reducefiltvol(1) General Commands Manual reducefiltvol(1)
NAME
reducefiltvol - Reduce a volume and/or filter it in Fourier space
SYNOPSIS
reducefiltvol [options] input_file output_file
DESCRIPTION
Reducefiltvol provides a wrapper script for two operations that produce
tomograms with higher signal-to-noise ratio suitable for visualization
of features, segmentation, and detection of particle positions: size
reduction and filtering. Either one or both of these operations can be
done. The reduction is done with antialias filtering by Binvol, so
large reduction factors can be used without introducing noise from
aliasing. The filtering is done on a 3-D Fourier transform with Mtf-
filter(1). The options here provide either a simple low-pass filter to
remove high frequencies, or a Wiener-like deconvolution filter that
matches what is implemented in Warp (Tegunov and Cramer, 2019, Nat.
Methods 16, 1146-1152) and IsoNet (Y. T. Yiu, et al., 2022, Nat. Comm.
13, 6482). The filter compensates for attenuations by the microscope
contrast transfer function (CTF), using an assumed signal-to-noise
ratio that starts high and falls off at a specified rate.
Pixel size and origin values in the header of the output file are set
so that the coordinate system matches that of the input file. Thus,
models drawn on the input file in 3dmod should load correctly onto the
output file, and vice versa. This coordinate system can be attached to
IMOD models generated on the reduced volume by external software using
the -i option to Imodtrans.
OPTIONS
Reducefiltvol 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 -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-input (-i) OR -InputFile File name
Input file with volume to be reduced and/or filtered
-output (-o) OR -OutputFile File name
Output file for reduced and/or filtered volume
-reduce (-r) OR -ReductionFactor Floating point
Overall reduction factor to apply, which will be used for X and
Y even if a different factor is entered for Z.
-zfactor (-z) OR -ZReductionFactor Floating point
Factor to reduce by in Z; the default is to reduce the same in
all dimensions. Can be non-integer.
-lowpass (-l) OR -LowPassRadiusSigma Two floats
Cutoff radius and sigma for a low pass filter that imposes a
high-frequency Gaussian roll-off to 0.0. This option cannot be
entered with -deconv.
-deconv (-dec) OR -DeconvolutionStrength Floating point
The option activates a deconvolution filter by specifying the
overall strength of the deconvolution, which controls the degree
to which low frequencies are boosted. Values around 0.25 to 1
may be useful. The bigger the value, the more low frequencies
are accentuated. This value is treated as it is in Warp; values
used in IsoNet need to be divided by 3 to have the same effect
here. This option cannot be entered with -lowpass.
The following 7 entries are used for the deconvolution filter.
-snr (-sn) OR -SNRFalloff Floating point
Falloff rate with frequency of the signal-to-noise ratio assumed
for computing the deconvolution filter; higher values attenuate
high frequencies more. Some users suggest keeping this value
comparable to the -deconv entry. The default is 0.7, the value
in IsoNet.
-dchigh (-dch) OR -HighPassNyquist Floating point
Cutoff frequency of a high-pass filter to prevent excessive
boosting of the lowest frequencies, where the CTF is low. For
consistency with Warp and IsoNet, the value is expressed as the
fraction of Nyquist, and is thus twice the usual frequency in
reciprocal pixels. The default is 0.02 as in IsoNet.
-pixel (-pi) OR -PixelSize Floating point
Pixel size in nanometers. This entry is needed only if the
pixel size in the image file header is incorrect, but the pro-
gram will try to determine is value by getting the raw stack
pixel size in the Ctfplotter command file and comparing pixel
sizes in the raw stack and input volume headers.
-volt (-v) OR -Voltage Integer
Microscope voltage in kV; the default is 300. The program will
try to determine this value from the Ctfplotter command file.
-cs (-c) OR -SphericalAberration Floating point
Spherical aberration (Cs) in mm; the default is 2.7. The pro-
gram will try to determine this value from the Ctfplotter
command file.
-defocus (-def) OR -DefocusInMicrons Floating point
The defocus in microns (underfocus positive). The program will
try to determine this from the lowest tilt view of the ".defo-
cus" file output by Ctfplotter. If that is not possible, the
value must be entered.
-dcphase (-dcp) OR -PhaseShift Floating point
Phase shift in degrees. This entry is needed if you want to
account for a phase shift; the program does not take it from the
".defocus" file.
-mode (-m) OR -ModeToOutput Integer
The storage mode of the output file from either Binvol or
Mtffilter; 0 for byte, 1 for 16-bit signed integer, 6 for
16-bit unsigned integer, 2 for 32-bit floating point, or 12 for
16-bit floating point. The default is the mode of the input
file. See the Mtffilter man page for some details about mode
12.
-setup (-se) OR -SetupChunksIfMemoryError
If Mtffilter exits with an error indicating that the memory
needed is bigger than the allowed amount, or that memory for the
image array could not be allocated, then run Chunksetup to
create command files for processing the volume in parallel.
-param (-pa) OR -ParameterFile Parameter file
Read parameter entries from file
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
If the output file already exists a backup of the original is created
with the ~ extension. If both reduction and filtering are being done,
a temporary file is created with the root name of the output file fol-
lowed by ".filttemp" and the extension of the output file.
AUTHOR
David Mastronarde <mast at colorado dot edu>
SEE ALSO
Binvol, Mtffilter
IMOD 5.2.0 reducefiltvol(1)