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sp_ctf_punisher
This version (2020/11/18 17:16) was approved by shaikh.
CTF Punisher

sp_ctf_punisher

Apply trapped CTF : Multiplies images by the contrast transfer function only after the first extremum.


Usage

Usage in command line:

sp_ctf_punish.py input_stack output_directory --plot --singlehdf --verbosity --debug 


Typical usage

The purpose of sp_ctf_punisher.py is to:

: multiply images by the contrast transfer function (CTF) only after the first extremum

The general choices for CTF-correction include (among others):

: doing nothing
: phase-flipping
: multiplying by the CTF

Multiplying by the CTF has the effect of flipping the phases where the CTF is negative, while avoiding the sharp filter edges during phase-flipping. (See 1D profile plot.)

However, multiplying by the CTF also dampens the data near the origin, which often adversely affects particle-recognition and alignment.

This program multiplies by the CTF, but only after the first extremum of the CTF. Before this extremum, the amplitudes are preserved. This strategy was referred to as a “trapped CTF” in SPIDER, or “ignore CTF until first peak” in RELION.

1D profiles of different CTF-correction strategies
Standard usage:

sp_ctf_punish.py input_stack output_directory
1) Padded image.2) CTF-multiplied image. 3) Phase-flipped image. 4) CTF-punished image. Images are low-pass filtered for clarity.


Input

Main Parameters

input_stack
Set of images. (default required string)
output_directory
Directory where outputs will be written. (default required string)
--plot
Writes plot of example CTF profiles (machine-specific, may not work)
--singlehdf
Writes a single HDF stack instead of a BDB stack pointing to MRC stacks.
--debug
Writes example of various CTF-correction strategies.


Output

bdb:ctfpunished
Filtered BDB stack
stkctfpunished.hdf
(optional) Filtered HDF stack
plotctf.png
1D profiles of example CTF


Description


Method


Reference

SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. Nat Protoc. 2008;3(12):1941-74. doi: 10.1038/nprot.2008.156.

Developer Notes


Author / Maintainer

Tapu Shaikh


Keywords

Category 1:: APPLICATIONS


Files

sphire/bin/sp_ctf_punisher.py


See also


Maturity

Beta:: Under evaluation and testing. Please let us know if there are any bugs.


Bugs

On some machines, the 1D profiles cannot be plotted.


sp_ctf_punisher.txt · Last modified: 2020/07/22 18:09 by shaikh