Feature #913
closedXMIPP normalize stack
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Description
Added a option to makestack2.py to perform an XMIPP normalization of the particles after the stack is created.
Unlike EMAN's proc2d "normalization", which only changes the pixel values to reflect a mean=0 & std=1, this option both removes ramp density (particularly useful for negative stain), and replaces pixel values above or below a specified sigma threshold with random pixel values that are within the threshold range.
I've been using this normalization for all my stack for the past 4 months, and find it to be very helpful in particle alignment, especially if doing CTF correction, which can sometimes introduce intensity spikes.
This normalization is performed AFTER storing the mean & std dev values of the particle images, so the meanfilt function isn't affected.
r14873
Updated by Neil Voss over 13 years ago
Hi Gabe, I had started working on putting the "ramping" into make stack using python for the Asturias, but the abruptly stopped using it, because they felt it was artificially creating fringes in their images. Think of applying the ramp to a picture of the edge of a hole and how it would overcut on one side and undercut on the other. They are now using a large high pass filter cutoff, which I feel is better any way.
Nonetheless, I should never complain about implementing more features.
Updated by Gabriel Lander over 13 years ago
That's interesting about the ramping issue - I'm not sure how exactly XMIPP is removing the ramp, but no one in the lab has noticed fringes or other introduced distortions in negative stain or cryo datasets. I'll keep a closer eye out for this - perhaps eventually we should have a separate option for the ramp?
Updated by Amber Herold over 13 years ago
- Status changed from New to In Code Review
Updated by Amber Herold about 10 years ago
- Status changed from In Code Review to Closed