Posted by
Herbie on
Oct 16, 2019; 6:10pm
URL: http://imagej.273.s1.nabble.com/how-does-ImageJ-measure-circular-ROI-tp5022481p5022546.html
Good day Charitra,
you've brought up your question on the ImageJ-Forum again but you didn't
reply to Michael's and my posts here on the ImageJ-list.
Would you please tell us what remains unclear after our replies?
To make things more obvious, you may run the following ImageJ-macro:
///////
newImage("Untitled", "8-bit noise", 8, 8, 1);
run("Set... ", "zoom=3200 x=4 y=4");
run("Specify...", "width=1 height=1 x=3.3 y=3.3 oval");
run("RGB Color");
setForegroundColor(255, 0, 255);
run("Fill", "slice");
exit()
///////
Paste the this macro code to an empty macro window
(Plugins >> New >> Macro) and run it.
Please tell us in detail what you don't understand when inspecting the
result.
Regards
Herbie
::::::::::::::::::::::::::::::::::::
Am 02.10.19 um 15:45 schrieb Herbie:
> Good day,
>
> this is a cross-post from the IJ-Forum:
> <
https://forum.image.sc/t/how-does-imagej-measure-pixels-in-circular-roi/30041>
>
>
> Please make sure that you understand what spatially discrete, i.e.
> sampled images mean. The fill command acts on the samples not the ROI
> circle that is a vector graphic. The number of pixels that are filled
> most likely depends on the next neighbor distances.
>
> Furthermore please not that pixels have no spatial extension, i.e. what
> you see as squares of equal gray is the common attempt (most simple
> interpolation scheme) to visualize the sample value. Per convention
> ImageJ assumes the sample coordinate at the upper left corner of the
> square.
>
> Did you consider to oversample your image using an adequate
> interpolation scheme?
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::
> Am 02.10.19 um 15:18 schrieb Charitra:
>> I am trying to measure photon counts from single molecules (7*7
>> pixels) by
>> defining a ROI around the single molecule. I localize the center of the
>> emitter (this could be subpixel) from ThunderSTORM and draw the ROI
>> around
>> it which makes everything sub-pixel. If the ROI is circular, some of the
>> pixels are excluded from measurement. Can someone tell me how exactly the
>> pixels for measurement are selected? Is it based on the amount of area
>> selected by the ROI boundaries or is it something else?
>> <
http://imagej.1557.x6.nabble.com/file/t382433/IMG_20191001_172953.jpg>
>> <
http://imagej.1557.x6.nabble.com/file/t382433/IMG_20191001_173241.jpg>
>>
>> In the above images, I specified a sub-pixel center and drew a
>> circular ROI
>> and filled it from the ROI Manager, but the fill seems to fall
>> completely at
>> a different location than the ROI specified. I am not able to
>> understand how
>> this works! Please help.
>>
>>
>>
>> --
>> Sent from:
http://imagej.1557.x6.nabble.com/>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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