Angular histogram plot

[CARL Philippe (LBP)]

Dear all,

I would like to make an angular histogram plot, similar to what can be found
in the following picture (taken from a publication):
<http://punias.free.fr/ImageJ/Graph.jpg>
http://punias.free.fr/ImageJ/Graph.jpg

Or by using Matlab: http://fr.mathworks.com/help/matlab/ref/rose.html

within ImageJ.

Is there already a plugin doing such graphs and if not would there be a
plugin that would be a good starting point for developing such a tool?

I thank you very much in advance for your hints about this.

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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[Herbie]

Bonjour Philippe,

referring to the example, I'm not sure what is actually plotted, or if
the angles run correctly...

Do you like to plot the integral values of directed sectors taken from
the gray shape?

What does the violet ellipse stand for and what does the green circle
indicate?

Somehow clueless,

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 15.09.16 um 10:17 schrieb Philippe CARL:

> Dear all,
>
> I would like to make an angular histogram plot, similar to what can be found
> in the following picture (taken from a publication):
> <http://punias.free.fr/ImageJ/Graph.jpg>
> http://punias.free.fr/ImageJ/Graph.jpg
>
> Or by using Matlab: http://fr.mathworks.com/help/matlab/ref/rose.html
>
> within ImageJ.
>
> Is there already a plugin doing such graphs and if not would there be a
> plugin that would be a good starting point for developing such a tool?
>
> I thank you very much in advance for your hints about this.
>
> 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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[CARL Philippe (LBP)]

Hallo Herbie,
Wie geht es dir?
The figure on the right of the picture I gave as example (i.e. taken from a publication) is not a real measurement, but just an illustration explaining how the calculations are done in the figure on the right.
Thus the violet ellipse is a represention of the cell nucleus and they are actually making the angle measurement between the nucleus centroid and the position of the green circle and then make an histogram plot (also called Windrose Graph) of the measured angles.
In my case I would like to make such a graph (i.e. Windrose Graph) of the angles of the displacement vectors of kinetical measurements.
Making the angle histograms divisions of the displacement vectors is quite trivial (i.e. I have a very small starting idea on how to make this calculation and think that I should be able to make it on my own), but I don't know how to generate such a Windrose Plot of the obtained results within ImageJ.
And if somebody has already done something similar or quite near to it, it would be a little bit stupid to reinvent the wheel.
Did I clarify my previous question with this answer (= alles klar herr kommissar?)
Kindest regards,
Philippe

Le Jeudi 15 Septembre 2016 11:17 CEST, Herbie <[hidden email]> a écrit:

> Bonjour Philippe,
>
> referring to the example, I'm not sure what is actually plotted, or if
> the angles run correctly...
>
> Do you like to plot the integral values of directed sectors taken from
> the gray shape?
>
> What does the violet ellipse stand for and what does the green circle
> indicate?
>
> Somehow clueless,
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::
> Am 15.09.16 um 10:17 schrieb Philippe CARL:
> > Dear all,
> >
> > I would like to make an angular histogram plot, similar to what can be found
> > in the following picture (taken from a publication):
> > <http://punias.free.fr/ImageJ/Graph.jpg>
> > http://punias.free.fr/ImageJ/Graph.jpg
> >
> > Or by using Matlab: http://fr.mathworks.com/help/matlab/ref/rose.html
> >
> > within ImageJ.
> >
> > Is there already a plugin doing such graphs and if not would there be a
> > plugin that would be a good starting point for developing such a tool?
> >
> > I thank you very much in advance for your hints about this.
> >
> > 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Herbie]

Merci Philippe,

tout va bien ici quelques semaines avant ma retraite...

Well, for the plot itself, I have no idea whether some IJ-compatible
code exists -- sorry. I'd export the data and use the Polar-plot option
of Kaleidagraph.

A bientôt

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::
Am 15.09.16 um 12:07 schrieb CARL Philippe (PHA):

