Path Intensity Profile Icy

Hello,

I have a little question regarding the path intensity Profile.
Is the principle is the same as the scan line in Fiji?

I attached a picture of what I have done. There is the ROI and the corresponding path profile.
So the “Point #” is all the pixels it’s measuring, the X, Y, Z, T the coordinates for that pixel, and then the channels.

So does this mean that the path profiler is measuring the average intensity for each column of pixels over the distance (like in “scan line” in Fiji)? Or is it giving the intensity of all the pixels inside the ROI?

Thank you in advance,
Virgínia

Hi Virginia,

Thanks for forwarding your message here !
Afaik the Path Intensity Profiler plugin only give you the intensity over the ROI edge, not for the interior of the ROI. So basically what you have in the table is just the position for each point of the ROI contour (as you guessed) and the intensity value for this single point. When a contour point is located between 2 pixels then the mean intensity of the 2 pixels is used.
Hope that reply your question !

Best,

– Stephane

Hi Stephane,

Thank you a lot for your answer! I understand now.

So if I want to use “Area” ROI with the Path intensity Profile it will give me the mean intensity of the pixels in the same column?

Thank you again.

Kindly,
Virginia

Hi Virginia,

If you use an Area ROI, the Path Intensity Profile will only give you the intensity for the contour pixels of this area, not intensity from the interior.
If you want to get the mean intensity from a complete ROI you directly have it in the ROI Table.
If you want intensity for each pixel of a ROI, you can use the ROI pixels CSV export script
But there is no such thing which allow to get the mean intensity for each row or column of pixels from a ROI. But that is easily doable using a script (starting from the one mentioned just above).

Best,

– Stephane

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Hi Stephane,

OK I see! Thank you a lot for the clarification.
I will take a look at the script also.

Thank you a lot for your help.

Kindly,
Virginia

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