FreehandRoi integrateddensity measures

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FreehandRoi integrateddensity measures

lougerard
Hi all ! I'm new here, so i'l try to be as clear as possible !

I'm using the FreehandRoi object in my project. I would like to know if it's
possible to measure the integrated density of a FreehandRoi object ?

I'm doing it well for rectangular Roi's (with the good results) via :
    [...]
    Analyzer.setMeasurements(Measurements.INTEGRATED_DENSITY);
    resultTable = myRoiManager.multiMeasure(MyImagePlus);
    resultTable.show("test");
    [...]

When i tried to do this with an FreehandRoi object, it doesn't work. I only
receive NaN for both (Inden and RawInDen) for all my frames in my ImagePlus.

Does someone have an idea ?

PS : the debug properties of myFreehand object is :
            bounds : null
            x,y,w,h: 57,32,1,1  
       as example, but i don't know if the two 1 and the null bounds are
normal


Thanks in advance !! Have a nice day.

Best regards,

Louis





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Re: FreehandRoi integrateddensity measures

Michael Schmid-3
Hi Louis,

probably your roi contains no pixels. You can have such Rois, e.g. with
the following macro command, which creates a roi where the line folds
back on itself, without encircling any pixels:
   makePolygon(7,8, 6,7, 7,8);
or (L-shaped):
   makePolygon(5,4, 5,3, 6,3, 5,3, 5,4);

You can also have a roi with non-zero area when looking at high
magnification. This can happen if a pixel is cut in half, but the pixel
is not inside the Roi by the ImageJ convention of how border pixels are
handled. Then ImageJ considers it a roi with no pixels enclosed, see
this macro example:
   makePolygon(8,6, 9,5, 9,6);

For Rois with zero pixels, a "Measure" command reports an area of 0 and
NaN values for Mean, Min, Max, IntDen, etc.


Michael
________________________________________________________________
On 27.03.19 14:53, lougerard wrote:

> Hi all ! I'm new here, so i'l try to be as clear as possible !
>
> I'm using the FreehandRoi object in my project. I would like to know if it's
> possible to measure the integrated density of a FreehandRoi object ?
>
> I'm doing it well for rectangular Roi's (with the good results) via :
>      [...]
>      Analyzer.setMeasurements(Measurements.INTEGRATED_DENSITY);
>      resultTable = myRoiManager.multiMeasure(MyImagePlus);
>      resultTable.show("test");
>      [...]
>
> When i tried to do this with an FreehandRoi object, it doesn't work. I only
> receive NaN for both (Inden and RawInDen) for all my frames in my ImagePlus.
>
> Does someone have an idea ?
>
> PS : the debug properties of myFreehand object is :
>              bounds : null
>              x,y,w,h: 57,32,1,1
>         as example, but i don't know if the two 1 and the null bounds are
> normal
>
>
> Thanks in advance !! Have a nice day.
>
> Best regards,
>
> Louis

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Re: FreehandRoi integrateddensity measures

lougerard
Thank you Michael !

I'll check that today !

Have a nice day !

Louis



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Re: FreehandRoi integrateddensity measures

lougerard
In reply to this post by Michael Schmid-3
It's working !

Thanks a lot !

Best regards,

Louis



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