Integrated Intensity


#1

Hi,
This is my first post and I would first like to thank you for CP. It is really a great tool!
So this is my question: after measuring object intensity, I do not get integer values as Integrated Intesity values. I was wondering why because I thought Integrated Intensity was calculated as the sum of pixel intensities which are integers ranging from 0 to 255.
Thanks
Best
Emmanuel


#2

CP doesn’t work with raw unscaled intensity values. Intensities are rescaled between 0 and 1. Whether rescaling factor is taken from image metadata, image bit-depth or manually provided value depends on “Set intensity range” field in NamesAndTypes module.


#3

Hi Emmanuel,
You could do me a favor and make some point here that it would be more scientific if the images were not rescaled :slight_smile: There currently is a super small change that the CP developers might consider changing this behavior…


#4

@Christian_Tischer
Honest question: why do you think it wold be more scientific not to rescale images?


#5

In the present case, I want to measure the decrease of EGFR staining at different time points after EGF stimulation and I took care not to change acquisition settings of these different time points. So I would prefer CP not to rescale image intensity… Is it possible?


#6

@emmanuel Why don’t you want to rescale intensities?

The rescaling is simply a division of raw intensities by a fixed factor. It’s NOT rescaling intensities between min and max recorded values. Say, if your image is acquired at 14 bits and if you choose “Set intensity range from Image metadata” in NamesAndTypes module, then intensity values are divided by 2^14=16’384. And this will happen for all your images.

If you really insist on sticking to raw intensities, just multiply your image using ImageMath module or multiply your final result in the spreadsheet by 2^{bit_depth}.

Also have a look at help for “Set intensity range from” field.


#7

OK, If all the images are divided by the same factor then it’s fine for me. I was worried that it could be different from images to images depending on the overall intensity of each image.
What happens if you chose No in the Metadata modules? Does it interfere with the “Set intensity range from Image metadata” in NamesAndTypes module?
Thanks for your help


#8

Hi,

There was a long discussion on github, please find my comments there:


#9

OK, If all the images are divided by the same factor then it’s fine for me. I was worried that it could be different from images to images depending on the overall intensity of each image.

This should not ever happen (and if it ever was different from image to image, it’d be due to a issue like the metadata in one of your images being corrupted, not due to the pixel values present); if you want to assure yourself that it everything is being scaled the same way, you can confirm in the Image_Scaling column that the scaling is consistent image-to-image.

What happens if you chose No in the Metadata modules? Does it interfere with the “Set intensity range from Image metadata” in NamesAndTypes module?

The metadata that sets bit-depth is pulled out whether or not you use the Metadata module or not, so no need to worry about that.