sp_ctf_punisher

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

sp_ctf_punisher [2020/07/22 18:09] (current)
shaikh created
Line 1: Line 1:
 +~~NOTOC~~
 +[{{ ::​ctf_punisher_blue2.png?​275|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.
 +
 +{{ :​plotctf.png?​600 |1D profiles of different CTF-correction strategies}}
 +\\ __Standard usage: __
 +
 +  sp_ctf_punish.py input_stack output_directory
 +[{{ ::​trapped_ctf_examples.png?​200|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