selfalign(1) General Commands Manual selfalign(1)
NAME
selfalign - Realign model based on fits to trajectories
SYNOPSIS
selfalign options root_name|input_file output_file
DESCRIPTION
selfalign will refine the alignment of a model of fibers that progress
through the Z-dimension, such as microtubules modeled through serial
sections, using the trajectories in the model. This provides a way of
smoothing a model without disrupting the spacings between fibers in a
section, which would happen if trajectories were smoothed independently
with mtsmooth. selfalign works by first running xfmodel to
obtain transformations relating each section to the previous one (f
transforms). The kind of transformation can be specified with the -t
option, e.g., full linear, rotations and translations only, etc. If
there are few fibers, it is appropriate to reduce the complexity of
transformations being solved for. In addition, one can specify the
range of sections in the model over which to solve for transformations,
and thus exclude regions near the ends of the model that have few
fibers. If sections are excluded at the start or end of the model,
selfalign supplies transforms for those sections by replicating the
first or last transform actually solved for, respectively. This pre-
vents artifacts when local fits are made to the trends in the trans-
forms. The f transforms are converted to g transforms using xftoxg,
using fitting parameters that can be adjusted with the -l and -o
options. The self-aligned model is produced by running imodtrans.
The program can be run with either one or two arguments after the
options. Use one argument to specify a root filename. The program
then assumes that the input model is root_name.mod and generates an
output model named root_name.selfmod. Alternatively, use two arguments
to specify the full names of the input and output models. In this
case, the root name for the other files is assumed to be the name of
the input model with any extension removed.
OPTIONS
Run selfalign with no arguments to get a usage statement listing the
default values of the parameters.
-s list
Solve for transformations over the range of sections given in
list. A single range (e.g., 3-32) will give best results. The
default is to solve over the whole extent of the model.
-l extent
Do local fits to transformation parameters over the number of
sections given in extent. This parameter is used in running
xftoxg.
-o order
Set the polynomial order for the local fits to order. This
parameter is also used in running xftoxg.
-t type
Specify the type of transformations to solve for; set type to 0
for general linear transforms, 2 for translations only, 3 for
rotations and translations, or 4 for magnifications, rotations
and translations.
-i file
Specify the name of the image stack upon which the model was
built. If no file is entered, the default is the root name of
the model with extension .ali. If such an image file is not
available, the program will extract the needed information about
image dimensions from the header of the model, and assume that
this will adequately represent the information that could be
extracted from the image file header.
FILES
In addition to the self-aligned model, the program creates files with
the f transforms (root_name.selfxf) and the g transforms
(root_name.selfxg). If any of the output files already exists a backup
of the original is created with the ~ extension.
AUTHOR
David Mastronarde <mast at colorado dot edu>
SEE ALSO
xfmodel, xftoxg, imodtrans
IMOD 4.11.0 selfalign(1)