Extracts individual pixel values from a selection or RIO

[zherxes]

Dear all,

I am struggling to extract individual pixel values from a selection or area
of interest. I have tried to save the image as a text file, but it is very
hard working to find and collect the pixels I am interested in. I have also
tried to extract the histogram values from the option "list" however, it put
several pixels with in a bin range and I want to extract every single
individual value.

Do you know any way to do this?

Many thanks in advance
:)



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[gankaku]

Hi Mirko,

the following macro should do what you need:

//------------------------------------------------
Roi.getBounds(rx, ry, width, height);
row = 0;

for(y=ry; y<ry+height; y++) {
    for(x=rx; x<rx+width; x++) {
        if(Roi.contains(x, y)==1) {
            setResult("X", row, x);
            setResult("Y", row, y);
            setResult("Value", row, getPixel(x, y));
            row++;
        }
    }
}
//------------------------------------------------

Hope this helps,
Jan


2018-02-16 13:03 GMT+01:00 zherxes <[hidden email]>:

> Dear all,
>
> I am struggling to extract individual pixel values from a selection or area
> of interest. I have tried to save the image as a text file, but it is very
> hard working to find and collect the pixels I am interested in. I have also
> tried to extract the histogram values from the option "list" however, it
> put
> several pixels with in a bin range and I want to extract every single
> individual value.
>
> Do you know any way to do this?
>
> Many thanks in advance
> :)
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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CEO: Dr. Jan Brocher
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[zherxes]

I love you!

This worked like a charm :)

Many many thanks Jan!



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[gankaku]

Be aware that actually the output is not perfectly exact because you can
draw ROIs similar to vector graphics partially independent of the pixels
representing squares.
thus, when you measure the area of your ROI it will not reflect exactly the
measured number of pixel values by the macro. This depends on if IJ
considers a respective pixel still inside or already outside the ROI.
Please consider that because of this accuracy is not perfect in this
analysis.

Regards,
Jan

2018-02-16 16:26 GMT+01:00 zherxes <[hidden email]>:

> I love you!
>
> This worked like a charm :)
>
> Many many thanks Jan!
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

CEO: Dr. Jan Brocher
phone: [phone]
e-mail: [hidden email]
info: [hidden email]
inquiries: [hidden email]
web: www.biovoxxel.de

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[gankaku]

Hi Mirko,

I didn't remember the function Herbie mentioned.
This is the better option, because it will not skip pixels dependent on the
relative position towards the selection line.

regards,
Jan

2018-02-16 13:03 GMT+01:00 zherxes <[hidden email]>:

> Dear all,
>
> I am struggling to extract individual pixel values from a selection or area
> of interest. I have tried to save the image as a text file, but it is very
> hard working to find and collect the pixels I am interested in. I have also
> tried to extract the histogram values from the option "list" however, it
> put
> several pixels with in a bin range and I want to extract every single
> individual value.
>
> Do you know any way to do this?
>
> Many thanks in advance
> :)
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

CEO: Dr. Jan Brocher
phone: [phone]
e-mail: [hidden email]
info: [hidden email]
inquiries: [hidden email]
web: www.biovoxxel.de

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Herbie]

Good day Mirko,

"Analyze >> Tools >> Save XY Coordinates..."

does what you want.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::
Am 16.02.18 um 13:03 schrieb zherxes:

> Dear all,
>
> I am struggling to extract individual pixel values from a selection or area
> of interest. I have tried to save the image as a text file, but it is very
> hard working to find and collect the pixels I am interested in. I have also
> tried to extract the histogram values from the option "list" however, it put
> several pixels with in a bin range and I want to extract every single
> individual value.
>
> Do you know any way to do this?
>
> Many thanks in advance
> :)

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[zherxes]

Hi Jan!

Yes I realized that is taking some background pixels. However the macro was
very comfortable since I have many RIOs to go through the same picture in
about 120 pictures. Because the background pixel values are so different
than the ones inside the RIOs, it was easy to filter them out. Nonetheless
Herbie's solution worked nicely too!

Many thanks again.



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[zherxes]

Hi Herbie!

Yes indeed it does exactly what I need :)

Thanks you very much!



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