Hi,
> processing producing typical greyscale images of 0-255
No. Perhaps you are looking at pixel values on screenshots
of relion_display, which is normalised only for display purpose.
Instead, right click on a class and choose
"show original image". Then clicking on the image shows
you the original pixel value on the console.
If you want to get whole raw data, you can read it into
Python by 'mrcfile' package.
Best regards,
Takanori Nakane
On 2018/11/30 19:14, Eric Verbeke wrote:
> Hi All,
>
> I am wondering how pixel intensity values are stored across image processing steps in RELION (from raw images to 2D classification). After running 2D classification, I would like to compare the pixel values between different 2D classes (essentially comparing their absolute intensity). However, it seems images are either normalized or thresholded during processing producing typical greyscale images of 0-255. This is an issue for me because the max pixel value of one 2D class (at 255) is not necessarily equal to the intensity of the max pixel value in another 2D class (also 255). I have tried excluding --norm in both extraction and 2D classification but the result is the same. Does anybody know where the actual signal intensity is stored? Thanks for any help!
>
> Eric Verbeke
> PhD Candidate
> David Taylor and Edward Marcotte labs
>
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