ctfphaseflip(1) ctfphaseflip(1)
NAME
ctfphaseflip - correct tilt series for microscope CTF by phase flipping
SYNOPSIS
ctfphaseflip options
DESCRIPTION
This program will correct the CTF of an input tilt series by simple
phase flipping. The user can select a subset of projection views of
the input tilt series to correct and can specify a defocus value for
each selected view through a text defocus file. The output file of
ctfplotter is usually used as the defocus file.
Ctfphaseflip corrects each view strip by strip. A strip is defined as
an image region whose defocus difference is less than a user specified
value, but the width is also limited to 256 pixels.
It can be run in a parallel mode similiar to the Tilt program by
setting the TotalViews option. The script Splitcorrection can be
used to prepare command files for running the program in parallel.
A sample command file for running the program with "subm" can be found
in the IMOD/com directory (ctfcorrection.com).
Options
Ctfphaseflip uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -):
-input OR -InputStack File name
Input stack that will be corrected
-output OR -OutputFileName File name
Name of output file for the corrected views
-angleFn OR -AngleFile File name
File containing tilt angles for the input stack. Each line of
this file is the tilt angle for a view of the input stack. The
angles are listed in order starting from view 1.
-defFn OR -DefocusFile File name
File with list of tilt angle ranges and defocus values in
nanometers, such as was output by ctfplotter. Each line
should have a starting and ending view number (numbered from 1),
a starting and ending tilt angle, and a defocus value. Defocus
is in nanometers, with positive values for underfocus. The pro-
gram will assign that defocus value to the midpoint of the range
of views. For a view at a given tilt angle, it will find the
defocus either by interpolating between two surrounding midpoint
angles, if there are such angles, or by taking the nearest defo-
cus value, if the angle is beyond the range of the available
midpoint angles. To correct a tilt series with a single value
of defocus, supply a file with a single line containing "20 20
0. 0. defocus_value".
-defTol OR -DefocusTol Integer
Defocus tolerance in nanometers that limits the width of the
strips. An image region with defocus difference less than this
tolerance is considered to have constant defocus and can be cor-
rected as one strip. The strip width is either the width of this
region or 256 pixels, whichever is smaller; but strips will also
be constrained to be at least 128 pixels wide. Each strip is
corrected based on the defocus at the center of the strip.
-iWidth OR -InterpolationWidth Integer
The distance in pixels between the center lines of two consecu-
tive strips. A pixel inside the region between those two center
lines resides in both strips. As the two strips are corrected
separately, that pixel will have 2 corrected values. The final
value for that pixel is a linear interpolation of the 2 cor-
rected values.
-pixelSize OR -PixelSize Floating point
Image pixel size in nanometers
-volt OR -Voltage Integer
Microscope voltage in kV
-cs OR -SphericalAberration Floating point
Microscope spherical aberration in millimeters
-ampContrast OR -AmplitudeContrast Floating point
The fraction of amplitude contrast. For Cryo-EM, it should be
between 0.07 and 0.14. The value should be the same as was used
when detecting the defocus.
-views OR -StartingEndingViews Two integers
The starting view and the ending view to correct in this run of
the program, numbered from 1. This is an optional field. The
default is to correct all views in the input stack.
-totalViews OR -TotalViews Two integers
The starting view and the ending view that need to be corrected
in all parallel runs of the program. This field is only needed
when doing parallel runs with direct writing to a single output
file. The program is run initially with a StartingEndingViews
entry of -1,-1 to set up the output file. Then it is run with
actual starting and ending views for each parallel run, and each
run writes to the existing output file.
-aAngle OR -AxisAngle Floating point
This option is not supported. The tilt axis has to be vertical,
i.e., to be coincident with the Y axis. Usually this means the
input stack has to be the aligned stack.
-param OR -Parameter Parameter file
Read parameter entries from this file.
-StandardInput
Read parameter entries from standard input
AUTHOR
Quanren Xiong
SEE ALSO
ctfplotter
BUGS
Email bug reports to xiongq at colorado dot edu.
BL3DEMC 3.11.2 ctfphaseflip(1)