> Hallo Herbie,
> Wie geht es dir?
> The figure on the right of the picture I gave as example (i.e. taken from a publication) is not a real measurement, but just an illustration explaining how the calculations are done in the figure on the right.
> Thus the violet ellipse is a represention of the cell nucleus and they are actually making the angle measurement between the nucleus centroid and the position of the green circle and then make an histogram plot (also called Windrose Graph) of the measured angles.
> In my case I would like to make such a graph (i.e. Windrose Graph) of the angles of the displacement vectors of kinetical measurements.
> Making the angle histograms divisions of the displacement vectors is quite trivial (i.e. I have a very small starting idea on how to make this calculation and think that I should be able to make it on my own), but I don't know how to generate such a Windrose Plot of the obtained results within ImageJ.
> And if somebody has already done something similar or quite near to it, it would be a little bit stupid to reinvent the wheel.
> Did I clarify my previous question with this answer (= alles klar herr kommissar?)
> Kindest regards,
> Philippe
>
> Le Jeudi 15 Septembre 2016 11:17 CEST, Herbie <[hidden email]> a écrit:
>
>> Bonjour Philippe,
>>
>> referring to the example, I'm not sure what is actually plotted, or if
>> the angles run correctly...
>>
>> Do you like to plot the integral values of directed sectors taken from
>> the gray shape?
>>
>> What does the violet ellipse stand for and what does the green circle
>> indicate?
>>
>> Somehow clueless,
>>
>> Herbie
>>
>> :::::::::::::::::::::::::::::::::::::::::::
>> Am 15.09.16 um 10:17 schrieb Philippe CARL:
>>> Dear all,
>>>
>>> I would like to make an angular histogram plot, similar to what can be found
>>> in the following picture (taken from a publication):
>>> <http://punias.free.fr/ImageJ/Graph.jpg>
>>> http://punias.free.fr/ImageJ/Graph.jpg
>>>
>>> Or by using Matlab: http://fr.mathworks.com/help/matlab/ref/rose.html
>>>
>>> within ImageJ.
>>>
>>> Is there already a plugin doing such graphs and if not would there be a
>>> plugin that would be a good starting point for developing such a tool?
>>>
>>> I thank you very much in advance for your hints about this.
>>>
>>> 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
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Tiago Ferreira-2]

Dear Philippe,

> Is there already a plugin doing such graphs and if not would there be a
> plugin that would be a good starting point for developing such a tool?

The BAR update site[1] has several scripts that use the jfreechart library[2] (bundled with Fiji) to perform advanced plotting from within ImageJ (see some examples here[3]).
I just uploaded a script[4] that allows you to create polar plots (XY lines plotted in polar coordinates - see this screenshot[5] to get an idea on how it looks like). Once you subscribe to the BAR update site, you will find it under "BAR>Data Analysis>Create Polar Plot." A cool feature of all these "BAR>Data Analysis>" commands is that they can read tabular values from multiple sources, not just the ImageJ Results table.

You could use it as a starting point for your polar histogram chart.
(It would be great if you could add such functionality to the existing script[6]).

Hope it helps,
-tiago

[1] http://imagej.net/BAR
[2] http://www.jfree.org/jfreechart/
[3] https://github.com/tferr/Scripts/tree/master/Data_Analysis#data-analysis
[4] https://github.com/tferr/Scripts/blob/master/Data_Analysis/Create_Polar_Plot.bsh
[5] https://cl.ly/401e0N1R292S/CreatePolarPlotScreenshot.png
[6] https://github.com/tferr/Scripts#help

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[CARL Philippe (LBP)]

Dear Tiago,
I was able to generate such a graph from your script and it will indeed make the job.
So thanks a lot for your help and advices.
I will now need to work on understanding how to best use this tool.
Have a nice week-end,
Philippe

Le Jeudi 15 Septembre 2016 21:07 CEST, Tiago Ferreira <[hidden email]> a écrit:

> Dear Philippe,
>
> > Is there already a plugin doing such graphs and if not would there be a
> > plugin that would be a good starting point for developing such a tool?
>
> The BAR update site[1] has several scripts that use the jfreechart library[2] (bundled with Fiji) to perform advanced plotting from within ImageJ (see some examples here[3]).
> I just uploaded a script[4] that allows you to create polar plots (XY lines plotted in polar coordinates - see this screenshot[5] to get an idea on how it looks like). Once you subscribe to the BAR update site, you will find it under "BAR>Data Analysis>Create Polar Plot." A cool feature of all these "BAR>Data Analysis>" commands is that they can read tabular values from multiple sources, not just the ImageJ Results table.
>
> You could use it as a starting point for your polar histogram chart.

> (It would be great if you could add such functionality to the existing script[6]).
>
> Hope it helps,
> -tiago
>
> [1] http://imagej.net/BAR
> [2] http://www.jfree.org/jfreechart/
> [3] https://github.com/tferr/Scripts/tree/master/Data_Analysis#data-analysis
> [4] https://github.com/tferr/Scripts/blob/master/Data_Analysis/Create_Polar_Plot.bsh
> [5] https://cl.ly/401e0N1R292S/CreatePolarPlotScreenshot.png
> [6] https://github.com/tferr/Scripts#help

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