2/7411 <http://forum.imagej.net/t/problem-with-li-plot-using-coloc2/7411>

Hope this helps a bit and at least you know for the future…

eta




> On Apr 15, 2018, at 4:42 PM, Jacob Keller <[hidden email]> wrote:
>
> Awesome--this is just what I needed! I actually also took the log of the 2D
> plot to see things a bit better, which worked excellently. All the best,
> and thanks for pointing me to this,
>
> Jacob Keller
>
> On Sun, Apr 15, 2018 at 4:46 PM, CARL Philippe (LBP) <
> [hidden email]> wrote:
>
>> Dear Jacob,
>> Please dowload and try the plugin found under this link:
>> http://punias.free.fr/ImageJ/Colocalization_Finder.jar
>> which is an improvement of the plugin originally developped by Jerôme
>> Mutterer found under this link:
>> https://imagej.nih.gov/ij/plugins/colocalization-finder.html
>> This plugin ables the use of whatever LUT for the ScatterPlot picture (as
>> you requested) as well as works for whatever type (even 32bits) of source
>> pictures.
>> A single click on the ScatterPlot picture will calculate the values
>> corresponding to the given selected ROI as a double click will save the ROI
>> position on the ScatterPlot.
>> As if you press the Ctrl key and move the mouse over the Composite
>> picture, the ROI within the ScatterPlot picture will center its position on
>> the corresponding seleted pixel in the ScatterPlot picture.
>> At last, it is possible to generate the x or y histogram of the
>> ScatterPlot picture with a Gaussian fit of it in order to extract the
>> histogram maximum position by using the numeric pad 4/6 or 2/8 keys.
>> Feel free to contact me if you have some questions about the plugin or
>> some requests for improving it.
>> My best regards,
>> Philippe
>>
>> Le Vendredi 13 Avril 2018 23:52 CEST, Jacob Keller <[hidden email]>
>> a écrit:
>>
>>> Dear Developers of Coloc2,
>>>
>>> It would seem to me really helpful to have the all of the resultant
>> images
>>> (esp the 2D histogram) output as images separately. Then one could use
>>> whatever LUTs and change contrast levels etc. Is this possible as is, and
>>> if not, wouldn't it be pretty easy to do? Are the images written
>> somewhere?
>>> As it is, it's a bit tricky to make them into publishable images.
>>>
>>> All the best,
>>>
>>> Jacob Keller
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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